diff --git a/.github/ISSUE_TEMPLATE/Formulaire-Droit-Image_photo_DCOM.docx b/.github/ISSUE_TEMPLATE/Formulaire-Droit-Image_photo_DCOM.docx deleted file mode 100644 index bd66146..0000000 Binary files a/.github/ISSUE_TEMPLATE/Formulaire-Droit-Image_photo_DCOM.docx and /dev/null differ diff --git a/.github/ISSUE_TEMPLATE/new-member.md b/.github/ISSUE_TEMPLATE/new-member.md deleted file mode 100644 index 2c84772..0000000 --- a/.github/ISSUE_TEMPLATE/new-member.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -name: New member -about: Add a new member. -title: '' -labels: '' -assignees: '' - ---- - -**Personal information** -- First name: -- Last name: -- Title: - -**Team** -- [ ] ARCHITECTURE -- [ ] BRAINOMICS -- [ ] GINKGO -- [ ] SIGNATURE -- [ ] CATI -- [ ] Platform - -**Position** -- [X] PI -- [ ] Post Doc -- [ ] PhD Student -- [ ] Engineer - -**Supervisors** -- Optionally, list your supervisors - -**Fixed-term contract** -- Start year: -- End year: - -**Personal site** -- Optionally, you can add a link to your personal website. diff --git a/.github/ISSUE_TEMPLATE/new-position.md b/.github/ISSUE_TEMPLATE/new-position.md deleted file mode 100644 index 730f873..0000000 --- a/.github/ISSUE_TEMPLATE/new-position.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -name: New position -about: Add a new position. -title: '' -labels: '' -assignees: '' - ---- - -**Which type of position do you want to offer?** -- [ ] PhD -- [ ] Post Doc -- [ ] Intern -- [ ] CDD -- [ ] CDI - -**Team** -- [ ] ARCHITECTURE -- [ ] BRAINOMICS -- [ ] GINKGO -- [ ] SIGNATURE -- [ ] CATI -- [ ] Platform - -**Position Description** -- Title: -- Profile: -- Team: -- URL to the full job description (if applicable): - -**Do not forget** -- Upload the job description (if applicable): \_\_\.pdf. diff --git a/.github/ISSUE_TEMPLATE/news-.md b/.github/ISSUE_TEMPLATE/news-.md deleted file mode 100644 index de85c2f..0000000 --- a/.github/ISSUE_TEMPLATE/news-.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -name: News! -about: Add a news. -title: '' -labels: '' -assignees: '' - ---- - -**News details** -- Provide a title for the news: -- If applicable, provide here a small description: -- If applicable, provide here an url: diff --git a/.github/ISSUE_TEMPLATE/research-news-.md b/.github/ISSUE_TEMPLATE/research-news-.md deleted file mode 100644 index a20be56..0000000 --- a/.github/ISSUE_TEMPLATE/research-news-.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -name: Research news! -about: Add a new story about your research. -title: '' -labels: '' -assignees: '' - ---- - -**Research details** -- Title: -- Associated paper/code URL: -- Teasing: a ~300 character sentence (including spaces) for an appealing introduction - -**Team** -- [ ] ARCHITECTURE -- [ ] BRAINOMICS -- [ ] GINKGO -- [ ] SIGNATURE -- [ ] CATI -- [ ] Platform - -**Do not forget** -- Upload a graphical abstract of your reserach story: \_\.png diff --git a/.github/ISSUE_TEMPLATE/update-biblio.md b/.github/ISSUE_TEMPLATE/update-biblio.md deleted file mode 100644 index f4eae02..0000000 --- a/.github/ISSUE_TEMPLATE/update-biblio.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -name: Update biblio -about: Update the bibliography -title: '' -labels: '' -assignees: '' - ---- - -**Team** -- [ ] ARCHITECTURE -- [ ] BRAINOMICS -- [ ] GINKGO -- [ ] SIGNATURE -- [ ] CATI -- [ ] Platform - -**Do not forget** -- Upload a valid bibtex that contains the references you want to add. diff --git a/README.md b/README.md index 7584c98..e76eb61 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ ![PoweredBy](https://img.shields.io/badge/Powered%20by-CEA%2FNeuroSpin-blue.svg) -![Build Static Pages](https://github.com/neurospin/gaia/workflows/Build%20Static%20Pages/badge.svg) +![Build Static Pages](https://github.com/neurospin/baobab/workflows/Build%20Static%20Pages/badge.svg) # Important links -- repository URL: https://github.com/neurospin/gaia -- site URL: https://neurospin.github.io/gaia +- repository URL: https://github.com/neurospin/baobab +- site URL: https://neurospin.github.io/baobab # How to contribute @@ -13,9 +13,8 @@ The easiest way to update the content of the site is to create an issue from the GitHub interface: - first, log in to your GitHub account. -- go to the issue page: https://github.com/neurospin/gaia/issues. +- go to the issue page: https://github.com/neurospin/baobab/issues. - click the "New issue" buttton. -- fill out the appropriate template. If you want to contribute more deeply: diff --git a/_collections/_biblio/architecture/architecture_aczel_consensus-based_2021.md b/_collections/_biblio/architecture/architecture_aczel_consensus-based_2021.md deleted file mode 100644 index 8c06ca2..0000000 --- a/_collections/_biblio/architecture/architecture_aczel_consensus-based_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Balazs Aczel et al. -title: Consensus-based guidance for conducting and reporting multi-analyst studies -journal: eLife -year: 2021 -type: article -url: https -//doi.org/10.7554/eLife.72185 -doi: 10.7554/eLife.72185 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_andoh_low-cost_2009.md b/_collections/_biblio/architecture/architecture_andoh_low-cost_2009.md deleted file mode 100644 index 2020d21..0000000 --- a/_collections/_biblio/architecture/architecture_andoh_low-cost_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Andoh et al. -title: A low-cost MRI-guided method for TMS coil positioning -journal: Brain Stimulation -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_andoh_modulation_2006.md b/_collections/_biblio/architecture/architecture_andoh_modulation_2006.md deleted file mode 100644 index 753b0a6..0000000 --- a/_collections/_biblio/architecture/architecture_andoh_modulation_2006.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Andoh et al. -title: Modulation of language areas with functional MR image-guided magnetic stimulation -journal: Neuroimage -year: 2006 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_andoh_priming_2008.md b/_collections/_biblio/architecture/architecture_andoh_priming_2008.md deleted file mode 100644 index 70c3ae4..0000000 --- a/_collections/_biblio/architecture/architecture_andoh_priming_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Andoh et al. -title: Priming frequencies of transcranial magnetic stimulation over Wernicke's area modulate word detection -journal: Cereb Cortex -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_andrade_detection_2001.md b/_collections/_biblio/architecture/architecture_andrade_detection_2001.md deleted file mode 100644 index aa99da7..0000000 --- a/_collections/_biblio/architecture/architecture_andrade_detection_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Andrade et al. -title: Detection of fMRI activation using cortical surface mapping -journal: Hum Brain Mapp -year: 2001 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_angioni_biomarkers_2022.md b/_collections/_biblio/architecture/architecture_angioni_biomarkers_2022.md deleted file mode 100644 index f6209f7..0000000 --- a/_collections/_biblio/architecture/architecture_angioni_biomarkers_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Angioni et al. -title: Biomarkers of Age-Related Frailty and Frailty Related to Diseases - An Exploratory, Cross-Sectional Analysis from the MAPT Study -journal: The Journal of nutrition, health and aging -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1279770723008448 -doi: 10.1007/s12603-022-1793-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_angioni_neuroimaging_2022.md b/_collections/_biblio/architecture/architecture_angioni_neuroimaging_2022.md deleted file mode 100644 index 869ceae..0000000 --- a/_collections/_biblio/architecture/architecture_angioni_neuroimaging_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Davide Angioni et al. -title: Neuroimaging correlates of persistent fatigue in older adults - A secondary analysis from the Multidomain Alzheimer Preventive Trial (MAPT) trial -journal: Aging \& Mental Health -year: 2022 -type: article -url: https -//doi.org/10.1080/13607863.2021.1932737 -doi: 10.1080/13607863.2021.1932737 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_assaf_connect_2013.md b/_collections/_biblio/architecture/architecture_assaf_connect_2013.md deleted file mode 100644 index d9290f5..0000000 --- a/_collections/_biblio/architecture/architecture_assaf_connect_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yaniv Assaf et al. -title: The CONNECT project - Combining macro- and micro-structure -journal: Neuroimage -year: 2013 -type: article -doi: 10.1016/j.neuroimage.2013.05.055 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_auzias_disco:_2009.md b/_collections/_biblio/architecture/architecture_auzias_disco:_2009.md deleted file mode 100644 index 582cfc4..0000000 --- a/_collections/_biblio/architecture/architecture_auzias_disco:_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: G. Auzias et al. -title: DISCO - a Coherent Diffeomorphic Framework for Brain Registration under Exhaustive Sulcal Constraints -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_auzias_model-driven_2015-1.md b/_collections/_biblio/architecture/architecture_auzias_model-driven_2015-1.md deleted file mode 100644 index 9ba9074..0000000 --- a/_collections/_biblio/architecture/architecture_auzias_model-driven_2015-1.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Guillaume Auzias et al. -title: Model-driven parameterization of fetal cortical surfaces -year: 2015 -type: inproceedings -doi: 10.1109/ISBI.2015.7164103 -booktitle: 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, Brooklyn, NY, USA, April 16-19, 2015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_auzias_model-driven_2015.md b/_collections/_biblio/architecture/architecture_auzias_model-driven_2015.md deleted file mode 100644 index f590db3..0000000 --- a/_collections/_biblio/architecture/architecture_auzias_model-driven_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: G. Auzias et al. -title: Model-driven parametrization of fetal cortical surfaces -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_auzias_multi-scale_2008.md b/_collections/_biblio/architecture/architecture_auzias_multi-scale_2008.md deleted file mode 100644 index 02a8022..0000000 --- a/_collections/_biblio/architecture/architecture_auzias_multi-scale_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: G. Auzias et al. -title: Multi-scale diffeomorphic cortical registration under manifold sulcal constraints -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_avila_inference_2019.md b/_collections/_biblio/architecture/architecture_avila_inference_2019.md deleted file mode 100644 index 4800309..0000000 --- a/_collections/_biblio/architecture/architecture_avila_inference_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicole Avila et al. -title: Inference of an Extended Short Fiber Bundle Atlas Using Sulcus-Based Constraints for a Diffeomorphic Inter-subject Alignment -year: 2019 -type: inproceedings -doi: 10.1007/978-3-030-05831-9_25 -booktitle: Computational Diffusion MRI ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_balbastre_primatologist:_2017.md b/_collections/_biblio/architecture/architecture_balbastre_primatologist:_2017.md deleted file mode 100644 index a59c710..0000000 --- a/_collections/_biblio/architecture/architecture_balbastre_primatologist:_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yaël Balbastre et al. -title: Primatologist - A modular segmentation pipeline for macaque brain morphometry -journal: NeuroImage -year: 2017 -type: article -doi: 10.1016/j.neuroimage.2017.09.007 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_balbastre_quantitative_2015.md b/_collections/_biblio/architecture/architecture_balbastre_quantitative_2015.md deleted file mode 100644 index c334fa2..0000000 --- a/_collections/_biblio/architecture/architecture_balbastre_quantitative_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yaël Balbastre et al. -title: A Quantitative Approach to Characterize MR Contrasts with Histology -year: 2015 -type: inproceedings -doi: 10.1007/978-3-319-30858-6_10 -booktitle: Brainlesion - Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - First International Workshop, Brainles 2015, Held in Conjunction with MICCAI 2015, Munich, Germany, October 5, 2015, Revised Selected Papers ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_balbastre_validation_2018.md b/_collections/_biblio/architecture/architecture_balbastre_validation_2018.md deleted file mode 100644 index ac2213a..0000000 --- a/_collections/_biblio/architecture/architecture_balbastre_validation_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yaël Balbastre et al. -title: A validation dataset for Macaque brain MRI segmentation -journal: Data in Brief -year: 2018 -type: article -doi: 10.1016/j.dib.2017.11.008 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_balzeau_a_2024.md b/_collections/_biblio/architecture/architecture_balzeau_a_2024.md deleted file mode 100644 index aabe0a8..0000000 --- a/_collections/_biblio/architecture/architecture_balzeau_a_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Antoine Balzeau et al. -title: À la recherche des particularités du cerveau d’Homo neanderthalensis et d’Homo sapiens -journal: Bulletins et mémoires de la Société d’Anthropologie de Paris. BMSAP -year: 2024 -type: article -url: https -//journals.openedition.org/bmsap/12394 -doi: 10.4000/bmsap.12394 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_balzeau_what_2021.md b/_collections/_biblio/architecture/architecture_balzeau_what_2021.md deleted file mode 100644 index 9797435..0000000 --- a/_collections/_biblio/architecture/architecture_balzeau_what_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Antoine Balzeau et al. -title: What Are the Synergies between Paleoanthropology and Brain Imaging? -journal: Symmetry -year: 2021 -type: article -url: https -//www.mdpi.com/2073-8994/13/10/1974 -doi: 10.3390/sym13101974 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_beaujoin_post-mortem_2018.md b/_collections/_biblio/architecture/architecture_beaujoin_post-mortem_2018.md deleted file mode 100644 index 439b97e..0000000 --- a/_collections/_biblio/architecture/architecture_beaujoin_post-mortem_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Justine Beaujoin et al. -title: Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-018-1617-1 -doi: 10.1007/s00429-018-1617-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_benezit_organising_2015.md b/_collections/_biblio/architecture/architecture_benezit_organising_2015.md deleted file mode 100644 index 132e8a3..0000000 --- a/_collections/_biblio/architecture/architecture_benezit_organising_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Audrey Bénézit et al. -title: Organising white matter in a brain without corpus callosum fibres -journal: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior -year: 2015 -type: article -doi: 10.1016/j.cortex.2014.08.022 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_berkovitch_disruption_2021.md b/_collections/_biblio/architecture/architecture_berkovitch_disruption_2021.md deleted file mode 100644 index b7f9695..0000000 --- a/_collections/_biblio/architecture/architecture_berkovitch_disruption_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lucie Berkovitch et al. -title: Disruption of Conscious Access in Psychosis Is Associated with Altered Structural Brain Connectivity -journal: Journal of Neuroscience -year: 2021 -type: article -url: https -//www.jneurosci.org/content/41/3/513 -doi: 10.1523/JNEUROSCI.0945-20.2020 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bertoux_sulcal_2019.md b/_collections/_biblio/architecture/architecture_bertoux_sulcal_2019.md deleted file mode 100644 index d5759eb..0000000 --- a/_collections/_biblio/architecture/architecture_bertoux_sulcal_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Maxime Bertoux et al. -title: Sulcal morphology in Alzheimer's disease - an effective marker of diagnosis and cognition -journal: Neurobiology of Aging -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0197458019302192 -doi: 10.1016/j.neurobiolaging.2019.07.015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_blanc_prodromal_2022.md b/_collections/_biblio/architecture/architecture_blanc_prodromal_2022.md deleted file mode 100644 index 2988359..0000000 --- a/_collections/_biblio/architecture/architecture_blanc_prodromal_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Frederic Blanc et al. -title: Prodromal characteristics of dementia with Lewy bodies - baseline results of the MEMENTO memory clinics nationwide cohort -journal: Alzheimer's Research \& Therapy -year: 2022 -type: article -url: https -//doi.org/10.1186/s13195-022-01037-0 -doi: 10.1186/s13195-022-01037-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bogart_cortical_2012.md b/_collections/_biblio/architecture/architecture_bogart_cortical_2012.md deleted file mode 100644 index 4c99381..0000000 --- a/_collections/_biblio/architecture/architecture_bogart_cortical_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Stephanie Bogart et al. -title: Cortical sulci asymmetries in chimpanzees and macaques - a new look at an old idea -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2012.03.082 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_borne_automatic_2020.md b/_collections/_biblio/architecture/architecture_borne_automatic_2020.md deleted file mode 100644 index c69e829..0000000 --- a/_collections/_biblio/architecture/architecture_borne_automatic_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Léonie Borne et al. -title: Automatic labeling of cortical sulci using patch- or CNN-based segmentation techniques combined with bottom-up geometric constraints -journal: Medical Image Analysis -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1361841520300189 -doi: 10.1016/j.media.2020.101651 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_borne_automatic_2021.md b/_collections/_biblio/architecture/architecture_borne_automatic_2021.md deleted file mode 100644 index d0c8745..0000000 --- a/_collections/_biblio/architecture/architecture_borne_automatic_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Léonie Borne et al. -title: Automatic recognition of specific local cortical folding patterns -journal: NeuroImage -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921004857 -doi: 10.1016/j.neuroimage.2021.118208 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_borne_combining_2019.md b/_collections/_biblio/architecture/architecture_borne_combining_2019.md deleted file mode 100644 index fdcd17b..0000000 --- a/_collections/_biblio/architecture/architecture_borne_combining_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Léonie Borne et al. -title: Combining 3D U-Net and bottom-up geometric constraints for automatic cortical sulci recognition -year: 2019 -type: inproceedings -url: https -//openreview.net/forum?id=ryl0VTZCtV ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_borne_patch-based_2018.md b/_collections/_biblio/architecture/architecture_borne_patch-based_2018.md deleted file mode 100644 index e20982e..0000000 --- a/_collections/_biblio/architecture/architecture_borne_patch-based_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Léonie Borne et al. -title: A Patch-Based Segmentation Approach with High Level Representation of the Data for Cortical Sulci Recognition -year: 2018 -type: inproceedings -doi: 10.1007/978-3-030-00500-9_13 -booktitle: Patch-Based Techniques in Medical Imaging ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_borst_folding_2014.md b/_collections/_biblio/architecture/architecture_borst_folding_2014.md deleted file mode 100644 index 49d1b6f..0000000 --- a/_collections/_biblio/architecture/architecture_borst_folding_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: G. Borst et al. -title: Folding of the anterior cingulate cortex partially explains inhibitory control during childhood - a longitudinal study -journal: Developmental Cognitive Neuroscience -year: 2014 -type: article -doi: 10.1016/j.dcn.2014.02.006 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bouhali_anatomical_2014.md b/_collections/_biblio/architecture/architecture_bouhali_anatomical_2014.md deleted file mode 100644 index 1bec5dd..0000000 --- a/_collections/_biblio/architecture/architecture_bouhali_anatomical_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Florence Bouhali et al. -title: Anatomical connections of the visual word form area -journal: The Journal of Neuroscience - The Official Journal of the Society for Neuroscience -year: 2014 -type: article -doi: 10.1523/JNEUROSCI.4918-13.2014 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_boulant_counteracting_2009.md b/_collections/_biblio/architecture/architecture_boulant_counteracting_2009.md deleted file mode 100644 index f325318..0000000 --- a/_collections/_biblio/architecture/architecture_boulant_counteracting_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Boulant et al. -title: Counteracting radio frequency inhomogeneity in the human brain at 7 Tesla using strongly modulating pulses -journal: Magn Reson Med -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bouteloup_p2-277_2018.md b/_collections/_biblio/architecture/architecture_bouteloup_p2-277_2018.md deleted file mode 100644 index c005a4e..0000000 --- a/_collections/_biblio/architecture/architecture_bouteloup_p2-277_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Vincent Bouteloup et al. -title: P2-277 - Cortical Sulci Width and Incident Dementia in Outpatients Attending French Memory Clinics - The Memento Cohort -journal: Alzheimer's \& Dementia -year: 2018 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1016/j.jalz.2018.06.966 -doi: 10.1016/j.jalz.2018.06.966 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bouyeure_three-dimensional_2018.md b/_collections/_biblio/architecture/architecture_bouyeure_three-dimensional_2018.md deleted file mode 100644 index 81238f5..0000000 --- a/_collections/_biblio/architecture/architecture_bouyeure_three-dimensional_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Antoine Bouyeure et al. -title: Three-Dimensional Probabilistic Maps of Mesial Temporal Lobe Structures in Children and Adolescents’ Brains -journal: Frontiers in Neuroanatomy -year: 2018 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnana.2018.00098 -doi: 10.3389/fnana.2018.00098 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_brion_noise_2013.md b/_collections/_biblio/architecture/architecture_brion_noise_2013.md deleted file mode 100644 index d4aa204..0000000 --- a/_collections/_biblio/architecture/architecture_brion_noise_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Véronique Brion et al. -title: Noise correction for HARDI and HYDI data obtained with multi-channel coils and sum of squares reconstruction - an anisotropic extension of the LMMSE -journal: Magnetic Resonance Imaging -year: 2013 -type: article -doi: 10.1016/j.mri.2013.04.002 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_bristow_hearing_2009.md b/_collections/_biblio/architecture/architecture_bristow_hearing_2009.md deleted file mode 100644 index 6d78b48..0000000 --- a/_collections/_biblio/architecture/architecture_bristow_hearing_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Bristow et al. -title: Hearing faces - How the infant brain matches the face it sees with the speech it hears -journal: J. Cognitive Neuroscience -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_cortical_2008.md b/_collections/_biblio/architecture/architecture_cachia_cortical_2008.md deleted file mode 100644 index 43f78ab..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_cortical_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Cachia et al. -title: Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations -journal: NeuroImage -year: 2008 -type: article -doi: 10.1016/j.neuroimage.2007.08.049 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_how_2018.md b/_collections/_biblio/architecture/architecture_cachia_how_2018.md deleted file mode 100644 index 47c1305..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_how_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Cachia et al. -title: How interindividual differences in brain anatomy shape reading accuracy -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-017-1516-x -doi: 10.1007/s00429-017-1516-x ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_longitudinal_2016.md b/_collections/_biblio/architecture/architecture_cachia_longitudinal_2016.md deleted file mode 100644 index 8b88946..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_longitudinal_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Cachia et al. -title: Longitudinal stability of the folding pattern of the anterior cingulate cortex during development -journal: Developmental Cognitive Neuroscience -year: 2016 -type: article -doi: 10.1016/j.dcn.2016.02.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_mapping_2022.md b/_collections/_biblio/architecture/architecture_cachia_mapping_2022.md deleted file mode 100644 index f0ee63a..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_mapping_2022.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Cachia et al. -title: Mapping the human brain from the prenatal period to infancy using 3D magnetic reonance imaging -journal: The Cambridge Handbook of Congitive Development -year: 2022 -type: article -url: https -//books.google.com/books?hl=en&lr=&id=zhhdEAAAQBAJ&oi=fnd&pg=PA50&dq=info -7CC4s-ZEMSoJ -scholar.google.com&ots=qbsUayXZdg&sig=vTKl0d3BqK4iZ-bIQsYrOovHCPo ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_shape_2014.md b/_collections/_biblio/architecture/architecture_cachia_shape_2014.md deleted file mode 100644 index 1e0930e..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_shape_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Cachia et al. -title: The shape of the ACC contributes to cognitive control efficiency in preschoolers -journal: Journal of Cognitive Neuroscience -year: 2014 -type: article -doi: 10.1162/jocn_a_00459 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_sulcus-based_2005.md b/_collections/_biblio/architecture/architecture_cachia_sulcus-based_2005.md deleted file mode 100644 index 50c7026..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_sulcus-based_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Cachia et al. -title: Sulcus-based morphometry of heteromodal cortex in schizophrenia patients with resistant auditory hallucinations. -year: 2005 -type: inproceedings -booktitle: Proc. 11th HBM CD-Rom Neuroimage vol 26 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cachia_towards_2021.md b/_collections/_biblio/architecture/architecture_cachia_towards_2021.md deleted file mode 100644 index 048c339..0000000 --- a/_collections/_biblio/architecture/architecture_cachia_towards_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Cachia et al. -title: Towards Deciphering the Fetal Foundation of Normal Cognition and Cognitive Symptoms From Sulcation of the Cortex -journal: Frontiers in Neuroanatomy -year: 2021 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnana.2021.712862 -doi: 10.3389/fnana.2021.712862 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cathier_registration_2006.md b/_collections/_biblio/architecture/architecture_cathier_registration_2006.md deleted file mode 100644 index 2f93c7b..0000000 --- a/_collections/_biblio/architecture/architecture_cathier_registration_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Cathier et al. -title: Registration of cortical connectivity matrices -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cavedo_road_2014.md b/_collections/_biblio/architecture/architecture_cavedo_road_2014.md deleted file mode 100644 index 3fe5a02..0000000 --- a/_collections/_biblio/architecture/architecture_cavedo_road_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: E. Cavedo et al. -title: The Road Ahead to Cure Alzheimer's Disease - Development of Biological Markers and Neuroimaging Methods for Prevention Trials Across all Stages and Target Populations -journal: The Journal of Prevention of Alzheimer's Disease -year: 2014 -type: article -doi: 10.14283/jpad.2014.32 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_chabriat_clinical_1999.md b/_collections/_biblio/architecture/architecture_chabriat_clinical_1999.md deleted file mode 100644 index 6b60355..0000000 --- a/_collections/_biblio/architecture/architecture_chabriat_clinical_1999.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: H. Chabriat et al. -title: Clinical severity in CADASIL related to ultrastructural damage in white matter - in vivo study with diffusion tensor MRI -journal: Stroke -year: 1999 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_charidimou_cerebral_2020.md b/_collections/_biblio/architecture/architecture_charidimou_cerebral_2020.md deleted file mode 100644 index e4c04e0..0000000 --- a/_collections/_biblio/architecture/architecture_charidimou_cerebral_2020.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Andreas Charidimou et al. -title: Cerebral Small Vessel Diseases - From Vessel Alterations to Cortical Parenchymal Injury -year: 2020 -type: book ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_chauvel_vivo_2023.md b/_collections/_biblio/architecture/architecture_chauvel_vivo_2023.md deleted file mode 100644 index a1b380f..0000000 --- a/_collections/_biblio/architecture/architecture_chauvel_vivo_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Maëlig Chauvel et al. -title: In vivo mapping of the deep and superficial white matter connectivity in the chimpanzee brain -journal: NeuroImage -year: 2023 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S105381192300513X -doi: 10.1016/j.neuroimage.2023.120362 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_chavas_unsupervised_2022.md b/_collections/_biblio/architecture/architecture_chavas_unsupervised_2022.md deleted file mode 100644 index 1e46091..0000000 --- a/_collections/_biblio/architecture/architecture_chavas_unsupervised_2022.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Joël Chavas et al. -title: Unsupervised Representation Learning of Cingulate Cortical Folding Patterns -year: 2022 -type: inproceedings -doi: 10.1007/978-3-031-16431-6_8 -booktitle: Medical Image Computing and Computer Assisted Intervention – MICCAI 2022 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_clouchoux_anatomically_2005.md b/_collections/_biblio/architecture/architecture_clouchoux_anatomically_2005.md deleted file mode 100644 index 557fd11..0000000 --- a/_collections/_biblio/architecture/architecture_clouchoux_anatomically_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Clouchoux et al. -title: Anatomically constrained surface parameterization for cortical localization -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_clouchoux_cortical_2006.md b/_collections/_biblio/architecture/architecture_clouchoux_cortical_2006.md deleted file mode 100644 index f21f1ed..0000000 --- a/_collections/_biblio/architecture/architecture_clouchoux_cortical_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Clouchoux et al. -title: Cortical localization via hemisphere surface parameterization -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_clouchoux_new_2006.md b/_collections/_biblio/architecture/architecture_clouchoux_new_2006.md deleted file mode 100644 index 1ca52da..0000000 --- a/_collections/_biblio/architecture/architecture_clouchoux_new_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Clouchoux et al. -title: A new cortical surface parcellation model and its automatic implementation -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_coarelli_safety_2022.md b/_collections/_biblio/architecture/architecture_coarelli_safety_2022.md deleted file mode 100644 index 75fcae5..0000000 --- a/_collections/_biblio/architecture/architecture_coarelli_safety_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Giulia Coarelli et al. -title: Safety and efficacy of riluzole in spinocerebellar ataxia type 2 in France (ATRIL) - a multicentre, randomised, double-blind, placebo-controlled trial -journal: The Lancet Neurology -year: 2022 -type: article -url: https -//www.thelancet.com/journals/laneur/article/PIIS1474-4422(21)00457-9/abstract -doi: 10.1016/S1474-4422(21)00457-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cohen_individual_2006.md b/_collections/_biblio/architecture/architecture_cohen_individual_2006.md deleted file mode 100644 index e71ce57..0000000 --- a/_collections/_biblio/architecture/architecture_cohen_individual_2006.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Cohen et al. -title: Individual cognitive training of reading disability improves word identification and sentence comprehension in adults with mild mental retardation -journal: Res Dev Disabil -year: 2006 -type: article -doi: S0891-4222(05)00069-7 [pii] 10.1016/j.ridd.2004.07.008 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_coulon_quasi-isometric_2015.md b/_collections/_biblio/architecture/architecture_coulon_quasi-isometric_2015.md deleted file mode 100644 index bc4d40b..0000000 --- a/_collections/_biblio/architecture/architecture_coulon_quasi-isometric_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: O. Coulon et al. -title: Quasi-isometric length parameterization of cortical sulci - application to handedness and the central sulcus morphology -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_coyle_cortical_2006.md b/_collections/_biblio/architecture/architecture_coyle_cortical_2006.md deleted file mode 100644 index 128cc7d..0000000 --- a/_collections/_biblio/architecture/architecture_coyle_cortical_2006.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: T. Coyle et al. -title: Cortical sulci and bipolar disorder -journal: NeuroReport -year: 2006 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cury_incomplete_2015.md b/_collections/_biblio/architecture/architecture_cury_incomplete_2015.md deleted file mode 100644 index 6559b00..0000000 --- a/_collections/_biblio/architecture/architecture_cury_incomplete_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Claire Cury et al. -title: Incomplete Hippocampal Inversion - A Comprehensive MRI Study of Over 2000 Subjects -journal: FRONTIERS IN NEUROANATOMY -year: 2015 -type: article -doi: 10.3389/fnana.2015.00160 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_cykowski_perisylvian_2008.md b/_collections/_biblio/architecture/architecture_cykowski_perisylvian_2008.md deleted file mode 100644 index 76109f4..0000000 --- a/_collections/_biblio/architecture/architecture_cykowski_perisylvian_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Cykowski et al. -title: Perisylvian Sulcal Morphology and Cerebral Asymmetry Patterns in Adults Who Stutter -journal: Cereb Cortex -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dalbis_local_2018.md b/_collections/_biblio/architecture/architecture_dalbis_local_2018.md deleted file mode 100644 index ba80c1b..0000000 --- a/_collections/_biblio/architecture/architecture_dalbis_local_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Marc-Antoine d'Albis et al. -title: Local structural connectivity is associated with social cognition in autism spectrum disorder -journal: Brain - A Journal of Neurology -year: 2018 -type: article -doi: 10.1093/brain/awy275 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dauguet_three-dimensional_2007.md b/_collections/_biblio/architecture/architecture_dauguet_three-dimensional_2007.md deleted file mode 100644 index a4f4f67..0000000 --- a/_collections/_biblio/architecture/architecture_dauguet_three-dimensional_2007.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Dauguet et al. -title: Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain -journal: J Neurosci Methods -year: 2007 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dauphinot_subjective_2020.md b/_collections/_biblio/architecture/architecture_dauphinot_subjective_2020.md deleted file mode 100644 index 074f2ce..0000000 --- a/_collections/_biblio/architecture/architecture_dauphinot_subjective_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Virginie Dauphinot et al. -title: Subjective cognitive and non-cognitive complaints and brain MRI biomarkers in the MEMENTO cohort -journal: Alzheimer's \& Dementia - Diagnosis, Assessment \& Disease Monitoring -year: 2020 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/dad2.12051 -doi: 10.1002/dad2.12051 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_guio_alteration_2019.md b/_collections/_biblio/architecture/architecture_de_guio_alteration_2019.md deleted file mode 100644 index d0896a2..0000000 --- a/_collections/_biblio/architecture/architecture_de_guio_alteration_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: François De Guio et al. -title: Alteration of the Cortex Shape as a Proxy of White Matter Swelling in Severe Cerebral Small Vessel Disease -journal: Frontiers in Neurology -year: 2019 -type: article -url: https -//www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2019.00753/full -doi: 10.3389/fneur.2019.00753 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_guio_study_2014.md b/_collections/_biblio/architecture/architecture_de_guio_study_2014.md deleted file mode 100644 index 27600ec..0000000 --- a/_collections/_biblio/architecture/architecture_de_guio_study_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: François De Guio et al. -title: A study of cortical morphology in children with fetal alcohol spectrum disorders -journal: Human Brain Mapping -year: 2014 -type: article -doi: 10.1002/hbm.22327 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_guio_white_2015.md b/_collections/_biblio/architecture/architecture_de_guio_white_2015.md deleted file mode 100644 index c8897d7..0000000 --- a/_collections/_biblio/architecture/architecture_de_guio_white_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Francois De Guio et al. -title: White Matter Edema at the Early Stage of Cerebral Autosomal-Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy -journal: STROKE -year: 2015 -type: article -doi: 10.1161/STROKEAHA.114.007018 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_vareilles_development_2023.md b/_collections/_biblio/architecture/architecture_de_vareilles_development_2023.md deleted file mode 100644 index 02cf3e2..0000000 --- a/_collections/_biblio/architecture/architecture_de_vareilles_development_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: H. Vareilles et al. -title: Development of cortical folds in the human brain - An attempt to review biological hypotheses, early neuroimaging investigations and functional correlates -journal: Developmental Cognitive Neuroscience -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1878929323000543 -doi: 10.1016/j.dcn.2023.101249 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_vareilles_exploring_2023.md b/_collections/_biblio/architecture/architecture_de_vareilles_exploring_2023.md deleted file mode 100644 index 563417d..0000000 --- a/_collections/_biblio/architecture/architecture_de_vareilles_exploring_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Héloïse De Vareilles et al. -title: Exploring the emergence of morphological asymmetries around the brain’s Sylvian fissure - a longitudinal study of shape variability in preterm infants -journal: Cerebral Cortex -year: 2023 -type: article -url: https -//doi.org/10.1093/cercor/bhac533 -doi: 10.1093/cercor/bhac533 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_vareilles_folding_2019.md b/_collections/_biblio/architecture/architecture_de_vareilles_folding_2019.md deleted file mode 100644 index aab7f75..0000000 --- a/_collections/_biblio/architecture/architecture_de_vareilles_folding_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Héloïse Vareilles et al. -title: Folding dynamics of the Central Sulcus - a longitudinal study on preterms Authors - Introduction -year: 2019 -type: inproceedings -url: https -//hal.science/hal-02876130/file/HeloiseOHBM.pdf ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_vareilles_longitudinal_2019.md b/_collections/_biblio/architecture/architecture_de_vareilles_longitudinal_2019.md deleted file mode 100644 index ceab28e..0000000 --- a/_collections/_biblio/architecture/architecture_de_vareilles_longitudinal_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Héloïse Vareilles et al. -title: A Longitudinal Study of the Evolution of the Central Sulcus’ Shape in Preterm Infants Using Manifold Learning -year: 2019 -type: inproceedings -doi: 10.1007/978-3-030-32875-7_16 -booktitle: Smart Ultrasound Imaging and Perinatal, Preterm and Paediatric Image Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_de_vareilles_shape_2022.md b/_collections/_biblio/architecture/architecture_de_vareilles_shape_2022.md deleted file mode 100644 index 55237cb..0000000 --- a/_collections/_biblio/architecture/architecture_de_vareilles_shape_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Héloïse Vareilles et al. -title: Shape variability of the central sulcus in the developing brain - A longitudinal descriptive and predictive study in preterm infants -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921011083 -doi: 10.1016/j.neuroimage.2021.118837 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dehaene_cerebral_2001.md b/_collections/_biblio/architecture/architecture_dehaene_cerebral_2001.md deleted file mode 100644 index 71340b5..0000000 --- a/_collections/_biblio/architecture/architecture_dehaene_cerebral_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Dehaene et al. -title: Cerebral mechanisms of word masking and unconscious repetition priming -journal: Nat Neurosci -year: 2001 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_delettre_comparison_2019.md b/_collections/_biblio/architecture/architecture_delettre_comparison_2019.md deleted file mode 100644 index 07e1f46..0000000 --- a/_collections/_biblio/architecture/architecture_delettre_comparison_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Céline Delettre et al. -title: Comparison between diffusion MRI tractography and histological tract-tracing of cortico-cortical structural connectivity in the ferret brain -journal: Network Neuroscience -year: 2019 -type: article -url: https -//doi.org/10.1162/netn_a_00098 -doi: 10.1162/netn_a_00098 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_delmaire_disorganized_2005.md b/_collections/_biblio/architecture/architecture_delmaire_disorganized_2005.md deleted file mode 100644 index 550da8a..0000000 --- a/_collections/_biblio/architecture/architecture_delmaire_disorganized_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Delmaire et al. -title: Disorganized somatotopy in the putamen of patients with focal hand dystonia -journal: Neurology -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_deman_intranat_2017.md b/_collections/_biblio/architecture/architecture_deman_intranat_2017.md deleted file mode 100644 index 36375bc..0000000 --- a/_collections/_biblio/architecture/architecture_deman_intranat_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Deman et al. -title: INTRANAT ELECTRODES - A FREE SOFTWARE TO VISUALIZE SEEG DATA IN PATIENT REFERENTIAL AND INITIATE GROUP STUDIES -year: 2017 -type: inproceedings -url: https -//scholar.google.com/scholar?cluster=11665156421866533739&hl=en&oi=scholarr -booktitle: EPILEPSIA ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_deman_intranat_2018.md b/_collections/_biblio/architecture/architecture_deman_intranat_2018.md deleted file mode 100644 index e697524..0000000 --- a/_collections/_biblio/architecture/architecture_deman_intranat_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Pierre Deman et al. -title: IntrAnat Electrodes - A Free Database and Visualization Software for Intracranial Electroencephalographic Data Processed for Case and Group Studies -journal: Frontiers in Neuroinformatics -year: 2018 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2018.00040 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_descoteaux_diffusion_2009.md b/_collections/_biblio/architecture/architecture_descoteaux_diffusion_2009.md deleted file mode 100644 index d3f60ac..0000000 --- a/_collections/_biblio/architecture/architecture_descoteaux_diffusion_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Maxime Descoteaux et al. -title: Diffusion propagator imaging - using Laplace's equation and multiple shell acquisitions to reconstruct the diffusion propagator -journal: Inf Process Med Imaging -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_devos_trial_2022.md b/_collections/_biblio/architecture/architecture_devos_trial_2022.md deleted file mode 100644 index 0339369..0000000 --- a/_collections/_biblio/architecture/architecture_devos_trial_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: David Devos et al. -title: Trial of Deferiprone in Parkinson’s Disease -journal: New England Journal of Medicine -year: 2022 -type: article -url: https -//doi.org/10.1056/NEJMoa2209254 -doi: 10.1056/NEJMoa2209254 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_[brain_2012.md b/_collections/_biblio/architecture/architecture_dubois_[brain_2012.md deleted file mode 100644 index 8d18b15..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_[brain_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Dubois et al. -title: [Brain development of infant and MRI by diffusion tensor imaging] -journal: Neurophysiologie Clinique = Clinical Neurophysiology -year: 2012 -type: article -doi: 10.1016/j.neucli.2011.08.001 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008-1.md b/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008-1.md deleted file mode 100644 index 1b9bf6e..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008-1.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jessica Dubois et al. -title: Asynchrony of the early maturation of white matter bundles in healthy infants - quantitative landmarks revealed noninvasively by diffusion tensor imaging -journal: Human Brain Mapping -year: 2008 -type: article -doi: 10.1002/hbm.20363 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008.md b/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008.md deleted file mode 100644 index 1dd7b2c..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_asynchrony_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Dubois et al. -title: Asynchrony of the early maturation of white matter bundles in healthy infants - quantitative landmarks revealed non-invasively by diffusion tensor imaging -journal: Human Brain Mapping -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_cognitive_2018.md b/_collections/_biblio/architecture/architecture_dubois_cognitive_2018.md deleted file mode 100644 index 3694754..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_cognitive_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Bruno Dubois et al. -title: Cognitive and neuroimaging features and brain β-amyloidosis in individuals at risk of Alzheimer's disease (INSIGHT-preAD) - a longitudinal observational study -journal: The Lancet Neurology -year: 2018 -type: article -url: https -//www.thelancet.com/journals/laneur/article/PIIS1474-4422(18)30029-2/abstract -doi: 10.1016/S1474-4422(18)30029-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_dynamics_2019.md b/_collections/_biblio/architecture/architecture_dubois_dynamics_2019.md deleted file mode 100644 index 0f03d66..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_dynamics_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jessica Dubois et al. -title: The dynamics of cortical folding waves and prematurity-related deviations revealed by spatial and spectral analysis of gyrification -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918301903 -doi: 10.1016/j.neuroimage.2018.03.005 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_exploring_2016.md b/_collections/_biblio/architecture/architecture_dubois_exploring_2016.md deleted file mode 100644 index 9af0b99..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_exploring_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jessica Dubois et al. -title: Exploring the successive waves of cortical folding in the developing brain using MRI and spectral analysis of gyrification -year: 2016 -type: inproceedings -doi: 10.1109/ISBI.2016.7493259 -booktitle: 13th IEEE International Symposium on Biomedical Imaging, ISBI 2016, Prague, Czech Republic, April 13-16, 2016 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dubois_structural_2009.md b/_collections/_biblio/architecture/architecture_dubois_structural_2009.md deleted file mode 100644 index c70a374..0000000 --- a/_collections/_biblio/architecture/architecture_dubois_structural_2009.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Dubois et al. -title: Structural asymmetries in the infant language and sensori-motor networks -journal: Cereb Cortex -year: 2009 -type: article -doi: bhn097 [pii] 10.1093/cercor/bhn097 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_duchesnay_classification_2007.md b/_collections/_biblio/architecture/architecture_duchesnay_classification_2007.md deleted file mode 100644 index 8cf2075..0000000 --- a/_collections/_biblio/architecture/architecture_duchesnay_classification_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edouard Duchesnay et al. -title: Classification based on cortical folding patterns -journal: IEEE Transactions on Medical Imaging -year: 2007 -type: article -doi: 10.1109/TMI.2007.892501 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_duchesnay_different_2018.md b/_collections/_biblio/architecture/architecture_duchesnay_different_2018.md deleted file mode 100644 index ea8f383..0000000 --- a/_collections/_biblio/architecture/architecture_duchesnay_different_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edouard Duchesnay et al. -title: Different Types of White Matter Hyperintensities in CADASIL -journal: Frontiers in Neurology -year: 2018 -type: article -doi: 10.3389/fneur.2018.00526 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_duchesnay_feature_2011.md b/_collections/_biblio/architecture/architecture_duchesnay_feature_2011.md deleted file mode 100644 index 68d3008..0000000 --- a/_collections/_biblio/architecture/architecture_duchesnay_feature_2011.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edouard Duchesnay et al. -title: Feature selection and classification of imbalanced datasets - Application to PET images of children with autistic spectrum disorders -journal: NeuroImage -year: 2011 -type: article -url: http -//www.sciencedirect.com/science/article/pii/S105381191100499X -doi: 10.1016/j.neuroimage.2011.05.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_duchesnay_guessing_2004.md b/_collections/_biblio/architecture/architecture_duchesnay_guessing_2004.md deleted file mode 100644 index 6ee80ba..0000000 --- a/_collections/_biblio/architecture/architecture_duchesnay_guessing_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edouard Duchesnay et al. -title: Guessing the Sex from the Shapes of Cortical Folds -year: 2004 -type: inproceedings -booktitle: HBM, Budapest ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_duchesnay_population_2004.md b/_collections/_biblio/architecture/architecture_duchesnay_population_2004.md deleted file mode 100644 index 8eaf8d1..0000000 --- a/_collections/_biblio/architecture/architecture_duchesnay_population_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edouard Duchesnay et al. -title: Population Classification Based on Structural Morphometry of Cortical Sulci -year: 2004 -type: inproceedings -booktitle: International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_dufouil_cognitive_2017.md b/_collections/_biblio/architecture/architecture_dufouil_cognitive_2017.md deleted file mode 100644 index 8604491..0000000 --- a/_collections/_biblio/architecture/architecture_dufouil_cognitive_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Carole Dufouil et al. -title: Cognitive and imaging markers in non-demented subjects attending a memory clinic - study design and baseline findings of the MEMENTO cohort -journal: Alzheimer's Research \& Therapy -year: 2017 -type: article -doi: 10.1186/s13195-017-0288-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_el_kouby_main_2005.md b/_collections/_biblio/architecture/architecture_el_kouby_main_2005.md deleted file mode 100644 index 7f66a87..0000000 --- a/_collections/_biblio/architecture/architecture_el_kouby_main_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: V. El Kouby et al. -title: Main fiber tracks detection through classification of MR diffusion imaging data -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_el_kouby_mr_2005.md b/_collections/_biblio/architecture/architecture_el_kouby_mr_2005.md deleted file mode 100644 index 45b60d8..0000000 --- a/_collections/_biblio/architecture/architecture_el_kouby_mr_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: V. El Kouby et al. -title: MR diffusion-based inference of a fiber bundle model from a population of subjects -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_epelbaum_neural_2018.md b/_collections/_biblio/architecture/architecture_epelbaum_neural_2018.md deleted file mode 100644 index 1a057d3..0000000 --- a/_collections/_biblio/architecture/architecture_epelbaum_neural_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Stephane Epelbaum et al. -title: Neural correlates of episodic memory in the Memento cohort -journal: Alzheimer's \& Dementia - Translational Research \& Clinical Interventions -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2352873718300209 -doi: 10.1016/j.trci.2018.03.010 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_favre_widespread_2019.md b/_collections/_biblio/architecture/architecture_favre_widespread_2019.md deleted file mode 100644 index f9d2dd5..0000000 --- a/_collections/_biblio/architecture/architecture_favre_widespread_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Pauline Favre et al. -title: Widespread white matter microstructural abnormalities in bipolar disorder - evidence from mega- and meta-analyses across 3033 individuals -journal: Neuropsychopharmacology -year: 2019 -type: article -url: https -//www.nature.com/articles/s41386-019-0485-6 -doi: 10.1038/s41386-019-0485-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_fillard_free_2009.md b/_collections/_biblio/architecture/architecture_fillard_free_2009.md deleted file mode 100644 index ec61c42..0000000 --- a/_collections/_biblio/architecture/architecture_fillard_free_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Fillard et al. -title: Free Spin Tracking - A Novel Global Tractography Algorithm -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_fillard_novel_2009.md b/_collections/_biblio/architecture/architecture_fillard_novel_2009.md deleted file mode 100644 index 78c82f0..0000000 --- a/_collections/_biblio/architecture/architecture_fillard_novel_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Fillard et al. -title: A Novel Global Tractography Framework based on an Adaptive Spin Glass Model -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_fillard_quantitative_2011.md b/_collections/_biblio/architecture/architecture_fillard_quantitative_2011.md deleted file mode 100644 index 1dafaa8..0000000 --- a/_collections/_biblio/architecture/architecture_fillard_quantitative_2011.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Pierre Fillard et al. -title: Quantitative evaluation of 10 tractography algorithms on a realistic diffusion MR phantom -journal: NEUROIMAGE -year: 2011 -type: article -doi: 10.1016/j.neuroimage.2011.01.032 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_fish_influences_2017.md b/_collections/_biblio/architecture/architecture_fish_influences_2017.md deleted file mode 100644 index a939bf6..0000000 --- a/_collections/_biblio/architecture/architecture_fish_influences_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Ari Fish et al. -title: Influences of Brain Size, Sex, and Sex Chromosome Complement on the Architecture of Human Cortical Folding -journal: Cerebral Cortex (New York, N.Y. - 1991) -year: 2017 -type: article -doi: 10.1093/cercor/bhw323 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_foubet_shapes_2023.md b/_collections/_biblio/architecture/architecture_foubet_shapes_2023.md deleted file mode 100644 index 0a9d808..0000000 --- a/_collections/_biblio/architecture/architecture_foubet_shapes_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Ophelie Foubet et al. -title: On the Shapes of the Precentral Gyrus of Humans and Chimpanzees -year: 2023 -type: misc -url: https -//hal.science/hal-04477128 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_fouquet_role_2012.md b/_collections/_biblio/architecture/architecture_fouquet_role_2012.md deleted file mode 100644 index 5289e0a..0000000 --- a/_collections/_biblio/architecture/architecture_fouquet_role_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Marine Fouquet et al. -title: Role of hippocampal CA1 atrophy in memory encoding deficits in amnestic Mild Cognitive Impairment -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2011.11.036 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_frison_diabetes_2021.md b/_collections/_biblio/architecture/architecture_frison_diabetes_2021.md deleted file mode 100644 index fbd2d2d..0000000 --- a/_collections/_biblio/architecture/architecture_frison_diabetes_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Eric Frison et al. -title: Diabetes Mellitus and Cognition -journal: Neurology -year: 2021 -type: article -url: https -//www.neurology.org/doi/full/10.1212/WNL.0000000000012440 -doi: 10.1212/WNL.0000000000012440 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_germanaud_larger_2012.md b/_collections/_biblio/architecture/architecture_germanaud_larger_2012.md deleted file mode 100644 index ba02b85..0000000 --- a/_collections/_biblio/architecture/architecture_germanaud_larger_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: David Germanaud et al. -title: Larger is twistier - spectral analysis of gyrification (SPANGY) applied to adult brain size polymorphism -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2012.07.053 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_germanaud_simplified_2014.md b/_collections/_biblio/architecture/architecture_germanaud_simplified_2014.md deleted file mode 100644 index 5501d13..0000000 --- a/_collections/_biblio/architecture/architecture_germanaud_simplified_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Germanaud et al. -title: Simplified gyral pattern in severe developmental microcephalies? New insights from allometric modeling for spatial and spectral analysis of gyrification -journal: NeuroImage -year: 2014 -type: article -doi: 10.1016/j.neuroimage.2014.07.057 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_gesierich_features_2016.md b/_collections/_biblio/architecture/architecture_gesierich_features_2016.md deleted file mode 100644 index 7c660f8..0000000 --- a/_collections/_biblio/architecture/architecture_gesierich_features_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Benno Gesierich et al. -title: Features and Determinants of Lacune Shape - Relationship With Fiber Tracts and Perforating Arteries -journal: Stroke -year: 2016 -type: article -doi: 10.1161/STROKEAHA.116.012779 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ghadery_r2*mapping_2015.md b/_collections/_biblio/architecture/architecture_ghadery_r2*mapping_2015.md deleted file mode 100644 index 08fe439..0000000 --- a/_collections/_biblio/architecture/architecture_ghadery_r2*mapping_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Christine Ghadery et al. -title: R2*mapping for brain iron - associations with cognition in normal aging -journal: NEUROBIOLOGY OF AGING -year: 2015 -type: article -doi: 10.1016/j.neurobiolaging.2014.09.013 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_gilson_network_2019.md b/_collections/_biblio/architecture/architecture_gilson_network_2019.md deleted file mode 100644 index 2c192ba..0000000 --- a/_collections/_biblio/architecture/architecture_gilson_network_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Matthieu Gilson et al. -title: Network analysis of whole-brain fMRI dynamics - A new framework based on dynamic communicability -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811919305889 -doi: 10.1016/j.neuroimage.2019.116007 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ginsburger_improving_2018.md b/_collections/_biblio/architecture/architecture_ginsburger_improving_2018.md deleted file mode 100644 index 9f0f52a..0000000 --- a/_collections/_biblio/architecture/architecture_ginsburger_improving_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Kévin Ginsburger et al. -title: Improving the Realism of White Matter Numerical Phantoms - A Step toward a Better Understanding of the Influence of Structural Disorders in Diffusion MRI -journal: Frontiers in Physics -year: 2018 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fphy.2018.00012 -doi: 10.3389/fphy.2018.00012 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ginsburger_medusa_2019.md b/_collections/_biblio/architecture/architecture_ginsburger_medusa_2019.md deleted file mode 100644 index c12868c..0000000 --- a/_collections/_biblio/architecture/architecture_ginsburger_medusa_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Kévin Ginsburger et al. -title: MEDUSA - A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S105381191930151X -doi: 10.1016/j.neuroimage.2019.02.055 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_glasel_robust_2011.md b/_collections/_biblio/architecture/architecture_glasel_robust_2011.md deleted file mode 100644 index 7611433..0000000 --- a/_collections/_biblio/architecture/architecture_glasel_robust_2011.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: H. Glasel et al. -title: A robust cerebral asymmetry in the infant brain - The rightward superior temporal sulcus -journal: NEUROIMAGE -year: 2011 -type: article -doi: 10.1016/j.neuroimage.2011.06.016 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_goicovich_fiber_2021.md b/_collections/_biblio/architecture/architecture_goicovich_fiber_2021.md deleted file mode 100644 index d549938..0000000 --- a/_collections/_biblio/architecture/architecture_goicovich_fiber_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Isaac Goicovich et al. -title: Fiber Clustering Acceleration With a Modified Kmeans++ Algorithm Using Data Parallelism -journal: Frontiers in Neuroinformatics -year: 2021 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2021.727859 -doi: 10.3389/fninf.2021.727859 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_gondova_predicting_2023.md b/_collections/_biblio/architecture/architecture_gondova_predicting_2023.md deleted file mode 100644 index e761289..0000000 --- a/_collections/_biblio/architecture/architecture_gondova_predicting_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Andrea Gondová et al. -title: Predicting neurodevelopmental outcomes from neonatal cortical microstructure - A conceptual replication study -journal: Neuroimage - Reports -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2666956023000156 -doi: 10.1016/j.ynirp.2023.100170 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_gonzalez-bautista_development_2023.md b/_collections/_biblio/architecture/architecture_gonzalez-bautista_development_2023.md deleted file mode 100644 index 53b26a7..0000000 --- a/_collections/_biblio/architecture/architecture_gonzalez-bautista_development_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Emmanuel Gonzalez-Bautista et al. -title: Development and Validation of a Cutoff for the Chair Stand Test as a Screening for Mobility Impairment in the Context of the Integrated Care for Older People Program -journal: The Journals of Gerontology - Series A -year: 2023 -type: article -url: https -//doi.org/10.1093/gerona/glac055 -doi: 10.1093/gerona/glac055 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_grasset_explaining_2022.md b/_collections/_biblio/architecture/architecture_grasset_explaining_2022.md deleted file mode 100644 index a732e5f..0000000 --- a/_collections/_biblio/architecture/architecture_grasset_explaining_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Leslie Grasset et al. -title: Explaining the association between social and lifestyle factors and cognitive functions - a pathway analysis in the Memento cohort -journal: Alzheimer's Research \& Therapy -year: 2022 -type: article -url: https -//doi.org/10.1186/s13195-022-01013-8 -doi: 10.1186/s13195-022-01013-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_grasset_physical_2023.md b/_collections/_biblio/architecture/architecture_grasset_physical_2023.md deleted file mode 100644 index 197f6a0..0000000 --- a/_collections/_biblio/architecture/architecture_grasset_physical_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Leslie Grasset et al. -title: Physical activity, biomarkers of brain pathologies and dementia risk - Results from the Memento clinical cohort -journal: Alzheimer's \& Dementia -year: 2023 -type: article -url: https -//alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.13360 -doi: 10.1002/alz.13360 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guen_regional_2017.md b/_collections/_biblio/architecture/architecture_guen_regional_2017.md deleted file mode 100644 index 645dd9d..0000000 --- a/_collections/_biblio/architecture/architecture_guen_regional_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Guen et al. -title: Regional study of the genetic influence on the sulcal pits -year: 2017 -type: inproceedings -doi: 10.1109/ISBI.2017.7950472 -booktitle: 14th IEEE International Symposium on Biomedical Imaging, ISBI 2017, Melbourne, Australia, April 18-21, 2017 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guerville_kidney_2021.md b/_collections/_biblio/architecture/architecture_guerville_kidney_2021.md deleted file mode 100644 index e98f77c..0000000 --- a/_collections/_biblio/architecture/architecture_guerville_kidney_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Florent Guerville et al. -title: Kidney Function and Cognitive Decline in Older Adults - Examining the Role of Neurodegeneration -journal: Journal of the American Geriatrics Society -year: 2021 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16954 -doi: 10.1111/jgs.16954 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_automatic_2012.md b/_collections/_biblio/architecture/architecture_guevara_automatic_2012.md deleted file mode 100644 index c2f72dc..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_automatic_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Guevara et al. -title: Automatic fiber bundle segmentation in massive tractography datasets using a multi-subject bundle atlas -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2012.02.071 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_automatic_2015.md b/_collections/_biblio/architecture/architecture_guevara_automatic_2015.md deleted file mode 100644 index 71ebf41..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_automatic_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Guevara et al. -title: Automatic segmentation of short association bundles using a new multi-subject atlas of the left hemisphere fronto-parietal brain connections -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2015 -type: article -doi: 10.1109/EMBC.2015.7318390 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_connectivity-based_2008.md b/_collections/_biblio/architecture/architecture_guevara_connectivity-based_2008.md deleted file mode 100644 index 5beb1ba..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_connectivity-based_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Guevara et al. -title: Connectivity-based parcellation of the cortical surface using Q-ball imaging -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_creation_2016.md b/_collections/_biblio/architecture/architecture_guevara_creation_2016.md deleted file mode 100644 index 655ab69..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_creation_2016.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Guevara et al. -title: Creation of a whole brain short association bundle atlas using a hybrid approach. -year: 2016 -type: inproceedings -doi: 10.1109/EMBC.2016.7590899 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_definition_2023.md b/_collections/_biblio/architecture/architecture_guevara_definition_2023.md deleted file mode 100644 index 95e44e0..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_definition_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Miguel Guevara et al. -title: Définition de la normalité du fer intracérébral par IRM/QSM pour le diagnostic des maladies neurodégénératives -year: 2023 -type: inproceedings -url: https -//hal.science/hal-04271807 -booktitle: Journées Francophones de Radiologie 2023 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_disentangling_2022.md b/_collections/_biblio/architecture/architecture_guevara_disentangling_2022.md deleted file mode 100644 index 6759294..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_disentangling_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Miguel Guevara et al. -title: Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922003214 -doi: 10.1016/j.neuroimage.2022.119197 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_identification_2019.md b/_collections/_biblio/architecture/architecture_guevara_identification_2019.md deleted file mode 100644 index 9f03912..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_identification_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Guevara et al. -title: Identification of U-Bundles Based on Sulcus Morphology -year: 2019 -type: inproceedings -doi: 10.1007/978-3-030-13835-6_1 -booktitle: Processing and Analysis of Biomedical Information ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_inference_2009.md b/_collections/_biblio/architecture/architecture_guevara_inference_2009.md deleted file mode 100644 index 8767dd6..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_inference_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Guevara et al. -title: Inference of a fiber bundle atlas using a two-level clustering strategy -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_reproducibility_2017.md b/_collections/_biblio/architecture/architecture_guevara_reproducibility_2017.md deleted file mode 100644 index a28f2f2..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_reproducibility_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Miguel Guevara et al. -title: Reproducibility of superficial white matter tracts using diffusion-weighted imaging tractography -journal: NeuroImage -year: 2017 -type: article -doi: 10.1016/j.neuroimage.2016.11.066 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guevara_superficial_2020.md b/_collections/_biblio/architecture/architecture_guevara_superficial_2020.md deleted file mode 100644 index 9d66549..0000000 --- a/_collections/_biblio/architecture/architecture_guevara_superficial_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Miguel Guevara et al. -title: Superficial white matter - A review on the dMRI analysis methods and applications -journal: NeuroImage -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811920301609 -doi: 10.1016/j.neuroimage.2020.116673 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guillon_detection_2021.md b/_collections/_biblio/architecture/architecture_guillon_detection_2021.md deleted file mode 100644 index 1385b14..0000000 --- a/_collections/_biblio/architecture/architecture_guillon_detection_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Louise Guillon et al. -title: Detection of Abnormal Folding Patterns with Unsupervised Deep Generative Models -year: 2021 -type: inproceedings -doi: 10.1007/978-3-030-87586-2_7 -booktitle: Machine Learning in Clinical Neuroimaging ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_guillon_identification_2024.md b/_collections/_biblio/architecture/architecture_guillon_identification_2024.md deleted file mode 100644 index 85871d5..0000000 --- a/_collections/_biblio/architecture/architecture_guillon_identification_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Louise Guillon et al. -title: Identification of rare cortical folding patterns using unsupervised deep learning -journal: Imaging Neuroscience -year: 2024 -type: article -url: https -//direct.mit.edu/imag/article/doi/10.1162/imag_a_00084/119130 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_habert_evaluation_2018.md b/_collections/_biblio/architecture/architecture_habert_evaluation_2018.md deleted file mode 100644 index 9648612..0000000 --- a/_collections/_biblio/architecture/architecture_habert_evaluation_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Marie-Odile Habert et al. -title: Evaluation of amyloid status in a cohort of elderly individuals with memory complaints - validation of the method of quantification and determination of positivity thresholds -journal: Annals of Nuclear Medicine -year: 2018 -type: article -url: https -//doi.org/10.1007/s12149-017-1221-0 -doi: 10.1007/s12149-017-1221-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_haeger_imaging_2020.md b/_collections/_biblio/architecture/architecture_haeger_imaging_2020.md deleted file mode 100644 index 209bf98..0000000 --- a/_collections/_biblio/architecture/architecture_haeger_imaging_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Alexa Haeger et al. -title: Imaging the aging brain - study design and baseline findings of the SENIOR cohort -journal: Alzheimer's Research \& Therapy -year: 2020 -type: article -url: https -//alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1 -doi: 10.1186/s13195-020-00642-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hamelin_sulcal_2015.md b/_collections/_biblio/architecture/architecture_hamelin_sulcal_2015.md deleted file mode 100644 index c1f4827..0000000 --- a/_collections/_biblio/architecture/architecture_hamelin_sulcal_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lorraine Hamelin et al. -title: Sulcal morphology as a new imaging marker for the diagnosis of early onset Alzheimer's disease -journal: Neurobiology of Aging -year: 2015 -type: article -doi: 10.1016/j.neurobiolaging.2015.04.019 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hanon_plasma_2018.md b/_collections/_biblio/architecture/architecture_hanon_plasma_2018.md deleted file mode 100644 index f720e18..0000000 --- a/_collections/_biblio/architecture/architecture_hanon_plasma_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Olivier Hanon et al. -title: Plasma amyloid levels within the Alzheimer's process and correlations with central biomarkers -journal: Alzheimer's \& Dementia -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1552526018300219 -doi: 10.1016/j.jalz.2018.01.004 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hanon_plasma_2022.md b/_collections/_biblio/architecture/architecture_hanon_plasma_2022.md deleted file mode 100644 index 32c41e5..0000000 --- a/_collections/_biblio/architecture/architecture_hanon_plasma_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Olivier Hanon et al. -title: Plasma amyloid beta predicts conversion to dementia in subjects with mild cognitive impairment - The BALTAZAR study -journal: Alzheimer's \& Dementia -year: 2022 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/alz.12613 -doi: 10.1002/alz.12613 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_harvey_increased_2021.md b/_collections/_biblio/architecture/architecture_harvey_increased_2021.md deleted file mode 100644 index 15d6159..0000000 --- a/_collections/_biblio/architecture/architecture_harvey_increased_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Adam Harvey et al. -title: Increased representation of the non-dominant hand in pianists demonstrated by measurement of 3D morphology of the central sulcus -journal: Psychoradiology -year: 2021 -type: article -url: https -//doi.org/10.1093/psyrad/kkab004 -doi: 10.1093/psyrad/kkab004 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_he_fiveyear_2021.md b/_collections/_biblio/architecture/architecture_he_fiveyear_2021.md deleted file mode 100644 index 77307fd..0000000 --- a/_collections/_biblio/architecture/architecture_he_fiveyear_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lingxiao He et al. -title: Five‐Year Lower Extremity Function is Associated with White Matter Abnormality in Older Adults -journal: Journal of the American Geriatrics Society -year: 2021 -type: article -url: https -//agsjournals.onlinelibrary.wiley.com/doi/10.1111/jgs.16989 -doi: 10.1111/jgs.16989 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_herve_shape_2005.md b/_collections/_biblio/architecture/architecture_herve_shape_2005.md deleted file mode 100644 index e54f869..0000000 --- a/_collections/_biblio/architecture/architecture_herve_shape_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Herve et al. -title: Shape and volume of lacunar infarcts - a 3D MRI study in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy -journal: Stroke -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hopkins_evolution_2014.md b/_collections/_biblio/architecture/architecture_hopkins_evolution_2014.md deleted file mode 100644 index 4d42ace..0000000 --- a/_collections/_biblio/architecture/architecture_hopkins_evolution_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: William Hopkins et al. -title: Evolution of the Central Sulcus Morphology in Primates -journal: Brain Behavior and Evolution -year: 2014 -type: article -doi: 10.1159/000362431 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hopkins_genetic_2023.md b/_collections/_biblio/architecture/architecture_hopkins_genetic_2023.md deleted file mode 100644 index 91d5f04..0000000 --- a/_collections/_biblio/architecture/architecture_hopkins_genetic_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: William Hopkins et al. -title: Genetic determinants of individual variation in the superior temporal sulcus of chimpanzees (Pan troglodytes) -journal: Cerebral Cortex -year: 2023 -type: article -url: https -//doi.org/10.1093/cercor/bhac183 -doi: 10.1093/cercor/bhac183 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hotier_social_2017.md b/_collections/_biblio/architecture/architecture_hotier_social_2017.md deleted file mode 100644 index b9162a7..0000000 --- a/_collections/_biblio/architecture/architecture_hotier_social_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Hotier et al. -title: Social cognition in autism is associated with the neurodevelopment of the posterior superior temporal sulcus -journal: Acta Psychiatrica Scandinavica -year: 2017 -type: article -doi: 10.1111/acps.12814 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hou_measurement_2019.md b/_collections/_biblio/architecture/architecture_hou_measurement_2019.md deleted file mode 100644 index 6255bf8..0000000 --- a/_collections/_biblio/architecture/architecture_hou_measurement_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lewis Hou et al. -title: Measurement of Sylvian Fissure asymmetry and occipital bending in humans and Pan troglodytes -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918307432 -doi: 10.1016/j.neuroimage.2018.08.045 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_hozer_lithium_2021.md b/_collections/_biblio/architecture/architecture_hozer_lithium_2021.md deleted file mode 100644 index 08318d0..0000000 --- a/_collections/_biblio/architecture/architecture_hozer_lithium_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Franz Hozer et al. -title: Lithium prevents grey matter atrophy in patients with bipolar disorder - an international multicenter study -journal: Psychological Medicine -year: 2021 -type: article -url: https -//www.cambridge.org/core/journals/psychological-medicine/article/abs/lithium-prevents-grey-matter-atrophy-in-patients-with-bipolar-disorder-an-international-multicenter-study/6267A7E11F17EFDF5857F06E4C233D4F -doi: 10.1017/S0033291719004112 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_huerta_inter-subject_2020.md b/_collections/_biblio/architecture/architecture_huerta_inter-subject_2020.md deleted file mode 100644 index 9a540f4..0000000 --- a/_collections/_biblio/architecture/architecture_huerta_inter-subject_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Isaías Huerta et al. -title: Inter-Subject Clustering of Brain Fibers from Whole-Brain Tractography -year: 2020 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9175342 -doi: 10.1109/EMBC44109.2020.9175342 -booktitle: 2020 42nd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_im_spatial_2010.md b/_collections/_biblio/architecture/architecture_im_spatial_2010.md deleted file mode 100644 index 536ed31..0000000 --- a/_collections/_biblio/architecture/architecture_im_spatial_2010.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Kiho Im et al. -title: Spatial Distribution of Deep Sulcal Landmarks and Hemispherical Asymmetry on the Cortical Surface -journal: CEREBRAL CORTEX -year: 2010 -type: article -doi: 10.1093/cercor/bhp127 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ji_increased_2019.md b/_collections/_biblio/architecture/architecture_ji_increased_2019.md deleted file mode 100644 index 01cf283..0000000 --- a/_collections/_biblio/architecture/architecture_ji_increased_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Ellen Ji et al. -title: Increased and Decreased Superficial White Matter Structural Connectivity in Schizophrenia and Bipolar Disorder -journal: Schizophrenia Bulletin -year: 2019 -type: article -url: https -//doi.org/10.1093/schbul/sbz015 -doi: 10.1093/schbul/sbz015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_jouvent_apathy_2011.md b/_collections/_biblio/architecture/architecture_jouvent_apathy_2011.md deleted file mode 100644 index 81e511b..0000000 --- a/_collections/_biblio/architecture/architecture_jouvent_apathy_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: E. Jouvent et al. -title: Apathy is related to cortex morphology in CADASIL A sulcal-based morphometry study -journal: NEUROLOGY -year: 2011 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_jouvent_longitudinal_2012.md b/_collections/_biblio/architecture/architecture_jouvent_longitudinal_2012.md deleted file mode 100644 index da7436b..0000000 --- a/_collections/_biblio/architecture/architecture_jouvent_longitudinal_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Eric Jouvent et al. -title: Longitudinal changes of cortical morphology in CADASIL -journal: Neurobiology of Aging -year: 2012 -type: article -doi: 10.1016/j.neurobiolaging.2011.09.013 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_jouvent_prediction_2016.md b/_collections/_biblio/architecture/architecture_jouvent_prediction_2016.md deleted file mode 100644 index e83ce93..0000000 --- a/_collections/_biblio/architecture/architecture_jouvent_prediction_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Eric Jouvent et al. -title: Prediction of 3-year clinical course in CADASIL -journal: Neurology -year: 2016 -type: article -doi: 10.1212/WNL.0000000000003252 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_jouvent_shape_2016.md b/_collections/_biblio/architecture/architecture_jouvent_shape_2016.md deleted file mode 100644 index 6a0d0aa..0000000 --- a/_collections/_biblio/architecture/architecture_jouvent_shape_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Eric Jouvent et al. -title: Shape of the Central Sulcus and Disability After Subcortical Stroke - A Motor Reserve Hypothesis -journal: Stroke -year: 2016 -type: article -doi: 10.1161/STROKEAHA.115.012562 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_karkar_genome-wide_2021.md b/_collections/_biblio/architecture/architecture_karkar_genome-wide_2021.md deleted file mode 100644 index 8fd570e..0000000 --- a/_collections/_biblio/architecture/architecture_karkar_genome-wide_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Slim Karkar et al. -title: Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects -journal: European Journal of Human Genetics -year: 2021 -type: article -url: https -//www.nature.com/articles/s41431-021-00827-8 -doi: 10.1038/s41431-021-00827-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_katz_similar_2016-1.md b/_collections/_biblio/architecture/architecture_katz_similar_2016-1.md deleted file mode 100644 index b968728..0000000 --- a/_collections/_biblio/architecture/architecture_katz_similar_2016-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Katz et al. -title: Similar white matter but opposite grey matter changes in schizophrenia and high‐functioning autism -journal: Acta Psychiatrica Scandinavica -year: 2016 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_katz_similar_2016.md b/_collections/_biblio/architecture/architecture_katz_similar_2016.md deleted file mode 100644 index e58ea14..0000000 --- a/_collections/_biblio/architecture/architecture_katz_similar_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Katz et al. -title: Similar white matter but opposite grey matter changes in schizophrenia and high-functioning autism -journal: Acta Psychiatrica Scandinavica -year: 2016 -type: article -doi: 10.1111/acps.12579 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kersbergen_relation_2016.md b/_collections/_biblio/architecture/architecture_kersbergen_relation_2016.md deleted file mode 100644 index af2434c..0000000 --- a/_collections/_biblio/architecture/architecture_kersbergen_relation_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Karina Kersbergen et al. -title: Relation between clinical risk factors, early cortical changes, and neurodevelopmental outcome in preterm infants -journal: NeuroImage -year: 2016 -type: article -doi: 10.1016/j.neuroimage.2016.07.010 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kezele_computing_2008.md b/_collections/_biblio/architecture/architecture_kezele_computing_2008.md deleted file mode 100644 index 29daf92..0000000 --- a/_collections/_biblio/architecture/architecture_kezele_computing_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: I. Kezele et al. -title: Computing strings of average HARDI models using Procrustes-Based Fibre Alignment -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kezele_importance_2009.md b/_collections/_biblio/architecture/architecture_kezele_importance_2009.md deleted file mode 100644 index 3e39367..0000000 --- a/_collections/_biblio/architecture/architecture_kezele_importance_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: I. Kezele et al. -title: Importance of Multiscale Analysis in HARDI Studies -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kezele_mean_2008.md b/_collections/_biblio/architecture/architecture_kezele_mean_2008.md deleted file mode 100644 index f1d5022..0000000 --- a/_collections/_biblio/architecture/architecture_kezele_mean_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: I. Kezele et al. -title: Mean Q-ball strings obtained by constrained Procrustes analysis with point sliding -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_klein_retinotopic_2004.md b/_collections/_biblio/architecture/architecture_klein_retinotopic_2004.md deleted file mode 100644 index 455f4d1..0000000 --- a/_collections/_biblio/architecture/architecture_klein_retinotopic_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Isabelle Klein et al. -title: Retinotopic organization of visual mental images as revealed by functional magnetic resonance imaging -journal: Brain Res Cogn Brain Res -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kochunov_age-related_2005.md b/_collections/_biblio/architecture/architecture_kochunov_age-related_2005.md deleted file mode 100644 index 756e466..0000000 --- a/_collections/_biblio/architecture/architecture_kochunov_age-related_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Kochunov et al. -title: Age-related morphology trends of cortical sulci -journal: Hum Brain Mapp. -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kochunov_development_2005.md b/_collections/_biblio/architecture/architecture_kochunov_development_2005.md deleted file mode 100644 index 03540b5..0000000 --- a/_collections/_biblio/architecture/architecture_kochunov_development_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Kochunov et al. -title: Development of high-resolution MRI imaging and image processing for live and post-mortem primates (Papio hamadryas) -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kochunov_genetic_2007.md b/_collections/_biblio/architecture/architecture_kochunov_genetic_2007.md deleted file mode 100644 index 24b118b..0000000 --- a/_collections/_biblio/architecture/architecture_kochunov_genetic_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Kochunov et al. -title: Genetic analysis of cerebral volume and cortical sulci in baboons -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kochunov_relationship_2007.md b/_collections/_biblio/architecture/architecture_kochunov_relationship_2007.md deleted file mode 100644 index 724dc8a..0000000 --- a/_collections/_biblio/architecture/architecture_kochunov_relationship_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Kochunov et al. -title: Relationship between regional FDG uptake and other markers of cerebral health in normal aging -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_kochunov_relationship_2008.md b/_collections/_biblio/architecture/architecture_kochunov_relationship_2008.md deleted file mode 100644 index 691d204..0000000 --- a/_collections/_biblio/architecture/architecture_kochunov_relationship_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Kochunov et al. -title: Relationship among neuroimaging indices of cerebral health during normal aging -journal: Human Brain Mapping -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_krainik_postoperative_2003.md b/_collections/_biblio/architecture/architecture_krainik_postoperative_2003.md deleted file mode 100644 index a03ee69..0000000 --- a/_collections/_biblio/architecture/architecture_krainik_postoperative_2003.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Krainik et al. -title: Postoperative speech disorder after medial frontal surgery - Role of the supplementary motor area -journal: Neurology -year: 2003 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_labra_comparative_2023.md b/_collections/_biblio/architecture/architecture_labra_comparative_2023.md deleted file mode 100644 index 59e7e81..0000000 --- a/_collections/_biblio/architecture/architecture_labra_comparative_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicole Labra et al. -title: Comparative study of manual identification of brain foldings in a living human brain using a proxy-endocast obtained from MRI -journal: Bulletins et mémoires de la Société d’Anthropologie de Paris. BMSAP -year: 2023 -type: article -url: https -//journals.openedition.org/bmsap/11242 -doi: 10.4000/bmsap.11242 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_labra_fast_2017.md b/_collections/_biblio/architecture/architecture_labra_fast_2017.md deleted file mode 100644 index bcd6d77..0000000 --- a/_collections/_biblio/architecture/architecture_labra_fast_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicole Labra et al. -title: Fast Automatic Segmentation of White Matter Streamlines Based on a Multi-Subject Bundle Atlas -journal: Neuroinformatics -year: 2017 -type: article -doi: 10.1007/s12021-016-9316-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_labra_gpu-based_2013.md b/_collections/_biblio/architecture/architecture_labra_gpu-based_2013.md deleted file mode 100644 index 243fb0e..0000000 --- a/_collections/_biblio/architecture/architecture_labra_gpu-based_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicole Labra et al. -title: GPU-based acceleration of an automatic white matter segmentation algorithm using CUDA -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2013 -type: article -doi: 10.1109/EMBC.2013.6609444 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_labra_what_2024.md b/_collections/_biblio/architecture/architecture_labra_what_2024.md deleted file mode 100644 index dd99d71..0000000 --- a/_collections/_biblio/architecture/architecture_labra_what_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicole Labra et al. -title: What do brain endocasts tell us? A comparative analysis of the accuracy of sulcal identification by experts and perspectives in palaeoanthropology -journal: Journal of Anatomy -year: 2024 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/joa.13966 -doi: 10.1111/joa.13966 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_laidi_cerebellar_2019.md b/_collections/_biblio/architecture/architecture_laidi_cerebellar_2019.md deleted file mode 100644 index a02d7ce..0000000 --- a/_collections/_biblio/architecture/architecture_laidi_cerebellar_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Laidi et al. -title: Cerebellar parcellation in schizophrenia and bipolar disorder -journal: Acta Psychiatrica Scandinavica -year: 2019 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/acps.13087 -doi: 10.1111/acps.13087 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_le_guen_chaotic_2018.md b/_collections/_biblio/architecture/architecture_le_guen_chaotic_2018.md deleted file mode 100644 index 52ada26..0000000 --- a/_collections/_biblio/architecture/architecture_le_guen_chaotic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Le Guen et al. -title: The chaotic morphology of the left superior temporal sulcus is genetically constrained -journal: NeuroImage -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918302568 -doi: 10.1016/j.neuroimage.2018.03.046 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_le_guen_enhancer_2020.md b/_collections/_biblio/architecture/architecture_le_guen_enhancer_2020.md deleted file mode 100644 index 10999b4..0000000 --- a/_collections/_biblio/architecture/architecture_le_guen_enhancer_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Le Guen et al. -title: Enhancer Locus in ch14q23.1 Modulates Brain Asymmetric Temporal Regions Involved in Language Processing -journal: Cerebral Cortex -year: 2020 -type: article -url: https -//doi.org/10.1093/cercor/bhaa112 -doi: 10.1093/cercor/bhaa112 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_le_guen_eqtl_2019.md b/_collections/_biblio/architecture/architecture_le_guen_eqtl_2019.md deleted file mode 100644 index 59a79dd..0000000 --- a/_collections/_biblio/architecture/architecture_le_guen_eqtl_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Le Guen et al. -title: eQTL of KCNK2 regionally influences the brain sulcal widening - evidence from 15,597 UK Biobank participants with neuroimaging data -journal: Brain Structure and Function -year: 2019 -type: article -url: https -//doi.org/10.1007/s00429-018-1808-9 -doi: 10.1007/s00429-018-1808-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_le_guen_genetic_2018.md b/_collections/_biblio/architecture/architecture_le_guen_genetic_2018.md deleted file mode 100644 index 67f96f3..0000000 --- a/_collections/_biblio/architecture/architecture_le_guen_genetic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Le Guen et al. -title: Genetic Influence on the Sulcal Pits - On the Origin of the First Cortical Folds -journal: Cerebral Cortex -year: 2018 -type: article -url: https -//doi.org/10.1093/cercor/bhx098 -doi: 10.1093/cercor/bhx098 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_le_guen_heritability_2019.md b/_collections/_biblio/architecture/architecture_le_guen_heritability_2019.md deleted file mode 100644 index a386993..0000000 --- a/_collections/_biblio/architecture/architecture_le_guen_heritability_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Le Guen et al. -title: Heritability of surface area and cortical thickness - a comparison between the Human Connectome Project and the UK Biobank dataset -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/8759539 -doi: 10.1109/ISBI.2019.8759539 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lebenberg_clustering_2015.md b/_collections/_biblio/architecture/architecture_lebenberg_clustering_2015.md deleted file mode 100644 index 7b640f3..0000000 --- a/_collections/_biblio/architecture/architecture_lebenberg_clustering_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jessica Lebenberg et al. -title: Clustering the infant brain tissues based on microstructural properties and maturation assessment using multi-parametric MRI -year: 2015 -type: inproceedings -doi: 10.1109/ISBI.2015.7163837 -booktitle: 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, Brooklyn, NY, USA, April 16-19, 2015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lebenberg_framework_2018.md b/_collections/_biblio/architecture/architecture_lebenberg_framework_2018.md deleted file mode 100644 index 4df5e4b..0000000 --- a/_collections/_biblio/architecture/architecture_lebenberg_framework_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Lebenberg et al. -title: A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-018-1735-9 -doi: 10.1007/s00429-018-1735-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lebenberg_mapping_2019.md b/_collections/_biblio/architecture/architecture_lebenberg_mapping_2019.md deleted file mode 100644 index 0e87a1e..0000000 --- a/_collections/_biblio/architecture/architecture_lebenberg_mapping_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Lebenberg et al. -title: Mapping the asynchrony of cortical maturation in the infant brain - A MRI multi-parametric clustering approach -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918306372 -doi: 10.1016/j.neuroimage.2018.07.022 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefevre_are_2015.md b/_collections/_biblio/architecture/architecture_lefevre_are_2015.md deleted file mode 100644 index 090cd43..0000000 --- a/_collections/_biblio/architecture/architecture_lefevre_are_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Lefèvre et al. -title: Are Developmental Trajectories of Cortical Folding Comparable Between Cross-sectional Datasets of Fetuses and Preterm Newborns? -journal: Cereb Cortex -year: 2015 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefevre_surface_2013-1.md b/_collections/_biblio/architecture/architecture_lefevre_surface_2013-1.md deleted file mode 100644 index 6f1f134..0000000 --- a/_collections/_biblio/architecture/architecture_lefevre_surface_2013-1.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Julien Lefèvre et al. -title: Surface Smoothing - A Way Back in Early Brain Morphogenesis -year: 2013 -type: inproceedings -doi: 10.1007/978-3-642-40811-3_74 -booktitle: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2013 - 16th International Conference, Nagoya, Japan, September 22-26, 2013, Proceedings, Part I ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefevre_surface_2013.md b/_collections/_biblio/architecture/architecture_lefevre_surface_2013.md deleted file mode 100644 index db84465..0000000 --- a/_collections/_biblio/architecture/architecture_lefevre_surface_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Julien Lefèvre et al. -title: Surface smoothing - a way back in early brain morphogenesis -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2013 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefranc_concomitant_2015.md b/_collections/_biblio/architecture/architecture_lefranc_concomitant_2015.md deleted file mode 100644 index 61672ab..0000000 --- a/_collections/_biblio/architecture/architecture_lefranc_concomitant_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Sandrine Lefranc et al. -title: Concomitant variability of the central sulcus morphology and adjacent connectivity patterns -year: 2015 -type: inproceedings -doi: 10.1109/ISBI.2015.7163907 -booktitle: 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, Brooklyn, NY, USA, April 16-19, 2015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefranc_groupwise_2016.md b/_collections/_biblio/architecture/architecture_lefranc_groupwise_2016.md deleted file mode 100644 index cc3a518..0000000 --- a/_collections/_biblio/architecture/architecture_lefranc_groupwise_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Sandrine Lefranc et al. -title: Groupwise connectivity-based parcellation of the whole human cortical surface using watershed-driven dimension reduction -journal: Medical Image Analysis -year: 2016 -type: article -doi: 10.1016/j.media.2016.01.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lefranc_validation_2014.md b/_collections/_biblio/architecture/architecture_lefranc_validation_2014.md deleted file mode 100644 index 4fb2a18..0000000 --- a/_collections/_biblio/architecture/architecture_lefranc_validation_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Sandrine Lefranc et al. -title: Validation of consistent inter-subject connectivity-based parcellation -year: 2014 -type: inproceedings -doi: 10.1109/ISBI.2014.6868022 -booktitle: IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014, April 29 - May 2, 2014, Beijing, Chin, Beijing, China ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lemaitre_genetic_2023.md b/_collections/_biblio/architecture/architecture_lemaitre_genetic_2023.md deleted file mode 100644 index d4a6b95..0000000 --- a/_collections/_biblio/architecture/architecture_lemaitre_genetic_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Herve Lemaitre et al. -title: Genetic variations within human gained enhancer elements affect human brain sulcal morphology -journal: NeuroImage -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922008941 -doi: 10.1016/j.neuroimage.2022.119773 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_leprince_combined_2015.md b/_collections/_biblio/architecture/architecture_leprince_combined_2015.md deleted file mode 100644 index d1e2699..0000000 --- a/_collections/_biblio/architecture/architecture_leprince_combined_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Leprince et al. -title: Combined Laplacian-equivolumic model for studying cortical lamination with ultra high field MRI (7 T) -year: 2015 -type: inproceedings -doi: 10.1109/ISBI.2015.7163940 -booktitle: 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, Brooklyn, NY, USA, April 16-19, 2015 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_leprince_morphological_2020.md b/_collections/_biblio/architecture/architecture_leprince_morphological_2020.md deleted file mode 100644 index b9f3584..0000000 --- a/_collections/_biblio/architecture/architecture_leprince_morphological_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yann Leprince et al. -title: The morphological evolution of the primate brain revealed by alignment of the cortical sulci -year: 2020 -type: inproceedings -url: https -//cea.hal.science/cea-02868500/document ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_leprince_optimization_2015.md b/_collections/_biblio/architecture/architecture_leprince_optimization_2015.md deleted file mode 100644 index 68fb0ff..0000000 --- a/_collections/_biblio/architecture/architecture_leprince_optimization_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Y. Leprince et al. -title: Optimization of sample preparation for MRI of formaldehyde-fixed brains -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_leroy_early_2011.md b/_collections/_biblio/architecture/architecture_leroy_early_2011.md deleted file mode 100644 index 0a1d617..0000000 --- a/_collections/_biblio/architecture/architecture_leroy_early_2011.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Francois Leroy et al. -title: Early Maturation of the Linguistic Dorsal Pathway in Human Infants -journal: JOURNAL OF NEUROSCIENCE -year: 2011 -type: article -doi: 10.1523/JNEUROSCI.4141-10.2011 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_leroy_new_2015.md b/_collections/_biblio/architecture/architecture_leroy_new_2015.md deleted file mode 100644 index 4bb755f..0000000 --- a/_collections/_biblio/architecture/architecture_leroy_new_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: François Leroy et al. -title: New human-specific brain landmark - the depth asymmetry of superior temporal sulcus -journal: Proceedings of the National Academy of Sciences of the United States of America -year: 2015 -type: article -doi: 10.1073/pnas.1412389112 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lespinasse_associations_2023.md b/_collections/_biblio/architecture/architecture_lespinasse_associations_2023.md deleted file mode 100644 index 83cf2f0..0000000 --- a/_collections/_biblio/architecture/architecture_lespinasse_associations_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jérémie Lespinasse et al. -title: Associations among hypertension, dementia biomarkers, and cognition - The MEMENTO cohort -journal: Alzheimer's \& Dementia -year: 2023 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/alz.12866 -doi: 10.1002/alz.12866 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lizarazu_neural_2021.md b/_collections/_biblio/architecture/architecture_lizarazu_neural_2021.md deleted file mode 100644 index 101bc68..0000000 --- a/_collections/_biblio/architecture/architecture_lizarazu_neural_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Mikel Lizarazu et al. -title: Neural entrainment to speech and nonspeech in dyslexia - Conceptual replication and extension of previous investigations -journal: Cortex -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0010945221000265 -doi: 10.1016/j.cortex.2020.12.024 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lopez-lopez_coarse_2020.md b/_collections/_biblio/architecture/architecture_lopez-lopez_coarse_2020.md deleted file mode 100644 index 8d1d74c..0000000 --- a/_collections/_biblio/architecture/architecture_lopez-lopez_coarse_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Narciso López-López et al. -title: From Coarse to Fine-Grained Parcellation of the Cortical Surface Using a Fiber-Bundle Atlas -journal: Frontiers in Neuroinformatics -year: 2020 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2020.00032 -doi: 10.3389/fninf.2020.00032 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lopez-lopez_geosp_2020.md b/_collections/_biblio/architecture/architecture_lopez-lopez_geosp_2020.md deleted file mode 100644 index cdaaf8f..0000000 --- a/_collections/_biblio/architecture/architecture_lopez-lopez_geosp_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Narciso Lopez-Lopez et al. -title: GeoSP - A parallel method for a cortical surface parcellation based on geodesic distance -year: 2020 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/9175779/ -doi: 10.1109/EMBC44109.2020.9175779 -booktitle: 2020 42nd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lu_associations_2021.md b/_collections/_biblio/architecture/architecture_lu_associations_2021.md deleted file mode 100644 index e56344f..0000000 --- a/_collections/_biblio/architecture/architecture_lu_associations_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Wan-Hsuan Lu et al. -title: Associations Between Nutritional Deficits and Physical Performance in Community-Dwelling Older Adults -journal: Frontiers in Nutrition -year: 2021 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnut.2021.771470 -doi: 10.3389/fnut.2021.771470 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lu_biological_2021.md b/_collections/_biblio/architecture/architecture_lu_biological_2021.md deleted file mode 100644 index c2368ad..0000000 --- a/_collections/_biblio/architecture/architecture_lu_biological_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Wan-Hsuan Lu et al. -title: Biological and Neuroimaging Markers as Predictors of 5-Year Incident Frailty in Older Adults - A Secondary Analysis of the MAPT Study -journal: The Journals of Gerontology - Series A -year: 2021 -type: article -url: https -//doi.org/10.1093/gerona/glaa296 -doi: 10.1093/gerona/glaa296 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_lu_cross-sectional_2020.md b/_collections/_biblio/architecture/architecture_lu_cross-sectional_2020.md deleted file mode 100644 index e5a693c..0000000 --- a/_collections/_biblio/architecture/architecture_lu_cross-sectional_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Wan-Hsuan Lu et al. -title: Cross-sectional and prospective associations between cerebral cortical thickness and frailty in older adults -journal: Experimental Gerontology -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0531556520303661 -doi: 10.1016/j.exger.2020.111018 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_maltais_prospective_2020-1.md b/_collections/_biblio/architecture/architecture_maltais_prospective_2020-1.md deleted file mode 100644 index 5771f78..0000000 --- a/_collections/_biblio/architecture/architecture_maltais_prospective_2020-1.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Mathieu Maltais et al. -title: Prospective associations between physical activity levels and white matter integrity in older adults - results from the MAPT study -journal: Maturitas -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0378512220302425 -doi: 10.1016/j.maturitas.2020.04.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_maltais_prospective_2020.md b/_collections/_biblio/architecture/architecture_maltais_prospective_2020.md deleted file mode 100644 index d74cde4..0000000 --- a/_collections/_biblio/architecture/architecture_maltais_prospective_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Mathieu Maltais et al. -title: Prospective Associations Between Diffusion Tensor Imaging Parameters and Frailty in Older Adults -journal: Journal of the American Geriatrics Society -year: 2020 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16343 -doi: 10.1111/jgs.16343 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_-vivo_2010.md b/_collections/_biblio/architecture/architecture_mangin_-vivo_2010.md deleted file mode 100644 index 4e56f90..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_-vivo_2010.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jean-François Mangin et al. -title: In-vivo measurement of cortical morphology - means and meanings -journal: Current Opinion in Neurology -year: 2010 -type: article -url: https -//journals.lww.com/co-neurology/Abstract/2010/08000/In_vivo_measurement_of_cortical_morphology__means.4.aspx -doi: 10.1097/WCO.0b013e32833a0afc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_analysing_2008.md b/_collections/_biblio/architecture/architecture_mangin_analysing_2008.md deleted file mode 100644 index 9bd681f..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_analysing_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Analysing the cortical folding patterns -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_brain_2004.md b/_collections/_biblio/architecture/architecture_mangin_brain_2004.md deleted file mode 100644 index b423615..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_brain_2004.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J.-F. Mangin et al. -title: Brain morphometry using 3D moment invariants -journal: Medical Image Analysis -year: 2004 -type: article -doi: 10.1016/j.media.2004.06.016 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_coordinate-based_2004.md b/_collections/_biblio/architecture/architecture_mangin_coordinate-based_2004.md deleted file mode 100644 index 5ab05c1..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_coordinate-based_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Coordinate-based versus structural approaches to brain image analysis -journal: Artif Intell Med -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_framework_2004.md b/_collections/_biblio/architecture/architecture_mangin_framework_2004.md deleted file mode 100644 index 0894814..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_framework_2004.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J.-F. Mangin et al. -title: A framework to study the cortical folding patterns -journal: NeuroImage -year: 2004 -type: article -doi: 10.1016/j.neuroimage.2004.07.019 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_hdr_2005.md b/_collections/_biblio/architecture/architecture_mangin_hdr_2005.md deleted file mode 100644 index 9fc3331..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_hdr_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: HDR = Une vision structurelle de l'analyse des images cérébrales -year: 2005 -type: Habilitation à diriger des recherches ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_image_2007.md b/_collections/_biblio/architecture/architecture_mangin_image_2007.md deleted file mode 100644 index d1fa8e8..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_image_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Image processing for Random Shapes -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_machine_2007.md b/_collections/_biblio/architecture/architecture_mangin_machine_2007.md deleted file mode 100644 index 5abe1c9..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_machine_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Machine learning for Early Diagnosis of Brain Diseases -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_modern_2009.md b/_collections/_biblio/architecture/architecture_mangin_modern_2009.md deleted file mode 100644 index 4fb9532..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_modern_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Modern Neuroimaging -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_morphometry_2007.md b/_collections/_biblio/architecture/architecture_mangin_morphometry_2007.md deleted file mode 100644 index 59e4027..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_morphometry_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Morphometry of the human cortical cortex -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_neocortical_2020.md b/_collections/_biblio/architecture/architecture_mangin_neocortical_2020.md deleted file mode 100644 index 0461ce7..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_neocortical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jean-Francois Mangin et al. -title: Neocortical morphometry in Huntington's disease - Indication of the coexistence of abnormal neurodevelopmental and neurodegenerative processes -journal: NeuroImage - Clinical -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2213158220300486 -doi: 10.1016/j.nicl.2020.102211 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_notitle_2010.md b/_collections/_biblio/architecture/architecture_mangin_notitle_2010.md deleted file mode 100644 index 0f90b6a..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_notitle_2010.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -year: 2010 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_object-based_2004.md b/_collections/_biblio/architecture/architecture_mangin_object-based_2004.md deleted file mode 100644 index 8fdb274..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_object-based_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Object-based morphometry of the cerebral cortex -journal: IEEE Transactions on Medical Imaging -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_plis_2019.md b/_collections/_biblio/architecture/architecture_mangin_plis_2019.md deleted file mode 100644 index a41b59b..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_plis_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jean-François Mangin et al. -title: “Plis de passage” Deserve a Role in Models of the Cortical Folding Process -journal: Brain Topography -year: 2019 -type: article -url: https -//doi.org/10.1007/s10548-019-00734-8 -doi: 10.1007/s10548-019-00734-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_signal_2007.md b/_collections/_biblio/architecture/architecture_mangin_signal_2007.md deleted file mode 100644 index f03ef9d..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_signal_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Signal Processing Institute -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_spatial_2016.md b/_collections/_biblio/architecture/architecture_mangin_spatial_2016.md deleted file mode 100644 index 5f784e3..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_spatial_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J.-F. Mangin et al. -title: Spatial normalization of brain images and beyond -journal: Medical Image Analysis -year: 2016 -type: article -doi: 10.1016/j.media.2016.06.008 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_statistical_2008.md b/_collections/_biblio/architecture/architecture_mangin_statistical_2008.md deleted file mode 100644 index af05e30..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_statistical_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Statistical Methods in Brain Research -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_structural_2007-1.md b/_collections/_biblio/architecture/architecture_mangin_structural_2007-1.md deleted file mode 100644 index 508ede5..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_structural_2007-1.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: The structural paradigm -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_structural_2007.md b/_collections/_biblio/architecture/architecture_mangin_structural_2007.md deleted file mode 100644 index a709aec..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_structural_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: The structural paradigm when analyzing diffusion data -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_structural_2010.md b/_collections/_biblio/architecture/architecture_mangin_structural_2010.md deleted file mode 100644 index 641a77d..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_structural_2010.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Structural approaches to study variability of brain architecture -year: 2010 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_sulci_2015.md b/_collections/_biblio/architecture/architecture_mangin_sulci_2015.md deleted file mode 100644 index 706d62c..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_sulci_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Sulci as Landmarks -year: 2015 -type: incollection -booktitle: Brain Mapping - An Encyclopedic Reference ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_sulcus_2015.md b/_collections/_biblio/architecture/architecture_mangin_sulcus_2015.md deleted file mode 100644 index 3c82677..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_sulcus_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Sulcus identification and Labeling -year: 2015 -type: incollection -booktitle: Brain Mapping - An Encyclopedic Reference ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_toward_2013.md b/_collections/_biblio/architecture/architecture_mangin_toward_2013.md deleted file mode 100644 index 1d78aa9..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_toward_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J.-F. Mangin et al. -title: Toward global tractography -journal: Neuroimage -year: 2013 -type: article -doi: 10.1016/j.neuroimage.2013.04.009 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_variability_2007.md b/_collections/_biblio/architecture/architecture_mangin_variability_2007.md deleted file mode 100644 index e51d1de..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_variability_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Variability of the cortical folding patterns -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_variability_2008.md b/_collections/_biblio/architecture/architecture_mangin_variability_2008.md deleted file mode 100644 index 27c5265..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_variability_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Variability of the cortical folding patterns and development -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_variability_2010.md b/_collections/_biblio/architecture/architecture_mangin_variability_2010.md deleted file mode 100644 index 8478021..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_variability_2010.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: Variability of cortical anatomy - a challenge for computer vision -year: 2010 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mangin_vie_2011.md b/_collections/_biblio/architecture/architecture_mangin_vie_2011.md deleted file mode 100644 index 9d00246..0000000 --- a/_collections/_biblio/architecture/architecture_mangin_vie_2011.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Mangin et al. -title: La vie des formes -year: 2011 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_marrakchi-kacem_mapping_2013.md b/_collections/_biblio/architecture/architecture_marrakchi-kacem_mapping_2013.md deleted file mode 100644 index 58da97b..0000000 --- a/_collections/_biblio/architecture/architecture_marrakchi-kacem_mapping_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Linda Marrakchi-Kacem et al. -title: Mapping cortico-striatal connectivity onto the cortical surface - a new tractography-based approach to study Huntington disease -journal: PloS One -year: 2013 -type: article -doi: 10.1371/journal.pone.0053135 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_marrakchi-kacem_multi-contrast_2009.md b/_collections/_biblio/architecture/architecture_marrakchi-kacem_multi-contrast_2009.md deleted file mode 100644 index 76d63af..0000000 --- a/_collections/_biblio/architecture/architecture_marrakchi-kacem_multi-contrast_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: L. Marrakchi-Kacem et al. -title: Multi-contrast T1 and DTI deep nuclei segmentation using a probablistic atlas -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_marrakchi-kacem_using_2009.md b/_collections/_biblio/architecture/architecture_marrakchi-kacem_using_2009.md deleted file mode 100644 index 5123e25..0000000 --- a/_collections/_biblio/architecture/architecture_marrakchi-kacem_using_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: L. Marrakchi-Kacem et al. -title: Using DTI to constrain the automatic segmentation of the deep nuclei from T1 contrast by surrounding fiber bundles -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_martinot_brain_2005-1.md b/_collections/_biblio/architecture/architecture_martinot_brain_2005-1.md deleted file mode 100644 index 4a24547..0000000 --- a/_collections/_biblio/architecture/architecture_martinot_brain_2005-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J.-L. Martinot et al. -title: Brain folding in schizophrenia -year: 2005 -type: inproceedings -booktitle: Proc. 8th World congress of biological psychiatry. The world journal of biological psychiatry vol 6 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_martinot_brain_2005.md b/_collections/_biblio/architecture/architecture_martinot_brain_2005.md deleted file mode 100644 index e15efde..0000000 --- a/_collections/_biblio/architecture/architecture_martinot_brain_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Martinot et al. -title: Brain folding in schizophrenia -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_martinot_cortical_2006.md b/_collections/_biblio/architecture/architecture_martinot_cortical_2006.md deleted file mode 100644 index 54f4f7d..0000000 --- a/_collections/_biblio/architecture/architecture_martinot_cortical_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Martinot et al. -title: Cortical gyrification and (developmental) pathopsychology -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mendoza_convex_2023.md b/_collections/_biblio/architecture/architecture_mendoza_convex_2023.md deleted file mode 100644 index 6469268..0000000 --- a/_collections/_biblio/architecture/architecture_mendoza_convex_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Cristóbal Mendoza et al. -title: CONVEX HULL BASED FILTERING OF SUPERFICIAL WHITE MATTER FIBER BUNDLES -journal: IBRO Neuroscience Reports -year: 2023 -type: article -url: https -//www.ibroneuroreports.org/article/S2667-2421(23)01672-X/fulltext -doi: 10.1016/j.ibneur.2023.08.1610 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mendoza_enhanced_2021.md b/_collections/_biblio/architecture/architecture_mendoza_enhanced_2021.md deleted file mode 100644 index c420481..0000000 --- a/_collections/_biblio/architecture/architecture_mendoza_enhanced_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Mendoza et al. -title: Enhanced Automatic Segmentation for Superficial White Matter Fiber Bundles for Probabilistic Tractography Datasets -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9630529 -doi: 10.1109/EMBC46164.2021.9630529 -booktitle: 2021 43rd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mendoza_superficial_2023.md b/_collections/_biblio/architecture/architecture_mendoza_superficial_2023.md deleted file mode 100644 index 993244a..0000000 --- a/_collections/_biblio/architecture/architecture_mendoza_superficial_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Cristobal Mendoza et al. -title: Superficial white matter shape characterization using hierarchical clustering and a multi-subject bundle atlas -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/2669738/Superficial-white-matter-shape-characterization-using-hierarchical-clustering-and-a/10.1117/12.2669738.full -doi: 10.1117/12.2669738 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_messe_structural_2023.md b/_collections/_biblio/architecture/architecture_messe_structural_2023.md deleted file mode 100644 index cbde8dc..0000000 --- a/_collections/_biblio/architecture/architecture_messe_structural_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arnaud Messé et al. -title: Structural basis of envelope and phase intrinsic coupling modes in the cerebral cortex -journal: NeuroImage -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811923003634 -doi: 10.1016/j.neuroimage.2023.120212 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molina_group-wise_2023.md b/_collections/_biblio/architecture/architecture_molina_group-wise_2023.md deleted file mode 100644 index 6cac013..0000000 --- a/_collections/_biblio/architecture/architecture_molina_group-wise_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Joaquín Molina et al. -title: Group-wise cortical parcellation based on structural connectivity and hierarchical clustering -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670L/Group-wise-cortical-parcellation-based-on-structural-connectivity-and-hierarchical/10.1117/12.2670138.full -doi: 10.1117/12.2670138 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_brain_2004.md b/_collections/_biblio/architecture/architecture_molko_brain_2004.md deleted file mode 100644 index aca3265..0000000 --- a/_collections/_biblio/architecture/architecture_molko_brain_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Molko et al. -title: Brain Anatomy in Turner Syndrome - Evidence for Impaired Social and Spatial-Numerical Networks -journal: Cereb Cortex -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_diffusion_2001.md b/_collections/_biblio/architecture/architecture_molko_diffusion_2001.md deleted file mode 100644 index a4b015d..0000000 --- a/_collections/_biblio/architecture/architecture_molko_diffusion_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Molko et al. -title: Diffusion tensor imaging study of subcortical gray matter in cadasil -journal: Stroke -year: 2001 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_estimation_2004.md b/_collections/_biblio/architecture/architecture_molko_estimation_2004.md deleted file mode 100644 index 87af2f2..0000000 --- a/_collections/_biblio/architecture/architecture_molko_estimation_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Molko et al. -title: Estimation of the hemodynamic response in event-related functional MRI - Bayesian networks as a framework for efficient bayesian modeling and inference -journal: IEEE transactions of Medical Imaging -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_functional_2003.md b/_collections/_biblio/architecture/architecture_molko_functional_2003.md deleted file mode 100644 index abbd495..0000000 --- a/_collections/_biblio/architecture/architecture_molko_functional_2003.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Molko et al. -title: Functional and structural alterations of the intraparietal sulcus in a developmental dyscalculia of genetic origin -journal: Neuron -year: 2003 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_monitoring_2002.md b/_collections/_biblio/architecture/architecture_molko_monitoring_2002.md deleted file mode 100644 index 55b4fe1..0000000 --- a/_collections/_biblio/architecture/architecture_molko_monitoring_2002.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nicolas Molko et al. -title: Monitoring disease progression in CADASIL with diffusion magnetic resonance imaging a study with whole brain histogram analysis -year: 2002 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_molko_visualizing_2002.md b/_collections/_biblio/architecture/architecture_molko_visualizing_2002.md deleted file mode 100644 index 1b17fd2..0000000 --- a/_collections/_biblio/architecture/architecture_molko_visualizing_2002.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: N. Molko et al. -title: Visualizing the neural bases of a disconnection syndrome with diffusion tensor imaging -journal: Journal of Cognitive Neuroscience -year: 2002 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_moon_association_2018.md b/_collections/_biblio/architecture/architecture_moon_association_2018.md deleted file mode 100644 index 2aa4216..0000000 --- a/_collections/_biblio/architecture/architecture_moon_association_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: So Moon et al. -title: Association Between Red Blood Cells Omega-3 Polyunsaturated Fatty Acids and White Matter Hyperintensities - The MAPT Study -journal: The Journal of nutrition, health and aging -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1279770723022443 -doi: 10.1007/s12603-017-0965-5 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_moon_associations_2017.md b/_collections/_biblio/architecture/architecture_moon_associations_2017.md deleted file mode 100644 index d5e59cd..0000000 --- a/_collections/_biblio/architecture/architecture_moon_associations_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: So Moon et al. -title: Associations between white matter hyperintensities and cognitive decline over three years in non-dementia older adults with memory complaints -journal: Journal of the Neurological Sciences -year: 2017 -type: article -doi: 10.1016/j.jns.2017.06.031 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_moon_physical_2018.md b/_collections/_biblio/architecture/architecture_moon_physical_2018.md deleted file mode 100644 index a4da094..0000000 --- a/_collections/_biblio/architecture/architecture_moon_physical_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: So Moon et al. -title: Physical Activity and Changes in White Matter Hyperintensities over Three Years -journal: The Journal of nutrition, health and aging -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1279770723021619 -doi: 10.1007/s12603-017-0959-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_moon_prospective_2018.md b/_collections/_biblio/architecture/architecture_moon_prospective_2018.md deleted file mode 100644 index 70572ea..0000000 --- a/_collections/_biblio/architecture/architecture_moon_prospective_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: So Moon et al. -title: Prospective associations between white matter hyperintensities and lower extremity function -journal: Neurology -year: 2018 -type: article -doi: 10.1212/WNL.0000000000005289 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_mortamais_sulcal_2022.md b/_collections/_biblio/architecture/architecture_mortamais_sulcal_2022.md deleted file mode 100644 index 8086075..0000000 --- a/_collections/_biblio/architecture/architecture_mortamais_sulcal_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Marion Mortamais et al. -title: Sulcal morphology as cognitive decline predictor in older adults with memory complaints -journal: Neurobiology of Aging -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0197458022000240 -doi: 10.1016/j.neurobiolaging.2022.02.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_muellner_altered_2015.md b/_collections/_biblio/architecture/architecture_muellner_altered_2015.md deleted file mode 100644 index d87514b..0000000 --- a/_collections/_biblio/architecture/architecture_muellner_altered_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Julia Muellner et al. -title: Altered Structure of Cortical Sulci in Gilles de la Tourette Syndrome - Further Support for Abnormal Brain Development -journal: MOVEMENT DISORDERS -year: 2015 -type: article -doi: 10.1002/mds.26207 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_operto_cati:_2016.md b/_collections/_biblio/architecture/architecture_operto_cati:_2016.md deleted file mode 100644 index dedf18e..0000000 --- a/_collections/_biblio/architecture/architecture_operto_cati:_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Grégory Operto et al. -title: CATI - A Large Distributed Infrastructure for the Neuroimaging of Cohorts -journal: Neuroinformatics -year: 2016 -type: article -doi: 10.1007/s12021-016-9295-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_operto_structural_2012.md b/_collections/_biblio/architecture/architecture_operto_structural_2012.md deleted file mode 100644 index 02e07ae..0000000 --- a/_collections/_biblio/architecture/architecture_operto_structural_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Grégory Operto et al. -title: Structural analysis of fMRI data - a surface-based framework for multi-subject studies -journal: Medical Image Analysis -year: 2012 -type: article -doi: 10.1016/j.media.2012.02.007 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_osorio_abrainvis_2021.md b/_collections/_biblio/architecture/architecture_osorio_abrainvis_2021.md deleted file mode 100644 index f1f2217..0000000 --- a/_collections/_biblio/architecture/architecture_osorio_abrainvis_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Ignacio Osorio et al. -title: ABrainVis - an android brain image visualization tool -journal: BioMedical Engineering OnLine -year: 2021 -type: article -url: https -//biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-021-00909-0 -doi: 10.1186/s12938-021-00909-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_paillere-martinot_active_2017.md b/_collections/_biblio/architecture/architecture_paillere-martinot_active_2017.md deleted file mode 100644 index 3227582..0000000 --- a/_collections/_biblio/architecture/architecture_paillere-martinot_active_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M.-L. Paillère-Martinot et al. -title: Active and placebo transcranial magnetic stimulation effects on external and internal auditory hallucinations of schizophrenia -journal: Acta Psychiatrica Scandinavica -year: 2017 -type: article -doi: 10.1111/acps.12680 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pappata_vivo_1996.md b/_collections/_biblio/architecture/architecture_pappata_vivo_1996.md deleted file mode 100644 index af98724..0000000 --- a/_collections/_biblio/architecture/architecture_pappata_vivo_1996.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Pappata et al. -title: In vivo imaging of human cerebral acetylcholinesterase -journal: J Neurochem -year: 1996 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pardo_study_2013.md b/_collections/_biblio/architecture/architecture_pardo_study_2013.md deleted file mode 100644 index da59de8..0000000 --- a/_collections/_biblio/architecture/architecture_pardo_study_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Edison Pardo et al. -title: Study of the variability of short association bundles on a HARDI database -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2013 -type: article -doi: 10.1109/EMBC.2013.6609441 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_patel_comparison_2005.md b/_collections/_biblio/architecture/architecture_patel_comparison_2005.md deleted file mode 100644 index f4faaae..0000000 --- a/_collections/_biblio/architecture/architecture_patel_comparison_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: R. Patel et al. -title: Comparison of age-related sulcal opening trends between bipolar II patients and normal individuals -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_penttila_cortical_2009-1.md b/_collections/_biblio/architecture/architecture_penttila_cortical_2009-1.md deleted file mode 100644 index e857d63..0000000 --- a/_collections/_biblio/architecture/architecture_penttila_cortical_2009-1.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jani Penttilä et al. -title: Cortical folding difference between patients with early-onset and patients with intermediate-onset bipolar disorder -journal: Bipolar Disorders -year: 2009 -type: article -doi: 10.1111/j.1399-5618.2009.00683.x ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_penttila_cortical_2009.md b/_collections/_biblio/architecture/architecture_penttila_cortical_2009.md deleted file mode 100644 index 48a79a1..0000000 --- a/_collections/_biblio/architecture/architecture_penttila_cortical_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jani Penttilä et al. -title: Cortical folding in patients with bipolar disorder or unipolar depression -journal: Journal of psychiatry \& neuroscience - JPN -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_penttila_global_2008.md b/_collections/_biblio/architecture/architecture_penttila_global_2008.md deleted file mode 100644 index 630101d..0000000 --- a/_collections/_biblio/architecture/architecture_penttila_global_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Penttilä et al. -title: Global and Temporal Cortical Folding in Patients With Early-Onset Schizophrenia -journal: Journal of the American Academy of Child \& Adolescent Psychiatry -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pepe_spectral_2015.md b/_collections/_biblio/architecture/architecture_pepe_spectral_2015.md deleted file mode 100644 index 17941cf..0000000 --- a/_collections/_biblio/architecture/architecture_pepe_spectral_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Pepe et al. -title: Spectral clustering based parcellation of fetal brain MRI -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrin_connectivity-based_2008.md b/_collections/_biblio/architecture/architecture_perrin_connectivity-based_2008.md deleted file mode 100644 index aeffa10..0000000 --- a/_collections/_biblio/architecture/architecture_perrin_connectivity-based_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Muriel Perrin et al. -title: Connectivity-based parcellation of the cortical mantle using q-ball diffusion imaging -journal: International Journal of Biomedical Imaging -year: 2008 -type: article -doi: 10.1155/2008/368406 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrin_fiber_2005.md b/_collections/_biblio/architecture/architecture_perrin_fiber_2005.md deleted file mode 100644 index a8b50ac..0000000 --- a/_collections/_biblio/architecture/architecture_perrin_fiber_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Perrin et al. -title: Fiber tracking in q-ball fields using regularized particle trajectories -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrin_q-ball_2006.md b/_collections/_biblio/architecture/architecture_perrin_q-ball_2006.md deleted file mode 100644 index fea9f8a..0000000 --- a/_collections/_biblio/architecture/architecture_perrin_q-ball_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Perrin et al. -title: Q-ball imaging simulation with a numerical diffusion fiber crossing phantom -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrin_regularized_2005.md b/_collections/_biblio/architecture/architecture_perrin_regularized_2005.md deleted file mode 100644 index d5f4f04..0000000 --- a/_collections/_biblio/architecture/architecture_perrin_regularized_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Perrin et al. -title: Regularized probabilistic tracking with Q-ball fields -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrin_validation_2005.md b/_collections/_biblio/architecture/architecture_perrin_validation_2005.md deleted file mode 100644 index 243c6e8..0000000 --- a/_collections/_biblio/architecture/architecture_perrin_validation_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Muriel Perrin et al. -title: Validation of q-ball imaging with a diffusion fibre-crossing phantom on a clinical scanner -journal: Philos Trans R Soc Lond B Biol Sci -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrot_identifying_2008.md b/_collections/_biblio/architecture/architecture_perrot_identifying_2008.md deleted file mode 100644 index ca886e8..0000000 --- a/_collections/_biblio/architecture/architecture_perrot_identifying_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Perrot et al. -title: Identifying cortical sulci from localizations, shape and local organization -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perrot_joint_2009.md b/_collections/_biblio/architecture/architecture_perrot_joint_2009.md deleted file mode 100644 index 7873351..0000000 --- a/_collections/_biblio/architecture/architecture_perrot_joint_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Perrot et al. -title: Joint Bayesian Cortical Sulci Recognition and Spatial Normalization -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perus_effects_2022.md b/_collections/_biblio/architecture/architecture_perus_effects_2022.md deleted file mode 100644 index 21c4034..0000000 --- a/_collections/_biblio/architecture/architecture_perus_effects_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lisa Perus et al. -title: Effects of preventive interventions on neuroimaging biomarkers in subjects at-risk to develop Alzheimer's disease - A systematic review -journal: Frontiers in Aging Neuroscience -year: 2022 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnagi.2022.1014559 -doi: 10.3389/fnagi.2022.1014559 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_perus_impact_2023.md b/_collections/_biblio/architecture/architecture_perus_impact_2023.md deleted file mode 100644 index 7bf2515..0000000 --- a/_collections/_biblio/architecture/architecture_perus_impact_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Lisa Perus et al. -title: Impact of multidomain preventive strategies on functional brain connectivity in older adults with cognitive complaint - Subset from the Montpellier center of the ancillary MAPT-MRI study -journal: Frontiers in Aging Neuroscience -year: 2023 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnagi.2022.971220 -doi: 10.3389/fnagi.2022.971220 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pinel_modulation_2001.md b/_collections/_biblio/architecture/architecture_pinel_modulation_2001.md deleted file mode 100644 index dd79280..0000000 --- a/_collections/_biblio/architecture/architecture_pinel_modulation_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Pinel et al. -title: Modulation of parietal activation by semantic distance in a number comparison task -journal: Neuroimage -year: 2001 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pizzagalli_reliability_2020.md b/_collections/_biblio/architecture/architecture_pizzagalli_reliability_2020.md deleted file mode 100644 index f68b5b0..0000000 --- a/_collections/_biblio/architecture/architecture_pizzagalli_reliability_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Fabrizio Pizzagalli et al. -title: The reliability and heritability of cortical folds and their genetic correlations across hemispheres -journal: Communications Biology -year: 2020 -type: article -url: https -//www.nature.com/articles/s42003-020-01163-1 -doi: 10.1038/s42003-020-01163-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_pizzagalli_sulcal-based_2018.md b/_collections/_biblio/architecture/architecture_pizzagalli_sulcal-based_2018.md deleted file mode 100644 index 1f2a15b..0000000 --- a/_collections/_biblio/architecture/architecture_pizzagalli_sulcal-based_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Fabrizio Pizzagalli et al. -title: Sulcal-based morphometry in Parkinson’s disease - a study of reliability and disease effects -year: 2018 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/10975/109750T/Sulcal-based-morphometry-in-Parkinsons-disease--a-study-of/10.1117/12.2511590.full -doi: 10.1117/12.2511590 -booktitle: 14th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_planche_clinical_2021.md b/_collections/_biblio/architecture/architecture_planche_clinical_2021.md deleted file mode 100644 index 175350e..0000000 --- a/_collections/_biblio/architecture/architecture_planche_clinical_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Vincent Planche et al. -title: Clinical relevance of brain atrophy subtypes categorization in memory clinics -journal: Alzheimer's \& Dementia -year: 2021 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/alz.12231 -doi: 10.1002/alz.12231 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_planche_validity_2023.md b/_collections/_biblio/architecture/architecture_planche_validity_2023.md deleted file mode 100644 index b892995..0000000 --- a/_collections/_biblio/architecture/architecture_planche_validity_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Vincent Planche et al. -title: Validity and Performance of Blood Biomarkers for Alzheimer Disease to Predict Dementia Risk in a Large Clinic-Based Cohort -journal: Neurology -year: 2023 -type: article -url: https -//www.neurology.org/doi/full/10.1212/WNL.0000000000201479 -doi: 10.1212/WNL.0000000000201479 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_plaze_brain_2009.md b/_collections/_biblio/architecture/architecture_plaze_brain_2009.md deleted file mode 100644 index 96898d6..0000000 --- a/_collections/_biblio/architecture/architecture_plaze_brain_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: M. Plaze et al. -title: A brain morphometry study of schizophrenia patients with inner or outer space hallucinations -journal: Schizophrenia Bulletin -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_plaze_who_2015.md b/_collections/_biblio/architecture/architecture_plaze_who_2015.md deleted file mode 100644 index c2673d4..0000000 --- a/_collections/_biblio/architecture/architecture_plaze_who_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Marion Plaze et al. -title: Who is talking to me? - Self-other attribution of auditory hallucinations and sulcation of the right temporoparietal junction -journal: Schizophrenia Research -year: 2015 -type: article -doi: 10.1016/j.schres.2015.10.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poo_brain_2023.md b/_collections/_biblio/architecture/architecture_poo_brain_2023.md deleted file mode 100644 index 46cf6ef..0000000 --- a/_collections/_biblio/architecture/architecture_poo_brain_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Elida Poo et al. -title: BRAIN FIBER BUNDLE SIMULATOR USING SPLINE CURVES -journal: IBRO Neuroscience Reports -year: 2023 -type: article -url: https -//www.ibroneuroreports.org/article/S2667-2421(23)01673-1/fulltext -doi: 10.1016/j.ibneur.2023.08.1611 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poo_fiber_2023.md b/_collections/_biblio/architecture/architecture_poo_fiber_2023.md deleted file mode 100644 index be61c34..0000000 --- a/_collections/_biblio/architecture/architecture_poo_fiber_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Elida Poo et al. -title: Fiber bundles simulator using exponential curves to validate fiber clustering algorithms -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670J/Fiber-bundles-simulator-using-exponential-curves-to-validate-fiber-clustering/10.1117/12.2669811.full -doi: 10.1117/12.2669811 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_atlas-based_2009.md b/_collections/_biblio/architecture/architecture_poupon_atlas-based_2009.md deleted file mode 100644 index bb4f7db..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_atlas-based_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: F. Poupon et al. -title: Atlas-Based Analysis of Human Brainstem Anatomy as Revealed by Gradient-Echo T2* Weighted MR Imaging at 7T -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_database_2006.md b/_collections/_biblio/architecture/architecture_poupon_database_2006.md deleted file mode 100644 index bd2bcb3..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_database_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: A database dedicated to anatomo-functional study of human brain connectivity -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_diffusion_2007.md b/_collections/_biblio/architecture/architecture_poupon_diffusion_2007.md deleted file mode 100644 index b0f7f4d..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_diffusion_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: Diffusion phantoms dedicated to the study and validation of HARDI models -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_millimeter_2009.md b/_collections/_biblio/architecture/architecture_poupon_millimeter_2009.md deleted file mode 100644 index a84b34b..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_millimeter_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: Millimeter analytical Q-ball fiber density function for a better separation of fiber populations at 7T -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_new_2007.md b/_collections/_biblio/architecture/architecture_poupon_new_2007.md deleted file mode 100644 index 16f1ac4..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_new_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: New diffusion phantoms dedicated to study and validation of HARDI diffusion models. -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_new_2008.md b/_collections/_biblio/architecture/architecture_poupon_new_2008.md deleted file mode 100644 index 55b69a7..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_new_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: New diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging (HARDI) models -journal: Magn Reson Med -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_real-time_2008-1.md b/_collections/_biblio/architecture/architecture_poupon_real-time_2008-1.md deleted file mode 100644 index 1037cb1..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_real-time_2008-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Cyril Poupon et al. -title: Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering -journal: Med Image Anal -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_real-time_2008.md b/_collections/_biblio/architecture/architecture_poupon_real-time_2008.md deleted file mode 100644 index d824f6f..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_real-time_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: F. Poupon et al. -title: Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_poupon_validation_2005.md b/_collections/_biblio/architecture/architecture_poupon_validation_2005.md deleted file mode 100644 index acf0972..0000000 --- a/_collections/_biblio/architecture/architecture_poupon_validation_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Poupon et al. -title: Validation of Q-ball imaging with a diffusion fiber crossing phantom on a clinical scanner -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_prieto_multiscale_2023.md b/_collections/_biblio/architecture/architecture_prieto_multiscale_2023.md deleted file mode 100644 index b76470f..0000000 --- a/_collections/_biblio/architecture/architecture_prieto_multiscale_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yarelis Prieto et al. -title: Multiscale cortical parcellation based on geodesic distance and hierarchical clustering -year: 2023 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/10373421 -doi: 10.1109/SIPAIM56729.2023.10373421 -booktitle: 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2021.md b/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2021.md deleted file mode 100644 index ea8dfcd..0000000 --- a/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jérémy Raffin et al. -title: Cross-sectional and longitudinal interaction effects of physical activity and \textitAPOE-\textitε4 on white matter integrity in older adults - The MAPT study -journal: Maturitas -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0378512221001158 -doi: 10.1016/j.maturitas.2021.06.010 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2023.md b/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2023.md deleted file mode 100644 index c00bb14..0000000 --- a/_collections/_biblio/architecture/architecture_raffin_cross-sectional_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jérémy Raffin et al. -title: Cross-sectional associations between cortical thickness and physical activity in older adults with spontaneous memory complaints - The MAPT Study -journal: Journal of Sport and Health Science -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S209525462100020X -doi: 10.1016/j.jshs.2021.01.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ragis_sulcal_2005.md b/_collections/_biblio/architecture/architecture_ragis_sulcal_2005.md deleted file mode 100644 index 2683ddd..0000000 --- a/_collections/_biblio/architecture/architecture_ragis_sulcal_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: J. Régis et al. -title: Sulcal root generic model - a hypothesis to overcome the variability of the human cortex folding patterns -journal: Neurol Med Chir (Tokyo) -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_redolfi_head--head_2015.md b/_collections/_biblio/architecture/architecture_redolfi_head--head_2015.md deleted file mode 100644 index 5e0140e..0000000 --- a/_collections/_biblio/architecture/architecture_redolfi_head--head_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Alberto Redolfi et al. -title: Head-to-Head Comparison of Two Popular Cortical Thickness Extraction Algorithms - A Cross-Sectional and Longitudinal Study -journal: PLOS ONE -year: 2015 -type: article -doi: 10.1371/journal.pone.0117692 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_regy_association_2022.md b/_collections/_biblio/architecture/architecture_regy_association_2022.md deleted file mode 100644 index 9e68a3a..0000000 --- a/_collections/_biblio/architecture/architecture_regy_association_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Mélina Régy et al. -title: Association of \textitAPOE ε4 with cerebral gray matter volumes in non-demented older adults - The MEMENTO cohort study -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922000957 -doi: 10.1016/j.neuroimage.2022.118966 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_reiner_sulcal_2012.md b/_collections/_biblio/architecture/architecture_reiner_sulcal_2012.md deleted file mode 100644 index 48eaa77..0000000 --- a/_collections/_biblio/architecture/architecture_reiner_sulcal_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Peggy Reiner et al. -title: Sulcal span in Azheimer's disease, amnestic mild cognitive impairment, and healthy controls -journal: Journal of Alzheimer's disease - JAD -year: 2012 -type: article -doi: 10.3233/JAD-2012-111622 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_ringuenet_cingulate_2005.md b/_collections/_biblio/architecture/architecture_ringuenet_cingulate_2005.md deleted file mode 100644 index 0934e4c..0000000 --- a/_collections/_biblio/architecture/architecture_ringuenet_cingulate_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Ringuenet et al. -title: Cingulate cortex and resistant depression - 3D sulci measurment and voxel-based morphometry abnormalities -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_riviere_anatomist:_2011.md b/_collections/_biblio/architecture/architecture_riviere_anatomist:_2011.md deleted file mode 100644 index 31c0775..0000000 --- a/_collections/_biblio/architecture/architecture_riviere_anatomist:_2011.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Rivière et al. -title: Anatomist - a python framework for interactive 3D visualization of neuroimaging data -year: 2011 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_riviere_brainvisa:_2009.md b/_collections/_biblio/architecture/architecture_riviere_brainvisa:_2009.md deleted file mode 100644 index f44dfde..0000000 --- a/_collections/_biblio/architecture/architecture_riviere_brainvisa:_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Riviere et al. -title: BrainVISA - an extensible software environment for sharing multimodal neuroimaging data and processing tools -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_riviere_browsing_2022.md b/_collections/_biblio/architecture/architecture_riviere_browsing_2022.md deleted file mode 100644 index 1c29a92..0000000 --- a/_collections/_biblio/architecture/architecture_riviere_browsing_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Denis Rivière et al. -title: Browsing Multiple Subjects When the Atlas Adaptation Cannot Be Achieved via a Warping Strategy -journal: Frontiers in Neuroinformatics -year: 2022 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2022.803934 -doi: 10.3389/fninf.2022.803934 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_riviere_focal_2011.md b/_collections/_biblio/architecture/architecture_riviere_focal_2011.md deleted file mode 100644 index 4ad132f..0000000 --- a/_collections/_biblio/architecture/architecture_riviere_focal_2011.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: D. Rivière et al. -title: Focal epileptogenic malformations of cortical development are associated with diffuse sulcal anomalies -year: 2011 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roca_sulcus-based_2015.md b/_collections/_biblio/architecture/architecture_roca_sulcus-based_2015.md deleted file mode 100644 index 3962174..0000000 --- a/_collections/_biblio/architecture/architecture_roca_sulcus-based_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Pauline Roca et al. -title: Sulcus-based MR analysis of focal cortical dysplasia located in the central region -journal: PloS One -year: 2015 -type: article -doi: 10.1371/journal.pone.0122252 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roca_tractography-based_2009.md b/_collections/_biblio/architecture/architecture_roca_tractography-based_2009.md deleted file mode 100644 index 067ff27..0000000 --- a/_collections/_biblio/architecture/architecture_roca_tractography-based_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: P. Roca et al. -title: Tractography-Based Parcellation of the Cortex using a Spatially-Informed Dimension Reduction of the Connectivity Matrix -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_rodrigo_human_2007.md b/_collections/_biblio/architecture/architecture_rodrigo_human_2007.md deleted file mode 100644 index 14e867e..0000000 --- a/_collections/_biblio/architecture/architecture_rodrigo_human_2007.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Rodrigo et al. -title: Human subinsular asymetry studied by diffusion tensor imaging and fiber tracking -journal: Am J Neuroradiol -year: 2007 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_rodrigo_uncinate_2007.md b/_collections/_biblio/architecture/architecture_rodrigo_uncinate_2007.md deleted file mode 100644 index c4b3fe9..0000000 --- a/_collections/_biblio/architecture/architecture_rodrigo_uncinate_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Rodrigo et al. -title: Uncinate fasciculus fiber tracking in mesial temporal lobe epilepsy. Initial findings -journal: European Radiology -year: 2007 -type: article -doi: 10.1007/s00330-006-0558-x ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_rolland_exploring_2019.md b/_collections/_biblio/architecture/architecture_rolland_exploring_2019.md deleted file mode 100644 index 17989c7..0000000 --- a/_collections/_biblio/architecture/architecture_rolland_exploring_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Rolland et al. -title: Exploring Microstructure Asymmetries in the Infant Brain Cortex - A Methodological Framework Combining Structural and Diffusion Mri -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/8759421 -doi: 10.1109/ISBI.2019.8759421 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roman_automatic_2015.md b/_collections/_biblio/architecture/architecture_roman_automatic_2015.md deleted file mode 100644 index 897c29c..0000000 --- a/_collections/_biblio/architecture/architecture_roman_automatic_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Roman et al. -title: Automatic clustering of short association white matter fibers from HARDI tractography datasets. -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roman_clustering_2017.md b/_collections/_biblio/architecture/architecture_roman_clustering_2017.md deleted file mode 100644 index e8d8330..0000000 --- a/_collections/_biblio/architecture/architecture_roman_clustering_2017.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Claudio Román et al. -title: Clustering of Whole-Brain White Matter Short Association Bundles Using HARDI Data -journal: Frontiers in Neuroinformatics -year: 2017 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2017.00073 -doi: 10.3389/fninf.2017.00073 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roman_short_2016.md b/_collections/_biblio/architecture/architecture_roman_short_2016.md deleted file mode 100644 index e2bd1e0..0000000 --- a/_collections/_biblio/architecture/architecture_roman_short_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Roman et al. -title: Short association bundle atlas based on inter-subject clustering from HARDI data -year: 2016 -type: inproceedings -doi: 10.1109/EMBC.2016.7591983 -booktitle: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roman_study_2021.md b/_collections/_biblio/architecture/architecture_roman_study_2021.md deleted file mode 100644 index 9ee04b0..0000000 --- a/_collections/_biblio/architecture/architecture_roman_study_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: C. Román et al. -title: Study Of Precentral-Postcentral Connections On Hcp Data Using Probabilistic Tractography And Fiber Clustering -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9434093 -doi: 10.1109/ISBI48211.2021.9434093 -booktitle: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_roman_superficial_2022.md b/_collections/_biblio/architecture/architecture_roman_superficial_2022.md deleted file mode 100644 index 5c83acf..0000000 --- a/_collections/_biblio/architecture/architecture_roman_superficial_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Claudio Román et al. -title: Superficial white matter bundle atlas based on hierarchical fiber clustering over probabilistic tractography data -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922006656 -doi: 10.1016/j.neuroimage.2022.119550 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_rybina_eosc-life_2023.md b/_collections/_biblio/architecture/architecture_rybina_eosc-life_2023.md deleted file mode 100644 index 6951ce2..0000000 --- a/_collections/_biblio/architecture/architecture_rybina_eosc-life_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Arina Rybina et al. -title: EOSC-Life Report on the work of the Open Call Projects -year: 2023 -type: techreport -url: https -//hal.science/hal-04185373 -doi: 10.5281/zenodo.8263074 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_corpus_2015.md b/_collections/_biblio/architecture/architecture_sarrazin_corpus_2015.md deleted file mode 100644 index 7ea85fd..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_corpus_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: Corpus callosum area in patients with bipolar disorder with and without psychotic features - an international multicentre study -journal: JOURNAL OF PSYCHIATRY \& NEUROSCIENCE -year: 2015 -type: article -doi: 10.1503/jpn.140262 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_higher_2019.md b/_collections/_biblio/architecture/architecture_sarrazin_higher_2019.md deleted file mode 100644 index 681a443..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_higher_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: Higher in vivo Cortical Intracellular Volume Fraction Associated with Lithium Therapy in Bipolar Disorder - A Multicenter NODDI Study -journal: Psychotherapy and Psychosomatics -year: 2019 -type: article -url: https -//doi.org/10.1159/000498854 -doi: 10.1159/000498854 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_mri_2011.md b/_collections/_biblio/architecture/architecture_sarrazin_mri_2011.md deleted file mode 100644 index ff2a7f3..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_mri_2011.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: MRI exploration of pineal volume in bipolar disorder -journal: JOURNAL OF AFFECTIVE DISORDERS -year: 2011 -type: article -doi: 10.1016/j.jad.2011.06.001 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_multicenter_2014.md b/_collections/_biblio/architecture/architecture_sarrazin_multicenter_2014.md deleted file mode 100644 index f0f5028..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_multicenter_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: A multicenter tractography study of deep white matter tracts in bipolar I disorder - psychotic features and interhemispheric disconnectivity -journal: JAMA psychiatry -year: 2014 -type: article -doi: 10.1001/jamapsychiatry.2013.4513 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_neurodevelopmental_2018.md b/_collections/_biblio/architecture/architecture_sarrazin_neurodevelopmental_2018.md deleted file mode 100644 index df8c309..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_neurodevelopmental_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: Neurodevelopmental subtypes of bipolar disorder are related to cortical folding patterns - An international multicenter study -journal: Bipolar Disorders -year: 2018 -type: article -doi: 10.1111/bdi.12664 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sarrazin_neuroimaging_2020.md b/_collections/_biblio/architecture/architecture_sarrazin_neuroimaging_2020.md deleted file mode 100644 index 3d04fae..0000000 --- a/_collections/_biblio/architecture/architecture_sarrazin_neuroimaging_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Samuel Sarrazin et al. -title: Neuroimaging Evidence for Increased Neurite Density in Patients Taking Lithium - A Replication Study -journal: Psychotherapy and Psychosomatics -year: 2020 -type: article -url: https -//doi.org/10.1159/000507556 -doi: 10.1159/000507556 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_schilling_tractography_2021.md b/_collections/_biblio/architecture/architecture_schilling_tractography_2021.md deleted file mode 100644 index 59c628d..0000000 --- a/_collections/_biblio/architecture/architecture_schilling_tractography_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Kurt Schilling et al. -title: Tractography dissection variability - What happens when 42 groups dissect 14 white matter bundles on the same dataset? -journal: NeuroImage -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921007758 -doi: 10.1016/j.neuroimage.2021.118502 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_schirner_brain_2022.md b/_collections/_biblio/architecture/architecture_schirner_brain_2022.md deleted file mode 100644 index 106684f..0000000 --- a/_collections/_biblio/architecture/architecture_schirner_brain_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Michael Schirner et al. -title: Brain simulation as a cloud service - The Virtual Brain on EBRAINS -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922001021 -doi: 10.1016/j.neuroimage.2022.118973 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_seiler_lower_2017.md b/_collections/_biblio/architecture/architecture_seiler_lower_2017.md deleted file mode 100644 index ad1e2bd..0000000 --- a/_collections/_biblio/architecture/architecture_seiler_lower_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Seiler et al. -title: Lower Magnetization Transfer Ratio in the Forceps Minor Is Associated with Poorer Gait Velocity in Older Adults -journal: AJNR. American journal of neuroradiology -year: 2017 -type: article -doi: 10.3174/ajnr.A5036 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_seiler_magnetization_2014.md b/_collections/_biblio/architecture/architecture_seiler_magnetization_2014.md deleted file mode 100644 index de52c52..0000000 --- a/_collections/_biblio/architecture/architecture_seiler_magnetization_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Stephan Seiler et al. -title: Magnetization transfer ratio relates to cognitive impairment in normal elderly -journal: FRONTIERS IN AGING NEUROSCIENCE -year: 2014 -type: article -doi: 10.3389/fnagi.2014.00263 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_senova_optogenetic_2018.md b/_collections/_biblio/architecture/architecture_senova_optogenetic_2018.md deleted file mode 100644 index 6952155..0000000 --- a/_collections/_biblio/architecture/architecture_senova_optogenetic_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: S. Senova et al. -title: Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates -journal: Scientific Reports -year: 2018 -type: article -doi: 10.1038/s41598-018-21486-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_siless_joint_2012.md b/_collections/_biblio/architecture/architecture_siless_joint_2012.md deleted file mode 100644 index af818ec..0000000 --- a/_collections/_biblio/architecture/architecture_siless_joint_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Viviana Siless et al. -title: Joint T1 and brain fiber log-demons registration using currents to model geometry -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2012 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_simon_automatized_2004.md b/_collections/_biblio/architecture/architecture_simon_automatized_2004.md deleted file mode 100644 index 1c39dd5..0000000 --- a/_collections/_biblio/architecture/architecture_simon_automatized_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: O. Simon et al. -title: Automatized clustering and functional geometry of human parietofrontal networks for language, space, and number -journal: Neuroimage -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_simon_topographical_2002.md b/_collections/_biblio/architecture/architecture_simon_topographical_2002.md deleted file mode 100644 index f04e094..0000000 --- a/_collections/_biblio/architecture/architecture_simon_topographical_2002.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: O. Simon et al. -title: Topographical layout of hand, eye, calculation, and language-related areas in the human parietal lobe -journal: Neuron -year: 2002 -type: article -doi: S0896627302005755 [pii] ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_automatic_2007.md b/_collections/_biblio/architecture/architecture_sun_automatic_2007.md deleted file mode 100644 index 1fe766f..0000000 --- a/_collections/_biblio/architecture/architecture_sun_automatic_2007.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Z. Sun et al. -title: Automatic inference of sulcus patterns using 3D moment invariants -year: 2007 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_constructing_2009.md b/_collections/_biblio/architecture/architecture_sun_constructing_2009.md deleted file mode 100644 index f3e8fd4..0000000 --- a/_collections/_biblio/architecture/architecture_sun_constructing_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Z. Sun et al. -title: Constructing a Dictionary of Human Brain Folding Patterns -year: 2009 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_defining_2008.md b/_collections/_biblio/architecture/architecture_sun_defining_2008.md deleted file mode 100644 index 4e2742b..0000000 --- a/_collections/_biblio/architecture/architecture_sun_defining_2008.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Zhong Sun et al. -title: Defining cortical sulcus patterns using partial clustering based on bootstrap and bagging -year: 2008 -type: inproceedings -url: http -//ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4541325 -doi: 10.1109/ISBI.2008.4541325 -booktitle: 2008 5th IEEE International Symposium on Biomedical Imaging - From Nano to Macro ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_effect_2012.md b/_collections/_biblio/architecture/architecture_sun_effect_2012.md deleted file mode 100644 index 3be97bf..0000000 --- a/_collections/_biblio/architecture/architecture_sun_effect_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Zhong Sun et al. -title: The effect of handedness on the shape of the central sulcus -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2011.12.050 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_linking_2016.md b/_collections/_biblio/architecture/architecture_sun_linking_2016.md deleted file mode 100644 index 6eeff46..0000000 --- a/_collections/_biblio/architecture/architecture_sun_linking_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Z. Sun et al. -title: Linking morphological and functional variability in hand movement and silent reading -journal: Brain Structure \& Function -year: 2016 -type: article -doi: 10.1007/s00429-015-1106-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_manifold-based_2019.md b/_collections/_biblio/architecture/architecture_sun_manifold-based_2019.md deleted file mode 100644 index 0f68834..0000000 --- a/_collections/_biblio/architecture/architecture_sun_manifold-based_2019.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Zhong Sun et al. -title: Manifold-based exploration of the links between cortical morphology and functional architecture -year: 2019 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_manifold-based_2020.md b/_collections/_biblio/architecture/architecture_sun_manifold-based_2020.md deleted file mode 100644 index 408e0d4..0000000 --- a/_collections/_biblio/architecture/architecture_sun_manifold-based_2020.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: ZY Sun et al. -title: Manifold-based exploration of the links between precentral sulcus interruptions and language-associated area 55b -year: 2020 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_new_2018.md b/_collections/_biblio/architecture/architecture_sun_new_2018.md deleted file mode 100644 index 7f2fc2c..0000000 --- a/_collections/_biblio/architecture/architecture_sun_new_2018.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Z. Sun et al. -title: New Anatomical Characterizations of the Posterior Sylvian Fissure using the Human Connectome Project Database -year: 2018 -type: inproceedings -url: https -//hal.science/hal-02876125/file/SunHBM2018abstract.pdf ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_sun_shape_2017.md b/_collections/_biblio/architecture/architecture_sun_shape_2017.md deleted file mode 100644 index 4233fdf..0000000 --- a/_collections/_biblio/architecture/architecture_sun_shape_2017.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Zhong Sun et al. -title: Shape analysis of the cingulum, uncinate and arcuate fasciculi in patients with bipolar disorder -journal: Journal of psychiatry \& neuroscience - JPN -year: 2017 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_tamura_advanced_2013.md b/_collections/_biblio/architecture/architecture_tamura_advanced_2013.md deleted file mode 100644 index a9dc75d..0000000 --- a/_collections/_biblio/architecture/architecture_tamura_advanced_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Manabu Tamura et al. -title: Advanced Image Coregistration within the Leksell Workstation for the Planning of Glioma Surgery - Initial Experience -journal: Journal of Neurological Surgery Reports -year: 2013 -type: article -doi: 10.1055/s-0033-1358380 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_tamura_integrated_2019.md b/_collections/_biblio/architecture/architecture_tamura_integrated_2019.md deleted file mode 100644 index d3ff283..0000000 --- a/_collections/_biblio/architecture/architecture_tamura_integrated_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Manabu Tamura et al. -title: Integrated datasets of normalized brain with functional localization using intra-operative electrical stimulation -journal: International Journal of Computer Assisted Radiology and Surgery -year: 2019 -type: article -url: https -//doi.org/10.1007/s11548-019-01957-7 -doi: 10.1007/s11548-019-01957-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_tamura_usefulness_2013.md b/_collections/_biblio/architecture/architecture_tamura_usefulness_2013.md deleted file mode 100644 index 8f75da8..0000000 --- a/_collections/_biblio/architecture/architecture_tamura_usefulness_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Manabu Tamura et al. -title: Usefulness of Leksell GammaPlan for preoperative planning of brain tumor resection - delineation of the cranial nerves and fusion of the neuroimaging data, including diffusion tensor imaging -journal: Acta Neurochirurgica. Supplement -year: 2013 -type: article -doi: 10.1007/978-3-7091-1376-9_27 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_teillac_colocalization_2016.md b/_collections/_biblio/architecture/architecture_teillac_colocalization_2016.md deleted file mode 100644 index cc10c4e..0000000 --- a/_collections/_biblio/architecture/architecture_teillac_colocalization_2016.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Achille Teillac et al. -title: Colocalization of Functional Activity and Neurite Density Within Cortical Areas -year: 2016 -type: inproceedings -url: https -//link.springer.com/chapter/10.1007/978-3-319-54130-3_15 -doi: 10.1007/978-3-319-54130-3_15 -booktitle: Computational Diffusion MRI ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_teillac_novel_2017.md b/_collections/_biblio/architecture/architecture_teillac_novel_2017.md deleted file mode 100644 index def73b9..0000000 --- a/_collections/_biblio/architecture/architecture_teillac_novel_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Achille Teillac et al. -title: A Novel Anatomically-Constrained Global Tractography Approach to Monitor Sharp Turns in Gyri -year: 2017 -type: inproceedings -doi: 10.1007/978-3-319-66182-7_61 -booktitle: Medical Image Computing and Computer Assisted Intervention - MICCAI 2017 - 20th International Conference, Quebec City, QC, Canada, September 11-13, 2017, Proceedings, Part I ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_thirion_high_2007.md b/_collections/_biblio/architecture/architecture_thirion_high_2007.md deleted file mode 100644 index 3250784..0000000 --- a/_collections/_biblio/architecture/architecture_thirion_high_2007.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Bertrand Thirion et al. -title: High level group analysis of FMRI data based on Dirichlet process mixture models -journal: Inf Process Med Imaging -year: 2007 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_thirion_structural_2007.md b/_collections/_biblio/architecture/architecture_thirion_structural_2007.md deleted file mode 100644 index ebf9d5a..0000000 --- a/_collections/_biblio/architecture/architecture_thirion_structural_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: B. Thirion et al. -title: Structural analysis of fMRI data revisited - improving the sensitivity and reliability of fMRI group studies -journal: IEEE Trans Med Imaging -year: 2007 -type: article -doi: 10.1109/TMI.2007.903226 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_tucholka_probabilistic_2008.md b/_collections/_biblio/architecture/architecture_tucholka_probabilistic_2008.md deleted file mode 100644 index 6847ac9..0000000 --- a/_collections/_biblio/architecture/architecture_tucholka_probabilistic_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Alan Tucholka et al. -title: Probabilistic anatomo-functional parcellation of the cortex - how many regions? -journal: Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv -year: 2008 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_tucholka_triangulating_2008.md b/_collections/_biblio/architecture/architecture_tucholka_triangulating_2008.md deleted file mode 100644 index d0f1038..0000000 --- a/_collections/_biblio/architecture/architecture_tucholka_triangulating_2008.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: A. Tucholka et al. -title: Triangulating cortical functional networks with anatomical landmarks -year: 2008 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vazquez_automatic_2020.md b/_collections/_biblio/architecture/architecture_vazquez_automatic_2020.md deleted file mode 100644 index a90d03c..0000000 --- a/_collections/_biblio/architecture/architecture_vazquez_automatic_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Andrea Vázquez et al. -title: Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information -journal: BioMedical Engineering OnLine -year: 2020 -type: article -url: https -//biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-020-00786-z -doi: 10.1186/s12938-020-00786-z ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vazquez_ffclust_2020.md b/_collections/_biblio/architecture/architecture_vazquez_ffclust_2020.md deleted file mode 100644 index bae463e..0000000 --- a/_collections/_biblio/architecture/architecture_vazquez_ffclust_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Andrea Vázquez et al. -title: FFClust - Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity -journal: NeuroImage -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811920305565 -doi: 10.1016/j.neuroimage.2020.117070 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vellas_mapt_2014.md b/_collections/_biblio/architecture/architecture_vellas_mapt_2014.md deleted file mode 100644 index b0c16dc..0000000 --- a/_collections/_biblio/architecture/architecture_vellas_mapt_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: B. Vellas et al. -title: MAPT STUDY - A MULTIDOMAIN APPROACH FOR PREVENTING ALZHEIMER'S DISEASE - DESIGN AND BASELINE DATA. -journal: J Prev Alzheimers Dis. -year: 2014 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vergara_group-wise_2021.md b/_collections/_biblio/architecture/architecture_vergara_group-wise_2021.md deleted file mode 100644 index e7c3992..0000000 --- a/_collections/_biblio/architecture/architecture_vergara_group-wise_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Christopher Vergara et al. -title: Group-Wise Cortical Surface Parcellation Based on Inter-Subject Fiber Clustering -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9631099 -doi: 10.1109/EMBC46164.2021.9631099 -booktitle: 2021 43rd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vidal_comparing_2023.md b/_collections/_biblio/architecture/architecture_vidal_comparing_2023.md deleted file mode 100644 index f8801d4..0000000 --- a/_collections/_biblio/architecture/architecture_vidal_comparing_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Natalia Vidal et al. -title: Comparing White Matter Fiber Bundle Segmentation Methods for Autism Prediction -year: 2023 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/10373470 -doi: 10.1109/SIPAIM56729.2023.10373470 -booktitle: 2023 19th International Symposium on Medical Information Processing and Analysis (SIPAIM) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vindas_geolab_2023.md b/_collections/_biblio/architecture/architecture_vindas_geolab_2023.md deleted file mode 100644 index 1bcc216..0000000 --- a/_collections/_biblio/architecture/architecture_vindas_geolab_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Nabil Vindas et al. -title: GeoLab - Geometry-Based Tractography Parcellation of Superficial White Matter -year: 2023 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/10230336 -doi: 10.1109/ISBI53787.2023.10230336 -booktitle: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_vonk_semantic_2020.md b/_collections/_biblio/architecture/architecture_vonk_semantic_2020.md deleted file mode 100644 index e6fa9f4..0000000 --- a/_collections/_biblio/architecture/architecture_vonk_semantic_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Jet Vonk et al. -title: Semantic loss marks early Alzheimer's disease-related neurodegeneration in older adults without dementia -journal: Alzheimer's \& Dementia - Diagnosis, Assessment \& Disease Monitoring -year: 2020 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/dad2.12066 -doi: 10.1002/dad2.12066 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_wang_framework_2024.md b/_collections/_biblio/architecture/architecture_wang_framework_2024.md deleted file mode 100644 index 6ed08e9..0000000 --- a/_collections/_biblio/architecture/architecture_wang_framework_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Xiaoyu Wang et al. -title: A framework to improve the alignment of individual cytoarchitectonic maps of the Julich-Brain atlas using cortical folding landmarks -journal: Cerebral Cortex -year: 2024 -type: article -url: https -//academic.oup.com/cercor/article-abstract/34/2/bhad538/7571378 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_worbe_altered_2015.md b/_collections/_biblio/architecture/architecture_worbe_altered_2015.md deleted file mode 100644 index da98ac5..0000000 --- a/_collections/_biblio/architecture/architecture_worbe_altered_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Yulia Worbe et al. -title: Altered structural connectivity of cortico-striato-pallido-thalamic networks in Gilles de la Tourette syndrome -journal: BRAIN -year: 2015 -type: article -doi: 10.1093/brain/awu311 ---- \ No newline at end of file diff --git a/_collections/_biblio/architecture/architecture_yoo_example-based_2015.md b/_collections/_biblio/architecture/architecture_yoo_example-based_2015.md deleted file mode 100644 index 7f90e99..0000000 --- a/_collections/_biblio/architecture/architecture_yoo_example-based_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: architecture -bestof: false -author: Sang Yoo et al. -title: An Example-Based Multi-Atlas Approach to Automatic Labeling of White Matter Tracts -journal: PLOS ONE -year: 2015 -type: article -doi: 10.1371/journal.pone.0133337 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_alentorn_p0588_2018.md b/_collections/_biblio/brainomics/brainomics_alentorn_p0588_2018.md deleted file mode 100644 index 2f18b46..0000000 --- a/_collections/_biblio/brainomics/brainomics_alentorn_p0588_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: A Alentorn et al. -title: P05.88 Radiomics analysis of brain metastases from non-small cell lung cancer brings relevant supplementary information to clinical scores -journal: Neuro-Oncology -year: 2018 -type: article -url: https -//www.ncbi.nlm.nih.gov/pmc/articles/PMC6144734/ -doi: 10.1093/neuonc/noy139.414 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_beaudoin_etude_2022.md b/_collections/_biblio/brainomics/brainomics_beaudoin_etude_2022.md deleted file mode 100644 index 4031353..0000000 --- a/_collections/_biblio/brainomics/brainomics_beaudoin_etude_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Annabelle Beaudoin et al. -title: Etude de la Pénalisation GraphNet en Analyse de Données Multi-blocs -year: 2022 -type: inproceedings -url: https -//pasteur.hal.science/pasteur-04131938 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_bragulat_dopaminergic_2007.md b/_collections/_biblio/brainomics/brainomics_bragulat_dopaminergic_2007.md deleted file mode 100644 index 0c285ea..0000000 --- a/_collections/_biblio/brainomics/brainomics_bragulat_dopaminergic_2007.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Véronique Bragulat et al. -title: Dopaminergic function in depressed patients with affective flattening or with impulsivity - [18F]fluoro-L-dopa positron emission tomography study with voxel-based analysis -journal: Psychiatry Res -year: 2007 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_calmon_radiogenomics_2021.md b/_collections/_biblio/brainomics/brainomics_calmon_radiogenomics_2021.md deleted file mode 100644 index 5942db2..0000000 --- a/_collections/_biblio/brainomics/brainomics_calmon_radiogenomics_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Raphaël Calmon et al. -title: Radiogenomics of diffuse intrinsic pontine gliomas (DIPGs) - correlation of histological and biological characteristics with multimodal MRI features -journal: European Radiology -year: 2021 -type: article -url: https -//doi.org/10.1007/s00330-021-07991-x -doi: 10.1007/s00330-021-07991-x ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_castel_transcriptomic_2018.md b/_collections/_biblio/brainomics/brainomics_castel_transcriptomic_2018.md deleted file mode 100644 index 4b4b56f..0000000 --- a/_collections/_biblio/brainomics/brainomics_castel_transcriptomic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: David Castel et al. -title: Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location -journal: Acta Neuropathologica Communications -year: 2018 -type: article -url: https -//doi.org/10.1186/s40478-018-0614-1 -doi: 10.1186/s40478-018-0614-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_charman_eu-aims_2017.md b/_collections/_biblio/brainomics/brainomics_charman_eu-aims_2017.md deleted file mode 100644 index a30eab6..0000000 --- a/_collections/_biblio/brainomics/brainomics_charman_eu-aims_2017.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: T. Charman et al. -title: The EU-AIMS Longitunal European Autism Project (LEAP) - clinical characterisation -journal: Molecular Autism -year: 2017 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_chegraoui_integrating_2023.md b/_collections/_biblio/brainomics/brainomics_chegraoui_integrating_2023.md deleted file mode 100644 index 5334901..0000000 --- a/_collections/_biblio/brainomics/brainomics_chegraoui_integrating_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Hamza Chegraoui et al. -title: Integrating multiomics and prior knowledge - a study of the Graphnet penalty impact -journal: Bioinformatics -year: 2023 -type: article -url: https -//doi.org/10.1093/bioinformatics/btad454 -doi: 10.1093/bioinformatics/btad454 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_chegraoui_object_2021.md b/_collections/_biblio/brainomics/brainomics_chegraoui_object_2021.md deleted file mode 100644 index 6c295e0..0000000 --- a/_collections/_biblio/brainomics/brainomics_chegraoui_object_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Hamza Chegraoui et al. -title: Object Detection Improves Tumour Segmentation in MR Images of Rare Brain Tumours -journal: Cancers -year: 2021 -type: article -url: https -//www.mdpi.com/2072-6694/13/23/6113 -doi: 10.3390/cancers13236113 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_chegraoui_prediction_2021.md b/_collections/_biblio/brainomics/brainomics_chegraoui_prediction_2021.md deleted file mode 100644 index 87461f0..0000000 --- a/_collections/_biblio/brainomics/brainomics_chegraoui_prediction_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Hamza Chegraoui et al. -title: Prediction Performance of Radiomic Features When Obtained using an Object Detection Framework -year: 2021 -type: inproceedings -doi: 10.1109/ISBI48211.2021.9434148 -booktitle: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_cury_incomplete_2015.md b/_collections/_biblio/brainomics/brainomics_cury_incomplete_2015.md deleted file mode 100644 index 027da2b..0000000 --- a/_collections/_biblio/brainomics/brainomics_cury_incomplete_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Claire Cury et al. -title: Incomplete Hippocampal Inversion - A Comprehensive MRI Study of Over 2000 Subjects -journal: FRONTIERS IN NEUROANATOMY -year: 2015 -type: article -doi: 10.3389/fnana.2015.00160 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_dalberto_individual_2018.md b/_collections/_biblio/brainomics/brainomics_dalberto_individual_2018.md deleted file mode 100644 index 75641d3..0000000 --- a/_collections/_biblio/brainomics/brainomics_dalberto_individual_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: N. D'Alberto et al. -title: Individual differences in stop-related activity are inflated by the adaptive algorithm in the stop signal task. -journal: Hum Brain Mapp. -year: 2018 -type: article -doi: 10.1002/hbm.2407 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_dauguet_three-dimensional_2007.md b/_collections/_biblio/brainomics/brainomics_dauguet_three-dimensional_2007.md deleted file mode 100644 index a45ea40..0000000 --- a/_collections/_biblio/brainomics/brainomics_dauguet_three-dimensional_2007.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: J. Dauguet et al. -title: Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain -journal: J Neurosci Methods -year: 2007 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_de_pierrefeu_structured_2018.md b/_collections/_biblio/brainomics/brainomics_de_pierrefeu_structured_2018.md deleted file mode 100644 index 44d217e..0000000 --- a/_collections/_biblio/brainomics/brainomics_de_pierrefeu_structured_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Amicie Pierrefeu et al. -title: Structured Sparse Principal Components Analysis With the TV-Elastic Net Penalty -journal: IEEE Transactions on Medical Imaging -year: 2018 -type: article -doi: 10.1109/TMI.2017.2749140 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_di_stefano_clinical_2020.md b/_collections/_biblio/brainomics/brainomics_di_stefano_clinical_2020.md deleted file mode 100644 index 15b0922..0000000 --- a/_collections/_biblio/brainomics/brainomics_di_stefano_clinical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Anna Di Stefano et al. -title: Clinical, molecular, and radiomic profile of gliomas with FGFR3-TACC3 fusions -journal: Neuro-Oncology -year: 2020 -type: article -url: https -//doi.org/10.1093/neuonc/noaa121 -doi: 10.1093/neuonc/noaa121 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_dubois_automated_2007.md b/_collections/_biblio/brainomics/brainomics_dubois_automated_2007.md deleted file mode 100644 index 07e12a1..0000000 --- a/_collections/_biblio/brainomics/brainomics_dubois_automated_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Albertine Dubois et al. -title: Automated three-dimensional analysis of histological and autoradiographic rat brain sections - application to an activation study -journal: Journal of Cerebral Blood Flow and Metabolism - Official Journal of the International Society of Cerebral Blood Flow and Metabolism -year: 2007 -type: article -doi: 10.1038/sj.jcbfm.9600470 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_dubois_predictive_2014.md b/_collections/_biblio/brainomics/brainomics_dubois_predictive_2014.md deleted file mode 100644 index 737fddf..0000000 --- a/_collections/_biblio/brainomics/brainomics_dubois_predictive_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: M. Dubois et al. -title: Predictive support recovery with TV-Elastic Net penalty and logistic regression - An application to structural MRI -year: 2014 -type: inproceedings -doi: 10.1109/PRNI.2014.6858517 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_dubois_quantitative_2008.md b/_collections/_biblio/brainomics/brainomics_dubois_quantitative_2008.md deleted file mode 100644 index 09b26eb..0000000 --- a/_collections/_biblio/brainomics/brainomics_dubois_quantitative_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Albertine Dubois et al. -title: Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes - application to unilateral visual stimulation -journal: NeuroImage -year: 2008 -type: article -doi: 10.1016/j.neuroimage.2007.11.054 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_duchesnay_methodes_2015.md b/_collections/_biblio/brainomics/brainomics_duchesnay_methodes_2015.md deleted file mode 100644 index ce78ec8..0000000 --- a/_collections/_biblio/brainomics/brainomics_duchesnay_methodes_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Edouard Duchesnay et al. -title: Méthodes de prédiction multivariées basées sur la neuroimagerie - application aux maladies psychiatriques -journal: Annales Médico-psychologiques, revue psychiatrique -year: 2015 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_ewald_role_2016.md b/_collections/_biblio/brainomics/brainomics_ewald_role_2016.md deleted file mode 100644 index ab769fe..0000000 --- a/_collections/_biblio/brainomics/brainomics_ewald_role_2016.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: A. Ewald et al. -title: The role of the cannabinoid receptor in adolescents' processing of facial expressions. -journal: Eur J Neurosci. -year: 2016 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_fouque_comparison_2013.md b/_collections/_biblio/brainomics/brainomics_fouque_comparison_2013.md deleted file mode 100644 index e2a82c5..0000000 --- a/_collections/_biblio/brainomics/brainomics_fouque_comparison_2013.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Anne-Laure Fouque et al. -title: Comparison of Features for Voxel-Based Analysis and Classification of Anatomical Neuroimaging Data -year: 2013 -type: inproceedings -url: http -//dl.acm.org/citation.cfm?id=2552484.2552547 -doi: 10.1109/PRNI.2013.55 -booktitle: 2013 International Workshop on Pattern Recognition in Neuroimaging ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_frouin_hdr_2009.md b/_collections/_biblio/brainomics/brainomics_frouin_hdr_2009.md deleted file mode 100644 index cd363ee..0000000 --- a/_collections/_biblio/brainomics/brainomics_frouin_hdr_2009.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: V. Frouin et al. -title: HDR = Applications de méthodes d'intégration d'informations en imagerie bio-médicale et génomique fonctionnelle -year: 2009 -type: Habilitation à diriger des recherches ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_gloaguen_multiway_2022.md b/_collections/_biblio/brainomics/brainomics_gloaguen_multiway_2022.md deleted file mode 100644 index 9471c09..0000000 --- a/_collections/_biblio/brainomics/brainomics_gloaguen_multiway_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Arnaud Gloaguen et al. -title: Multiway generalized canonical correlation analysis -journal: Biostatistics -year: 2022 -type: article -url: https -//doi.org/10.1093/biostatistics/kxaa010 -doi: 10.1093/biostatistics/kxaa010 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_goya-outi_can_2019.md b/_collections/_biblio/brainomics/brainomics_goya-outi_can_2019.md deleted file mode 100644 index 57c9af5..0000000 --- a/_collections/_biblio/brainomics/brainomics_goya-outi_can_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Jessica Goya-Outi et al. -title: Can Structural MRI Radiomics Predict DIPG Histone H3 Mutation and Patient Overall Survival at Diagnosis Time? -year: 2019 -type: inproceedings -doi: 10.1109/BHI.2019.8834524 -booktitle: 2019 IEEE EMBS International Conference on Biomedical \& Health Informatics (BHI) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_guigui_network_2019.md b/_collections/_biblio/brainomics/brainomics_guigui_network_2019.md deleted file mode 100644 index 3c1144f..0000000 --- a/_collections/_biblio/brainomics/brainomics_guigui_network_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: N. Guigui et al. -title: Network Regularization in Imaging Genetics Improves Prediction Performances and Model Interpretability on Alzheimer’s Disease -year: 2019 -type: inproceedings -doi: 10.1109/ISBI.2019.8759593 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_guillemot_introducing_2021.md b/_collections/_biblio/brainomics/brainomics_guillemot_introducing_2021.md deleted file mode 100644 index 54b441b..0000000 --- a/_collections/_biblio/brainomics/brainomics_guillemot_introducing_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Vincent Guillemot et al. -title: Introducing group-sparsity and orthogonality constraints in RGCCA -year: 2021 -type: inproceedings -url: https -//hal.science/hal-03264640 -booktitle: JdS2021 - 52èmes Journées de Statistique ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_guillemot_multi-block_2013.md b/_collections/_biblio/brainomics/brainomics_guillemot_multi-block_2013.md deleted file mode 100644 index c1099ed..0000000 --- a/_collections/_biblio/brainomics/brainomics_guillemot_multi-block_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Vincent Guillemot et al. -title: A multi-block approach in imaging genetics -year: 2013 -type: inproceedings -booktitle: 9th International Imaging Genetics Conference ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_habert_evaluation_2018.md b/_collections/_biblio/brainomics/brainomics_habert_evaluation_2018.md deleted file mode 100644 index 54136da..0000000 --- a/_collections/_biblio/brainomics/brainomics_habert_evaluation_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Marie-Odile Habert et al. -title: Evaluation of amyloid status in a cohort of elderly individuals with memory complaints - validation of the method of quantification and determination of positivity thresholds -journal: Annals of Nuclear Medicine -year: 2018 -type: article -url: https -//doi.org/10.1007/s12149-017-1221-0 -doi: 10.1007/s12149-017-1221-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_hadj-selem_continuation_2018.md b/_collections/_biblio/brainomics/brainomics_hadj-selem_continuation_2018.md deleted file mode 100644 index bb061ca..0000000 --- a/_collections/_biblio/brainomics/brainomics_hadj-selem_continuation_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Fouad Hadj-Selem et al. -title: Continuation of Nesterov's Smoothing for Regression With Structured Sparsity in High-Dimensional Neuroimaging -journal: IEEE Transactions on Medical Imaging -year: 2018 -type: article -doi: 10.1109/TMI.2018.2829802 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_hadj-selem_supplementary_2018.md b/_collections/_biblio/brainomics/brainomics_hadj-selem_supplementary_2018.md deleted file mode 100644 index aa246e3..0000000 --- a/_collections/_biblio/brainomics/brainomics_hadj-selem_supplementary_2018.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Fouad Hadj-Selem et al. -title: Supplementary material - Continuation of Nesterov's Smoothing for Regression with Structured Sparsity in High-Dimensional Neuroimaging -year: 2018 -type: misc -url: https -//hal-cea.archives-ouvertes.fr/cea-01324021/document ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_ibrahim_modeling_2017.md b/_collections/_biblio/brainomics/brainomics_ibrahim_modeling_2017.md deleted file mode 100644 index 8c3ab83..0000000 --- a/_collections/_biblio/brainomics/brainomics_ibrahim_modeling_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: El Ibrahim et al. -title: Modeling a linkage between blood transcriptional expression and activity in brain regions to infer the phenotype of schizophrenia patients -journal: NPJ schizophrenia -year: 2017 -type: article -doi: 10.1038/s41537-017-0027-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_jurk_personality_2015.md b/_collections/_biblio/brainomics/brainomics_jurk_personality_2015.md deleted file mode 100644 index 1de5874..0000000 --- a/_collections/_biblio/brainomics/brainomics_jurk_personality_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Sarah Jurk et al. -title: Personality and Substance Use - Psychometric Evaluation and Validation of the Substance Use Risk Profile Scale (SURPS) in English, Irish, French, and German Adolescents -journal: ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH -year: 2015 -type: article -doi: 10.1111/acer.12886 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_karkar_alzheimers_2020.md b/_collections/_biblio/brainomics/brainomics_karkar_alzheimers_2020.md deleted file mode 100644 index 01a4631..0000000 --- a/_collections/_biblio/brainomics/brainomics_karkar_alzheimers_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Slim Karkar et al. -title: Alzheimer's polygenic risk score in general population reveals new biomarkers for early diagnosis -journal: Alzheimer's \& Dementia -year: 2020 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/alz.043396 -doi: 10.1002/alz.043396 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_karkar_genome-wide_2021.md b/_collections/_biblio/brainomics/brainomics_karkar_genome-wide_2021.md deleted file mode 100644 index 1cc3587..0000000 --- a/_collections/_biblio/brainomics/brainomics_karkar_genome-wide_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Slim Karkar et al. -title: Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects -journal: European Journal of Human Genetics -year: 2021 -type: article -url: https -//www.nature.com/articles/s41431-021-00827-8 -doi: 10.1038/s41431-021-00827-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_karkar_multivariate_2019.md b/_collections/_biblio/brainomics/brainomics_karkar_multivariate_2019.md deleted file mode 100644 index 5dbbdf4..0000000 --- a/_collections/_biblio/brainomics/brainomics_karkar_multivariate_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: S. Karkar et al. -title: Multivariate Haplotype Analysis Of 96 Sulci Opening For 15,612 UK-Biobank Sujects -year: 2019 -type: inproceedings -doi: 10.1109/ISBI.2019.8759497 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_karkar_study_2018.md b/_collections/_biblio/brainomics/brainomics_karkar_study_2018.md deleted file mode 100644 index d1e9749..0000000 --- a/_collections/_biblio/brainomics/brainomics_karkar_study_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Slim Karkar et al. -title: A study of feasibility for genome-wide haplotype association of complex traits in imaging genetics -year: 2018 -type: inproceedings -doi: 10.1109/BIBM.2018.8621306 -booktitle: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_khalid_multimodal_2023.md b/_collections/_biblio/brainomics/brainomics_khalid_multimodal_2023.md deleted file mode 100644 index 7de08b8..0000000 --- a/_collections/_biblio/brainomics/brainomics_khalid_multimodal_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Fahad Khalid et al. -title: Multimodal MRI radiomic models to predict genomic mutations in diffuse intrinsic pontine glioma with missing imaging modalities -journal: Frontiers in Medicine -year: 2023 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fmed.2023.1071447 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_labreche_genome-wide_2019.md b/_collections/_biblio/brainomics/brainomics_labreche_genome-wide_2019.md deleted file mode 100644 index 0267c66..0000000 --- a/_collections/_biblio/brainomics/brainomics_labreche_genome-wide_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Karim Labreche et al. -title: A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1 - a LOC Network study -journal: Neuro-Oncology -year: 2019 -type: article -url: https -//doi.org/10.1093/neuonc/noz088 -doi: 10.1093/neuonc/noz088 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_floch_bridging_2011.md b/_collections/_biblio/brainomics/brainomics_le_floch_bridging_2011.md deleted file mode 100644 index fe6883f..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_floch_bridging_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Edith Le Floch et al. -title: Bridging the gap between imaging and genetics - a multivariate statistical investigation -year: 2011 -type: inproceedings -booktitle: Human brain mapping ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_floch_cluster-level_2010.md b/_collections/_biblio/brainomics/brainomics_le_floch_cluster-level_2010.md deleted file mode 100644 index 5023330..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_floch_cluster-level_2010.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Edith Le Floch et al. -title: Cluster-level Inference and Resampling-Based Multiple Testing applied to Imaging Genetics Studies -year: 2010 -type: inproceedings -booktitle: Human brain mapping ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_floch_dimension_2012.md b/_collections/_biblio/brainomics/brainomics_le_floch_dimension_2012.md deleted file mode 100644 index e4c5679..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_floch_dimension_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: E. Le Floch et al. -title: Dimension reduction and regularisation combined with Partial Least Squares in high dimensional imaging-genetics studies -year: 2012 -type: inproceedings -booktitle: Partial Least Squares ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_floch_discovering_2012.md b/_collections/_biblio/brainomics/brainomics_le_floch_discovering_2012.md deleted file mode 100644 index 59a74a5..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_floch_discovering_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Edith Le Floch et al. -title: Discovering associations in high dimensional imaging-genetics data - A comparison study of dimension reduction and regularisation strategies combined with partial least squares -year: 2012 -type: inproceedings -booktitle: International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_floch_significant_2012.md b/_collections/_biblio/brainomics/brainomics_le_floch_significant_2012.md deleted file mode 100644 index 4798a3a..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_floch_significant_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Edith Le Floch et al. -title: Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse Partial Least Squares -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2012.06.061 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_guen_enhancer_2020.md b/_collections/_biblio/brainomics/brainomics_le_guen_enhancer_2020.md deleted file mode 100644 index 1b84662..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_guen_enhancer_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yann Le Guen et al. -title: Enhancer Locus in ch14q23.1 Modulates Brain Asymmetric Temporal Regions Involved in Language Processing -journal: Cerebral Cortex -year: 2020 -type: article -url: https -//doi.org/10.1093/cercor/bhaa112 -doi: 10.1093/cercor/bhaa112 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_guen_eqtl_2019.md b/_collections/_biblio/brainomics/brainomics_le_guen_eqtl_2019.md deleted file mode 100644 index 1a45f65..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_guen_eqtl_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yann Le Guen et al. -title: eQTL of KCNK2 regionally influences the brain sulcal widening - evidence from 15,597 UK Biobank participants with neuroimaging data -journal: Brain Structure and Function -year: 2019 -type: article -url: https -//doi.org/10.1007/s00429-018-1808-9 -doi: 10.1007/s00429-018-1808-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_guen_genetic_2018.md b/_collections/_biblio/brainomics/brainomics_le_guen_genetic_2018.md deleted file mode 100644 index 3e65c5b..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_guen_genetic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yann Le Guen et al. -title: Genetic Influence on the Sulcal Pits - On the Origin of the First Cortical Folds -journal: Cerebral Cortex -year: 2018 -type: article -url: https -//doi.org/10.1093/cercor/bhx098 -doi: 10.1093/cercor/bhx098 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_le_guen_heritability_2019.md b/_collections/_biblio/brainomics/brainomics_le_guen_heritability_2019.md deleted file mode 100644 index daff7aa..0000000 --- a/_collections/_biblio/brainomics/brainomics_le_guen_heritability_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yann Le Guen et al. -title: Heritability of surface area and cortical thickness - a comparison between the Human Connectome Project and the UK Biobank dataset -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/8759539 -doi: 10.1109/ISBI.2019.8759539 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_lemaitre_genetic_2023.md b/_collections/_biblio/brainomics/brainomics_lemaitre_genetic_2023.md deleted file mode 100644 index 3c37109..0000000 --- a/_collections/_biblio/brainomics/brainomics_lemaitre_genetic_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Herve Lemaitre et al. -title: Genetic variations within human gained enhancer elements affect human brain sulcal morphology -journal: NeuroImage -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922008941 -doi: 10.1016/j.neuroimage.2022.119773 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_lobon-iglesias_diffuse_2018.md b/_collections/_biblio/brainomics/brainomics_lobon-iglesias_diffuse_2018.md deleted file mode 100644 index 7ec4501..0000000 --- a/_collections/_biblio/brainomics/brainomics_lobon-iglesias_diffuse_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: M. Lobon-Iglesias et al. -title: Diffuse intrinsic pontine gliomas (DIPG) at recurrence - is there a window to test new therapies in some patients? -journal: Journal of Neuro-Oncology -year: 2018 -type: article -doi: 10.1007/s11060-017-2702-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_lofstedt_analysis_2014.md b/_collections/_biblio/brainomics/brainomics_lofstedt_analysis_2014.md deleted file mode 100644 index ce6a576..0000000 --- a/_collections/_biblio/brainomics/brainomics_lofstedt_analysis_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Tommy Lofstedt et al. -title: Analysis, Structured variable selection for generalized canonical correlation -year: 2014 -type: inproceedings -booktitle: International Conference on Partial Least Squares and Related Methods ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_lofstedt_simulated_2014.md b/_collections/_biblio/brainomics/brainomics_lofstedt_simulated_2014.md deleted file mode 100644 index eb28ec1..0000000 --- a/_collections/_biblio/brainomics/brainomics_lofstedt_simulated_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Tommy Lofstedt et al. -title: Simulated Data for Linear Regression with Structured and Sparse Penalties -year: 2014 -type: misc -url: https -//hal-cea.archives-ouvertes.fr/cea-00914960/document ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_lofstedt_structured_2016.md b/_collections/_biblio/brainomics/brainomics_lofstedt_structured_2016.md deleted file mode 100644 index dee471f..0000000 --- a/_collections/_biblio/brainomics/brainomics_lofstedt_structured_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Tommy Lofstedt et al. -title: Structured Variable Selection for Regularized Generalized Canonical Correlation Analysis, The Multiple Facets of Partial Least Squares and Related Methods -year: 2016 -type: incollection -url: https -//hal-centralesupelec.archives-ouvertes.fr/hal-01396614 -booktitle: Springer Proceedings in Mathematics and Statistics ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_loth_eu-aims_2017.md b/_collections/_biblio/brainomics/brainomics_loth_eu-aims_2017.md deleted file mode 100644 index 934e51d..0000000 --- a/_collections/_biblio/brainomics/brainomics_loth_eu-aims_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Eva Loth et al. -title: The EU-AIMS Longitudinal European Autism Project (LEAP) - design and methodologies to identify and validate stratification biomarkers for autism spectrum disorders -journal: Molecular Autism -year: 2017 -type: article -doi: 10.1186/s13229-017-0146-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_maroy_segmentation_2008.md b/_collections/_biblio/brainomics/brainomics_maroy_segmentation_2008.md deleted file mode 100644 index 47386f1..0000000 --- a/_collections/_biblio/brainomics/brainomics_maroy_segmentation_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Renaud Maroy et al. -title: Segmentation of rodent whole-body dynamic PET images - an unsupervised method based on voxel dynamics -journal: IEEE Transactions on Medical Imaging -year: 2008 -type: article -doi: 10.1109/TMI.2007.905106 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_mekki_genetic_2022.md b/_collections/_biblio/brainomics/brainomics_mekki_genetic_2022.md deleted file mode 100644 index ad78b87..0000000 --- a/_collections/_biblio/brainomics/brainomics_mekki_genetic_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yasmina Mekki et al. -title: The genetic architecture of language functional connectivity -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921010661 -doi: 10.1016/j.neuroimage.2021.118795 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_mekki_heritability_2019.md b/_collections/_biblio/brainomics/brainomics_mekki_heritability_2019.md deleted file mode 100644 index 328e54c..0000000 --- a/_collections/_biblio/brainomics/brainomics_mekki_heritability_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Yasmina Mekki et al. -title: Heritability of the language network using resting state fMRI data -year: 2019 -type: inproceedings -url: https -//hal-cea.archives-ouvertes.fr/cea-02289470 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_mihailov_cortical_2020.md b/_collections/_biblio/brainomics/brainomics_mihailov_cortical_2020.md deleted file mode 100644 index b416d75..0000000 --- a/_collections/_biblio/brainomics/brainomics_mihailov_cortical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Angeline Mihailov et al. -title: Cortical signatures in behaviorally clustered autistic traits subgroups - a population-based study -journal: Translational Psychiatry -year: 2020 -type: article -url: https -//www.nature.com/articles/s41398-020-00894-3 -doi: 10.1038/s41398-020-00894-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_orlhac_postreconstruction_2018.md b/_collections/_biblio/brainomics/brainomics_orlhac_postreconstruction_2018.md deleted file mode 100644 index 3141adb..0000000 --- a/_collections/_biblio/brainomics/brainomics_orlhac_postreconstruction_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Fanny Orlhac et al. -title: A Postreconstruction Harmonization Method for Multicenter Radiomic Studies in PET -journal: Journal of Nuclear Medicine - Official Publication, Society of Nuclear Medicine -year: 2018 -type: article -doi: 10.2967/jnumed.117.199935 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_ortuno-sierra_new_2015.md b/_collections/_biblio/brainomics/brainomics_ortuno-sierra_new_2015.md deleted file mode 100644 index 5d1acfc..0000000 --- a/_collections/_biblio/brainomics/brainomics_ortuno-sierra_new_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Javier Ortuno-Sierra et al. -title: New evidence of factor structure and measurement invariance of the SDQ across five European nations -journal: EUROPEAN CHILD \& ADOLESCENT PSYCHIATRY -year: 2015 -type: article -doi: 10.1007/s00787-015-0729-x ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_papadopoulos_orfanos_brainomics_localizer_2015.md b/_collections/_biblio/brainomics/brainomics_papadopoulos_orfanos_brainomics_localizer_2015.md deleted file mode 100644 index 22b2f7e..0000000 --- a/_collections/_biblio/brainomics/brainomics_papadopoulos_orfanos_brainomics_localizer_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: D. Papadopoulos Orfanos et al. -title: The Brainomics/Localizer database. -journal: Neuroimage -year: 2015 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_pappata_vivo_2002.md b/_collections/_biblio/brainomics/brainomics_pappata_vivo_2002.md deleted file mode 100644 index 8152fbb..0000000 --- a/_collections/_biblio/brainomics/brainomics_pappata_vivo_2002.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: S. Pappata et al. -title: In Vivo Detection of Striatal Dopamine Release during Reward - A PET Study with [(11)C]Raclopride and a Single Dynamic Scan Approach -journal: Neuroimage -year: 2002 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_poline_imaging_2010.md b/_collections/_biblio/brainomics/brainomics_poline_imaging_2010.md deleted file mode 100644 index 263c75b..0000000 --- a/_collections/_biblio/brainomics/brainomics_poline_imaging_2010.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Jean-Baptiste Poline et al. -title: Imaging Genetics - Bio-Informatics and Bio-Statistics Challenges -year: 2010 -type: inproceedings -url: http -//www.springerlink.com/index/10.1007/978-3-7908-2604-3 -doi: 10.1007/978-3-7908-2604-3 -booktitle: compstat ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_ragis_sulcal_2005.md b/_collections/_biblio/brainomics/brainomics_ragis_sulcal_2005.md deleted file mode 100644 index 6296583..0000000 --- a/_collections/_biblio/brainomics/brainomics_ragis_sulcal_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: J. Régis et al. -title: Sulcal root generic model - a hypothesis to overcome the variability of the human cortex folding patterns -journal: Neurol Med Chir (Tokyo) -year: 2005 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_rebei_contribution_2021.md b/_collections/_biblio/brainomics/brainomics_rebei_contribution_2021.md deleted file mode 100644 index 107f947..0000000 --- a/_collections/_biblio/brainomics/brainomics_rebei_contribution_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Amine Rebei et al. -title: Contribution Of Imaging-Genetics To Overall Survival Prediction Compared To Clinical Status For Pcnsl Patients -year: 2021 -type: inproceedings -doi: 10.1109/ISBI48211.2021.9433785 -booktitle: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_spechler_cannabis_2015.md b/_collections/_biblio/brainomics/brainomics_spechler_cannabis_2015.md deleted file mode 100644 index 834d8ee..0000000 --- a/_collections/_biblio/brainomics/brainomics_spechler_cannabis_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Philip Spechler et al. -title: Cannabis use in early adolescence - Evidence of amygdala hypersensitivity to signals of threat -journal: DEVELOPMENTAL COGNITIVE NEUROSCIENCE -year: 2015 -type: article -doi: 10.1016/j.dcn.2015.08.007 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_stacey_translational_2016.md b/_collections/_biblio/brainomics/brainomics_stacey_translational_2016.md deleted file mode 100644 index 68a4dd0..0000000 --- a/_collections/_biblio/brainomics/brainomics_stacey_translational_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: David Stacey et al. -title: A translational systems biology approach in both animals and humans identifies a functionally related module of accumbal genes involved in the regulation of reward processing and binge drinking in males -journal: JOURNAL OF PSYCHIATRY \& NEUROSCIENCE -year: 2016 -type: article -doi: 10.1503/jpn.150138 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_stringaris_brains_2015.md b/_collections/_biblio/brainomics/brainomics_stringaris_brains_2015.md deleted file mode 100644 index 1a10881..0000000 --- a/_collections/_biblio/brainomics/brainomics_stringaris_brains_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Argyris Stringaris et al. -title: The Brain's Response to Reward Anticipation and Depression in Adolescence - Dimensionality, Specificity, and Longitudinal Predictions in a Community-Based Sample -journal: AMERICAN JOURNAL OF PSYCHIATRY -year: 2015 -type: article -doi: 10.1176/appi.ajp.2015.14101298 ---- \ No newline at end of file diff --git a/_collections/_biblio/brainomics/brainomics_tenenhaus_three-way_2018.md b/_collections/_biblio/brainomics/brainomics_tenenhaus_three-way_2018.md deleted file mode 100644 index 0db7a4d..0000000 --- a/_collections/_biblio/brainomics/brainomics_tenenhaus_three-way_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: brainomics -bestof: false -author: Arthur Tenenhaus et al. -title: Three-Way Generalized Canonical Correlation Analysis -year: 2018 -type: inproceedings -url: https -//hal.science/hal-03111188 -booktitle: SIAM Conference on Applied Linear Algebra ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_artiges_ginkgo_nodate.md b/_collections/_biblio/ginkgo/ginkgo_artiges_ginkgo_nodate.md deleted file mode 100644 index 79eda0d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_artiges_ginkgo_nodate.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Anaïs Artiges et al. -title: Ginkgo - a novel modular and and Open Source MRI pulse sequence development framework dedicated to MRI systems -type: inproceedings -url: https -//archive.ismrm.org/2022/2778.html -doi: 10.58530/2022/2778 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_assaf_connect_2013.md b/_collections/_biblio/ginkgo/ginkgo_assaf_connect_2013.md deleted file mode 100644 index d09d5ee..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_assaf_connect_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Yaniv Assaf et al. -title: The CONNECT project - Combining macro- and micro-structure -journal: Neuroimage -year: 2013 -type: article -doi: 10.1016/j.neuroimage.2013.05.055 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_avila_inference_2019.md b/_collections/_biblio/ginkgo/ginkgo_avila_inference_2019.md deleted file mode 100644 index fd74139..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_avila_inference_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nicole Avila et al. -title: Inference of an Extended Short Fiber Bundle Atlas Using Sulcus-Based Constraints for a Diffeomorphic Inter-subject Alignment -year: 2019 -type: inproceedings -doi: 10.1007/978-3-030-05831-9_25 -booktitle: Computational Diffusion MRI ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_beaujoin_post-mortem_2018.md b/_collections/_biblio/ginkgo/ginkgo_beaujoin_post-mortem_2018.md deleted file mode 100644 index 20eb6d0..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_beaujoin_post-mortem_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Justine Beaujoin et al. -title: Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-018-1617-1 -doi: 10.1007/s00429-018-1617-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_benezit_organising_2015.md b/_collections/_biblio/ginkgo/ginkgo_benezit_organising_2015.md deleted file mode 100644 index cca377f..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_benezit_organising_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Audrey Bénézit et al. -title: Organising white matter in a brain without corpus callosum fibres -journal: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior -year: 2015 -type: article -doi: 10.1016/j.cortex.2014.08.022 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_berkovitch_perturbations_2018.md b/_collections/_biblio/ginkgo/ginkgo_berkovitch_perturbations_2018.md deleted file mode 100644 index 9f981ce..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_berkovitch_perturbations_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: L. Berkovitch et al. -title: Perturbations de l’accès conscient et de la connectivité cérébrale longue-distance dans la psychose -journal: French Journal of Psychiatry -year: 2018 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S2590241519303824 -doi: 10.1016/S2590-2415(19)30382-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_berre_effet_2023.md b/_collections/_biblio/ginkgo/ginkgo_berre_effet_2023.md deleted file mode 100644 index 25c74ed..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_berre_effet_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Alice Berre et al. -title: Effet de l’électroconvulsivothérapie sur la microstructure hippocampique dans la dépression sévère - une étude en neurite orientation dispersion and density imaging (NODDI) -journal: Journal of Neuroradiology -year: 2023 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0150986123000482 -doi: 10.1016/j.neurad.2023.01.041 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_bouhali_anatomical_2014.md b/_collections/_biblio/ginkgo/ginkgo_bouhali_anatomical_2014.md deleted file mode 100644 index 83828fc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_bouhali_anatomical_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Florence Bouhali et al. -title: Anatomical connections of the visual word form area -journal: The Journal of Neuroscience - The Official Journal of the Society for Neuroscience -year: 2014 -type: article -doi: 10.1523/JNEUROSCI.4918-13.2014 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_boutet_detection_2014.md b/_collections/_biblio/ginkgo/ginkgo_boutet_detection_2014.md deleted file mode 100644 index 38da6c6..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_boutet_detection_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Claire Boutet et al. -title: Detection of volume loss in hippocampal layers in Alzheimer's disease using 7 T MRI - a feasibility study -journal: NeuroImage. Clinical -year: 2014 -type: article -doi: 10.1016/j.nicl.2014.07.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_brion_noise_2013.md b/_collections/_biblio/ginkgo/ginkgo_brion_noise_2013.md deleted file mode 100644 index fe5e86c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_brion_noise_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Véronique Brion et al. -title: Noise correction for HARDI and HYDI data obtained with multi-channel coils and sum of squares reconstruction - an anisotropic extension of the LMMSE -journal: Magnetic Resonance Imaging -year: 2013 -type: article -doi: 10.1016/j.mri.2013.04.002 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_brulle_large-scale_nodate.md b/_collections/_biblio/ginkgo/ginkgo_brulle_large-scale_nodate.md deleted file mode 100644 index 00e8b03..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_brulle_large-scale_nodate.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Alexis Brullé et al. -title: Large-scale simulations to create large collections of realistic white matter samples using MEDUSA -type: inproceedings -url: https -//archive.ismrm.org/2022/2726.html -doi: 10.58530/2022/2726 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_bzdok_formal_2016.md b/_collections/_biblio/ginkgo/ginkgo_bzdok_formal_2016.md deleted file mode 100644 index 107d655..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_bzdok_formal_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Danilo Bzdok et al. -title: Formal Models of the Network Co-occurrence Underlying Mental Operations -journal: PLoS computational biology -year: 2016 -type: article -doi: 10.1371/journal.pcbi.1004994 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_chauvel_comparative_2023.md b/_collections/_biblio/ginkgo/ginkgo_chauvel_comparative_2023.md deleted file mode 100644 index 4bc5602..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_chauvel_comparative_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Maëlig Chauvel et al. -title: Comparative analysis of the chimpanzee and human brain superficial structural connectivities -year: 2023 -type: preprint -url: https -//www.researchsquare.com/article/rs-3772776/v1 -doi: 10.21203/rs.3.rs-3772776/v1 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate-1.md b/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate-1.md deleted file mode 100644 index 25c73dc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Maëlig Chauvel et al. -title: Investigation of the inferior fronto-occipital fasciculus in the macaque fascicularis brain using 11.7 T ultra-high field diffusion data -type: inproceedings -url: https -//archive.ismrm.org/2022/2102.html -doi: 10.58530/2022/2102 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate.md b/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate.md deleted file mode 100644 index 7fd4db4..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_chauvel_investigation_nodate.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Maëlig Chauvel et al. -title: Investigation of the singularity of the chimpanzee brain superficial white matter bundles using diffusion MRI and clustering-based approaches -type: inproceedings -url: https -//archive.ismrm.org/2022/2107.html -doi: 10.58530/2022/2107 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_chauvel_vivo_2023.md b/_collections/_biblio/ginkgo/ginkgo_chauvel_vivo_2023.md deleted file mode 100644 index 0216e83..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_chauvel_vivo_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Maëlig Chauvel et al. -title: In vivo mapping of the deep and superficial white matter connectivity in the chimpanzee brain -journal: NeuroImage -year: 2023 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S105381192300513X -doi: 10.1016/j.neuroimage.2023.120362 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dalbis_local_2018.md b/_collections/_biblio/ginkgo/ginkgo_dalbis_local_2018.md deleted file mode 100644 index 766d2ff..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dalbis_local_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Marc-Antoine d'Albis et al. -title: Local structural connectivity is associated with social cognition in autism spectrum disorder -journal: Brain - A Journal of Neurology -year: 2018 -type: article -doi: 10.1093/brain/awy275 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dalbis_p806_2019.md b/_collections/_biblio/ginkgo/ginkgo_dalbis_p806_2019.md deleted file mode 100644 index 64ab56f..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dalbis_p806_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: M.A. D'Albis et al. -title: P.806 Whole brain long-range study of white matter cellular microstructure using diffusion microscopy MRI in subjects with autism spectrum disorders -journal: European Neuropsychopharmacology -year: 2019 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0924977X19315469 -doi: 10.1016/j.euroneuro.2019.09.672 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dalbis_study_2019.md b/_collections/_biblio/ginkgo/ginkgo_dalbis_study_2019.md deleted file mode 100644 index 0c5865c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dalbis_study_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: M.A. D'Albis et al. -title: Study of corpus callosum cellular microstructure using diffusion microscopy MRI in subjects with autism spectrum disorders -journal: European Neuropsychopharmacology -year: 2019 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0924977X18317309 -doi: 10.1016/j.euroneuro.2018.11.883 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_daudin_bin1_2018.md b/_collections/_biblio/ginkgo/ginkgo_daudin_bin1_2018.md deleted file mode 100644 index e0ca312..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_daudin_bin1_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: R Daudin et al. -title: BIN1 genetic risk factor for Alzheimer is sufficient to induce early structural tract alterations in entorhinal-hippocampal area and memory-related hippocampal multi-scale impairments -year: 2018 -type: preprint -url: http -//biorxiv.org/lookup/doi/10.1101/437228 -doi: 10.1101/437228 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_drobnjak_physical_2021.md b/_collections/_biblio/ginkgo/ginkgo_drobnjak_physical_2021.md deleted file mode 100644 index 7d9a3b5..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_drobnjak_physical_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ivana Drobnjak et al. -title: Physical and digital phantoms for validating tractography and assessing artifacts -journal: NeuroImage -year: 2021 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S1053811921009769 -doi: 10.1016/j.neuroimage.2021.118704 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dubois_correction_2014.md b/_collections/_biblio/ginkgo/ginkgo_dubois_correction_2014.md deleted file mode 100644 index 1db8bc3..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dubois_correction_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Jessica Dubois et al. -title: Correction strategy for diffusion-weighted images corrupted with motion - application to the DTI evaluation of infants' white matter -journal: Magnetic Resonance Imaging -year: 2014 -type: article -doi: 10.1016/j.mri.2014.05.007 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dubois_early_2014.md b/_collections/_biblio/ginkgo/ginkgo_dubois_early_2014.md deleted file mode 100644 index d3c0be0..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dubois_early_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J. Dubois et al. -title: The early development of brain white matter - a review of imaging studies in fetuses, newborns and infants -journal: Neuroscience -year: 2014 -type: article -doi: 10.1016/j.neuroscience.2013.12.044 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dubois_exploring_2016.md b/_collections/_biblio/ginkgo/ginkgo_dubois_exploring_2016.md deleted file mode 100644 index 6113ab0..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dubois_exploring_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Jessica Dubois et al. -title: Exploring the Early Organization and Maturation of Linguistic Pathways in the Human Infant Brain -journal: Cerebral Cortex (New York, N.Y. - 1991) -year: 2016 -type: article -doi: 10.1093/cercor/bhv082 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dubois_kerker_2018.md b/_collections/_biblio/ginkgo/ginkgo_dubois_kerker_2018.md deleted file mode 100644 index e754b72..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dubois_kerker_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Marc Dubois et al. -title: Kerker Effect in Ultrahigh-Field Magnetic Resonance Imaging -journal: Physical Review X -year: 2018 -type: article -url: https -//link.aps.org/doi/10.1103/PhysRevX.8.031083 -doi: 10.1103/PhysRevX.8.031083 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_dubois_mri_2016.md b/_collections/_biblio/ginkgo/ginkgo_dubois_mri_2016.md deleted file mode 100644 index 9339655..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_dubois_mri_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Jessica Dubois et al. -title: MRI and M/EEG studies of the White Matter Development in Human Fetuses and Infants - Review and Opinion -journal: Brain Plasticity (Amsterdam, Netherlands) -year: 2016 -type: article -doi: 10.3233/BPL-160031 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ewenczyk_antisaccades_2017.md b/_collections/_biblio/ginkgo/ginkgo_ewenczyk_antisaccades_2017.md deleted file mode 100644 index 28c8d6d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ewenczyk_antisaccades_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Claire Ewenczyk et al. -title: Antisaccades in Parkinson disease - A new marker of postural control? -journal: Neurology -year: 2017 -type: article -doi: 10.1212/WNL.0000000000003658 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_favre_white_2016.md b/_collections/_biblio/ginkgo/ginkgo_favre_white_2016.md deleted file mode 100644 index ed5a351..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_favre_white_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pauline Favre et al. -title: White Matter Plasticity Induced by Psychoeducation in Bipolar Patients - A Controlled Diffusion Tensor Imaging Study -journal: Psychotherapy and Psychosomatics -year: 2016 -type: article -doi: 10.1159/000441009 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gallea_pedunculopontine_2017.md b/_collections/_biblio/ginkgo/ginkgo_gallea_pedunculopontine_2017.md deleted file mode 100644 index 4a6ebbe..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gallea_pedunculopontine_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Cecile Gallea et al. -title: Pedunculopontine network dysfunction in Parkinson's disease with postural control and sleep disorders -journal: Movement Disorders - Official Journal of the Movement Disorder Society -year: 2017 -type: article -doi: 10.1002/mds.26923 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gallea_rad51_2013.md b/_collections/_biblio/ginkgo/ginkgo_gallea_rad51_2013.md deleted file mode 100644 index 1df2462..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gallea_rad51_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Cécile Gallea et al. -title: RAD51 deficiency disrupts the corticospinal lateralization of motor control -journal: Brain - A Journal of Neurology -year: 2013 -type: article -doi: 10.1093/brain/awt258 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_garcia-lorenzo_coeruleus_subcoeruleus_2013.md b/_collections/_biblio/ginkgo/ginkgo_garcia-lorenzo_coeruleus_subcoeruleus_2013.md deleted file mode 100644 index 2490a10..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_garcia-lorenzo_coeruleus_subcoeruleus_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Daniel García-Lorenzo et al. -title: The coeruleus/subcoeruleus complex in rapid eye movement sleep behaviour disorders in Parkinson's disease -journal: Brain - A Journal of Neurology -year: 2013 -type: article -doi: 10.1093/brain/awt152 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_georget_stacked_2017.md b/_collections/_biblio/ginkgo/ginkgo_georget_stacked_2017.md deleted file mode 100644 index 9d88861..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_georget_stacked_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Elodie Georget et al. -title: Stacked magnetic resonators for MRI RF coils decoupling -journal: Journal of Magnetic Resonance (San Diego, Calif. - 1997) -year: 2017 -type: article -doi: 10.1016/j.jmr.2016.11.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gilson_network_2019.md b/_collections/_biblio/ginkgo/ginkgo_gilson_network_2019.md deleted file mode 100644 index 19c3838..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gilson_network_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Matthieu Gilson et al. -title: Network analysis of whole-brain fMRI dynamics - A new framework based on dynamic communicability -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811919305889 -doi: 10.1016/j.neuroimage.2019.116007 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ginsburger_improving_2018.md b/_collections/_biblio/ginkgo/ginkgo_ginsburger_improving_2018.md deleted file mode 100644 index 70fdb0a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ginsburger_improving_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Kévin Ginsburger et al. -title: Improving the Realism of White Matter Numerical Phantoms - A Step toward a Better Understanding of the Influence of Structural Disorders in Diffusion MRI -journal: Frontiers in Physics -year: 2018 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fphy.2018.00012 -doi: 10.3389/fphy.2018.00012 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ginsburger_medusa_2019.md b/_collections/_biblio/ginkgo/ginkgo_ginsburger_medusa_2019.md deleted file mode 100644 index 93ec155..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ginsburger_medusa_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Kévin Ginsburger et al. -title: MEDUSA - A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S105381191930151X -doi: 10.1016/j.neuroimage.2019.02.055 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_goicovich_fiber_2021.md b/_collections/_biblio/ginkgo/ginkgo_goicovich_fiber_2021.md deleted file mode 100644 index 9c101dd..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_goicovich_fiber_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Isaac Goicovich et al. -title: Fiber Clustering Acceleration With a Modified Kmeans++ Algorithm Using Data Parallelism -journal: Frontiers in Neuroinformatics -year: 2021 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2021.727859 -doi: 10.3389/fninf.2021.727859 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2013.md b/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2013.md deleted file mode 100644 index ec29897..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: Bayesian atlas estimation for the variability analysis of shape complexes -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2013 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2017.md b/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2017.md deleted file mode 100644 index ab41a00..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_bayesian_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: A Bayesian framework for joint morphometry of surface and curve meshes in multi-object complexes -journal: Medical Image Analysis -year: 2017 -type: article -doi: 10.1016/j.media.2016.08.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_double_2018.md b/_collections/_biblio/ginkgo/ginkgo_gori_double_2018.md deleted file mode 100644 index 87c5c91..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_double_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: Double Diffeomorphism - Combining Morphometry and Structural Connectivity Analysis -journal: IEEE transactions on medical imaging -year: 2018 -type: article -doi: 10.1109/TMI.2018.2813062 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_joint_2015.md b/_collections/_biblio/ginkgo/ginkgo_gori_joint_2015.md deleted file mode 100644 index 87c6b61..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_joint_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: Joint Morphometry of Fiber Tracts and Gray Matter Structures Using Double Diffeomorphisms -journal: Information Processing in Medical Imaging - Proceedings of the ... Conference -year: 2015 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_parsimonious_2016.md b/_collections/_biblio/ginkgo/ginkgo_gori_parsimonious_2016.md deleted file mode 100644 index 99610e9..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_parsimonious_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: Parsimonious Approximation of Streamline Trajectories in White Matter Fiber Bundles -journal: IEEE transactions on medical imaging -year: 2016 -type: article -doi: 10.1109/TMI.2016.2591080 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gori_prototype_2014.md b/_collections/_biblio/ginkgo/ginkgo_gori_prototype_2014.md deleted file mode 100644 index 586c0f1..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gori_prototype_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Pietro Gori et al. -title: A prototype representation to approximate white matter bundles with weighted currents -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2014 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_gramfort_denoising_2014.md b/_collections/_biblio/ginkgo/ginkgo_gramfort_denoising_2014.md deleted file mode 100644 index 8732bba..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_gramfort_denoising_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: A. Gramfort et al. -title: Denoising and fast diffusion imaging with physically constrained sparse dictionary learning -journal: Medical Image Analysis -year: 2014 -type: article -doi: 10.1016/j.media.2013.08.006 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_guevara_automatic_2015.md b/_collections/_biblio/ginkgo/ginkgo_guevara_automatic_2015.md deleted file mode 100644 index 01bf6fb..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_guevara_automatic_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: M. Guevara et al. -title: Automatic segmentation of short association bundles using a new multi-subject atlas of the left hemisphere fronto-parietal brain connections -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2015 -type: article -doi: 10.1109/EMBC.2015.7318390 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_guevara_creation_2016.md b/_collections/_biblio/ginkgo/ginkgo_guevara_creation_2016.md deleted file mode 100644 index 920cfab..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_guevara_creation_2016.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: M. Guevara et al. -title: Creation of a whole brain short association bundle atlas using a hybrid approach. -year: 2016 -type: inproceedings -doi: 10.1109/EMBC.2016.7590899 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_guevara_disentangling_2022.md b/_collections/_biblio/ginkgo/ginkgo_guevara_disentangling_2022.md deleted file mode 100644 index 9af2cdc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_guevara_disentangling_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Miguel Guevara et al. -title: Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922003214 -doi: 10.1016/j.neuroimage.2022.119197 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_guevara_reproducibility_2017.md b/_collections/_biblio/ginkgo/ginkgo_guevara_reproducibility_2017.md deleted file mode 100644 index 9aeff54..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_guevara_reproducibility_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Miguel Guevara et al. -title: Reproducibility of superficial white matter tracts using diffusion-weighted imaging tractography -journal: NeuroImage -year: 2017 -type: article -doi: 10.1016/j.neuroimage.2016.11.066 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_haeger_imaging_2020.md b/_collections/_biblio/ginkgo/ginkgo_haeger_imaging_2020.md deleted file mode 100644 index 4b247be..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_haeger_imaging_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Alexa Haeger et al. -title: Imaging the aging brain - study design and baseline findings of the SENIOR cohort -journal: Alzheimer's Research \& Therapy -year: 2020 -type: article -url: https -//alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1 -doi: 10.1186/s13195-020-00642-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_herlin_cross-subject_2023.md b/_collections/_biblio/ginkgo/ginkgo_herlin_cross-subject_2023.md deleted file mode 100644 index e7febdc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_herlin_cross-subject_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: B. Herlin et al. -title: Cross-subject variability of the optic radiation anatomy in a cohort of 1065 healthy subjects -journal: Surgical and Radiologic Anatomy -year: 2023 -type: article -url: https -//link.springer.com/10.1007/s00276-023-03161-4 -doi: 10.1007/s00276-023-03161-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_houenou_cytomegalovirus_2014.md b/_collections/_biblio/ginkgo/ginkgo_houenou_cytomegalovirus_2014.md deleted file mode 100644 index 278e3c2..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_houenou_cytomegalovirus_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J. Houenou et al. -title: Cytomegalovirus seropositivity and serointensity are associated with hippocampal volume and verbal memory in schizophrenia and bipolar disorder -journal: Progress in Neuro-Psychopharmacology \& Biological Psychiatry -year: 2014 -type: article -doi: 10.1016/j.pnpbp.2013.09.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_houenou_multilevel_2017.md b/_collections/_biblio/ginkgo/ginkgo_houenou_multilevel_2017.md deleted file mode 100644 index 7f7d61d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_houenou_multilevel_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Josselin Houenou et al. -title: A Multilevel Functional Study of a SNAP25 At-Risk Variant for Bipolar Disorder and Schizophrenia -journal: The Journal of Neuroscience - The Official Journal of the Society for Neuroscience -year: 2017 -type: article -doi: 10.1523/JNEUROSCI.1040-17.2017 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_huerta_inter-subject_2020.md b/_collections/_biblio/ginkgo/ginkgo_huerta_inter-subject_2020.md deleted file mode 100644 index 0d0662b..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_huerta_inter-subject_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Isaías Huerta et al. -title: Inter-Subject Clustering of Brain Fibers from Whole-Brain Tractography -year: 2020 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9175342 -doi: 10.1109/EMBC44109.2020.9175342 -booktitle: 2020 42nd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ji_alterations_2020.md b/_collections/_biblio/ginkgo/ginkgo_ji_alterations_2020.md deleted file mode 100644 index c07569c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ji_alterations_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ellen Ji et al. -title: Alterations In Short-Range Structural Connectivity Across The Psychosis Spectrum - Findings From The B-Snip Study -journal: Schizophrenia Bulletin -year: 2020 -type: article -url: https -//academic.oup.com/schizophreniabulletin/article/46/Supplement_1/S97/5839281 -doi: 10.1093/schbul/sbaa031.226 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ji_increased_2019.md b/_collections/_biblio/ginkgo/ginkgo_ji_increased_2019.md deleted file mode 100644 index b57094a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ji_increased_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ellen Ji et al. -title: Increased and Decreased Superficial White Matter Structural Connectivity in Schizophrenia and Bipolar Disorder -journal: Schizophrenia Bulletin -year: 2019 -type: article -url: https -//doi.org/10.1093/schbul/sbz015 -doi: 10.1093/schbul/sbz015 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_ji_t240_2018.md b/_collections/_biblio/ginkgo/ginkgo_ji_t240_2018.md deleted file mode 100644 index d2b6a51..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_ji_t240_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ellen Ji et al. -title: T240. Relationship Between Cognitive Performance and Superficial White Matter Integrity in the Cingulate Cortex in Schizophrenia - A DWI Study Using a Novel Atlas -journal: Biological Psychiatry -year: 2018 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0006322318306796 -doi: 10.1016/j.biopsych.2018.02.577 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_kaden_diffeomorphic_2018.md b/_collections/_biblio/ginkgo/ginkgo_kaden_diffeomorphic_2018.md deleted file mode 100644 index 97d7890..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_kaden_diffeomorphic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Kévin Ginsburger et al. -title: Diffeomorphic Registration of Diffusion Mean Apparent Propagator Fields Using Dynamic Programming on a Minimum Spanning Tree -year: 2018 -type: incollection -url: http -//link.springer.com/10.1007/978-3-319-73839-0_6 -doi: 10.1007/978-3-319-73839-0_6 -booktitle: Computational Diffusion MRI ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_katz_similar_2016.md b/_collections/_biblio/ginkgo/ginkgo_katz_similar_2016.md deleted file mode 100644 index b6f2dca..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_katz_similar_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J. Katz et al. -title: Similar white matter but opposite grey matter changes in schizophrenia and high-functioning autism -journal: Acta Psychiatrica Scandinavica -year: 2016 -type: article -doi: 10.1111/acps.12579 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_kulikova_multi-parametric_2015.md b/_collections/_biblio/ginkgo/ginkgo_kulikova_multi-parametric_2015.md deleted file mode 100644 index 9790583..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_kulikova_multi-parametric_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: S. Kulikova et al. -title: Multi-parametric evaluation of the white matter maturation -journal: Brain Structure \& Function -year: 2015 -type: article -doi: 10.1007/s00429-014-0881-y ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_kulikova_new_2016.md b/_collections/_biblio/ginkgo/ginkgo_kulikova_new_2016.md deleted file mode 100644 index c642bf5..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_kulikova_new_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Sofya Kulikova et al. -title: A New Strategy for Fast MRI-Based Quantification of the Myelin Water Fraction - Application to Brain Imaging in Infants -journal: PloS One -year: 2016 -type: article -doi: 10.1371/journal.pone.0163143 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_labra_fast_2017.md b/_collections/_biblio/ginkgo/ginkgo_labra_fast_2017.md deleted file mode 100644 index 5f70164..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_labra_fast_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nicole Labra et al. -title: Fast Automatic Segmentation of White Matter Streamlines Based on a Multi-Subject Bundle Atlas -journal: Neuroinformatics -year: 2017 -type: article -doi: 10.1007/s12021-016-9316-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_labra_gpu-based_2013.md b/_collections/_biblio/ginkgo/ginkgo_labra_gpu-based_2013.md deleted file mode 100644 index 34e8696..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_labra_gpu-based_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nicole Labra et al. -title: GPU-based acceleration of an automatic white matter segmentation algorithm using CUDA -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2013 -type: article -doi: 10.1109/EMBC.2013.6609444 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_labra_interactive_2014.md b/_collections/_biblio/ginkgo/ginkgo_labra_interactive_2014.md deleted file mode 100644 index 33ca380..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_labra_interactive_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nicole Labra et al. -title: Interactive segmentation of white-matter fibers using a multi-subject atlas -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2014 -type: article -doi: 10.1109/EMBC.2014.6944099 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_laidi_cerebellar_2015.md b/_collections/_biblio/ginkgo/ginkgo_laidi_cerebellar_2015.md deleted file mode 100644 index 772ecfb..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_laidi_cerebellar_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Laidi et al. -title: Cerebellar volume in schizophrenia and bipolar I disorder with and without psychotic features -journal: Acta Psychiatr Scand -year: 2015 -type: article -doi: doi - 10.1111/acps.12363. Epub 2014 Nov 28. ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lebenberg_framework_2018.md b/_collections/_biblio/ginkgo/ginkgo_lebenberg_framework_2018.md deleted file mode 100644 index 4abff2b..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lebenberg_framework_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J. Lebenberg et al. -title: A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-018-1735-9 -doi: 10.1007/s00429-018-1735-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lebenberg_mapping_2019.md b/_collections/_biblio/ginkgo/ginkgo_lebenberg_mapping_2019.md deleted file mode 100644 index 9b2dd68..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lebenberg_mapping_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J. Lebenberg et al. -title: Mapping the asynchrony of cortical maturation in the infant brain - A MRI multi-parametric clustering approach -journal: NeuroImage -year: 2019 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918306372 -doi: 10.1016/j.neuroimage.2018.07.022 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lechanoine_wikibrainstem_2021.md b/_collections/_biblio/ginkgo/ginkgo_lechanoine_wikibrainstem_2021.md deleted file mode 100644 index b9695f2..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lechanoine_wikibrainstem_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: François Lechanoine et al. -title: WIKIBrainStem - An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI -journal: NeuroImage -year: 2021 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S1053811921003578 -doi: 10.1016/j.neuroimage.2021.118080 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lefranc_groupwise_2016.md b/_collections/_biblio/ginkgo/ginkgo_lefranc_groupwise_2016.md deleted file mode 100644 index 047841a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lefranc_groupwise_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Sandrine Lefranc et al. -title: Groupwise connectivity-based parcellation of the whole human cortical surface using watershed-driven dimension reduction -journal: Medical Image Analysis -year: 2016 -type: article -doi: 10.1016/j.media.2016.01.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lehericy_7_2014.md b/_collections/_biblio/ginkgo/ginkgo_lehericy_7_2014.md deleted file mode 100644 index e957c6e..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lehericy_7_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Stéphane Lehéricy et al. -title: 7 Tesla magnetic resonance imaging - a closer look at substantia nigra anatomy in Parkinson's disease -journal: Movement Disorders - Official Journal of the Movement Disorder Society -year: 2014 -type: article -doi: 10.1002/mds.26043 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lepore_identification_2019.md b/_collections/_biblio/ginkgo/ginkgo_lepore_identification_2019.md deleted file mode 100644 index 51e1510..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lepore_identification_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: M. Guevara et al. -title: Identification of U-Bundles Based on Sulcus Morphology -year: 2019 -type: incollection -url: http -//link.springer.com/10.1007/978-3-030-13835-6_1 -doi: 10.1007/978-3-030-13835-6_1 -booktitle: Processing and Analysis of Biomedical Information ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_leroi_simultaneous_2018.md b/_collections/_biblio/ginkgo/ginkgo_leroi_simultaneous_2018.md deleted file mode 100644 index 48dfdbc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_leroi_simultaneous_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Lisa Leroi et al. -title: Simultaneous multi-parametric mapping of total sodium concentration, T1, T2 and ADC at 7 T using a multi-contrast unbalanced SSFP -journal: Magnetic Resonance Imaging -year: 2018 -type: article -doi: 10.1016/j.mri.2018.07.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_leroy_new_2015.md b/_collections/_biblio/ginkgo/ginkgo_leroy_new_2015.md deleted file mode 100644 index 71647fd..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_leroy_new_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: François Leroy et al. -title: New human-specific brain landmark - the depth asymmetry of superior temporal sulcus -journal: Proceedings of the National Academy of Sciences of the United States of America -year: 2015 -type: article -doi: 10.1073/pnas.1412389112 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_li_numerical_2014.md b/_collections/_biblio/ginkgo/ginkgo_li_numerical_2014.md deleted file mode 100644 index a95dde7..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_li_numerical_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Jing-Rebecca Li et al. -title: Numerical simulation of diffusion MRI signals using an adaptive time-stepping method -journal: Physics in Medicine and Biology -year: 2014 -type: article -doi: 10.1088/0031-9155/59/2/441 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_linke_impaired_2013.md b/_collections/_biblio/ginkgo/ginkgo_linke_impaired_2013.md deleted file mode 100644 index 3a59968..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_linke_impaired_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Julia Linke et al. -title: Impaired anatomical connectivity and related executive functions - differentiating vulnerability and disease marker in bipolar disorder -journal: Biological Psychiatry -year: 2013 -type: article -doi: 10.1016/j.biopsych.2013.04.010 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_coarse_2020.md b/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_coarse_2020.md deleted file mode 100644 index 3bb7e4a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_coarse_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Narciso López-López et al. -title: From Coarse to Fine-Grained Parcellation of the Cortical Surface Using a Fiber-Bundle Atlas -journal: Frontiers in Neuroinformatics -year: 2020 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2020.00032 -doi: 10.3389/fninf.2020.00032 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_cortical_2019.md b/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_cortical_2019.md deleted file mode 100644 index baac70f..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_cortical_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Narciso Lopez-Lopez et al. -title: Cortical surface parcellation based on intra-subject white matter fiber clustering -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8988066/ -doi: 10.1109/CHILECON47746.2019.8988066 -booktitle: 2019 IEEE CHILEAN Conference on Electrical, Electronics Engineering, Information and Communication Technologies (CHILECON) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_geosp_2020.md b/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_geosp_2020.md deleted file mode 100644 index aa56979..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lopez-lopez_geosp_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Narciso Lopez-Lopez et al. -title: GeoSP - A parallel method for a cortical surface parcellation based on geodesic distance -year: 2020 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/9175779/ -doi: 10.1109/EMBC44109.2020.9175779 -booktitle: 2020 42nd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_lyoubi-idrissi_diffusion_2017.md b/_collections/_biblio/ginkgo/ginkgo_lyoubi-idrissi_diffusion_2017.md deleted file mode 100644 index 17a2b26..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_lyoubi-idrissi_diffusion_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: A. Lyoubi-Idrissi et al. -title: Diffusion magnetic resonance imaging in cerebral small vessel disease -journal: Revue Neurologique -year: 2017 -type: article -doi: 10.1016/j.neurol.2017.03.005 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_magalhaes_white_2017.md b/_collections/_biblio/ginkgo/ginkgo_magalhaes_white_2017.md deleted file mode 100644 index 8a9da7f..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_magalhaes_white_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: R. Magalhães et al. -title: White matter changes in microstructure associated with a maladaptive response to stress in rats -journal: Translational Psychiatry -year: 2017 -type: article -doi: 10.1038/tp.2016.283 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_mangin_spatial_2016.md b/_collections/_biblio/ginkgo/ginkgo_mangin_spatial_2016.md deleted file mode 100644 index 3fa85c2..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_mangin_spatial_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J.-F. Mangin et al. -title: Spatial normalization of brain images and beyond -journal: Medical Image Analysis -year: 2016 -type: article -doi: 10.1016/j.media.2016.06.008 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_mangin_toward_2013.md b/_collections/_biblio/ginkgo/ginkgo_mangin_toward_2013.md deleted file mode 100644 index cae802c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_mangin_toward_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: J.-F. Mangin et al. -title: Toward global tractography -journal: Neuroimage -year: 2013 -type: article -doi: 10.1016/j.neuroimage.2013.04.009 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_mapping_2013.md b/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_mapping_2013.md deleted file mode 100644 index 4606be4..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_mapping_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Linda Marrakchi-Kacem et al. -title: Mapping cortico-striatal connectivity onto the cortical surface - a new tractography-based approach to study Huntington disease -journal: PloS One -year: 2013 -type: article -doi: 10.1371/journal.pone.0053135 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_robust_2016.md b/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_robust_2016.md deleted file mode 100644 index cdb48be..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_marrakchi-kacem_robust_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Linda Marrakchi-Kacem et al. -title: Robust imaging of hippocampal inner structure at 7T - in vivo acquisition protocol and methodological choices -journal: Magma (New York, N.Y.) -year: 2016 -type: article -doi: 10.1007/s10334-016-0552-5 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_mendoza_enhanced_2021.md b/_collections/_biblio/ginkgo/ginkgo_mendoza_enhanced_2021.md deleted file mode 100644 index dd1e7e4..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_mendoza_enhanced_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Mendoza et al. -title: Enhanced Automatic Segmentation for Superficial White Matter Fiber Bundles for Probabilistic Tractography Datasets -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9630529 -doi: 10.1109/EMBC46164.2021.9630529 -booktitle: 2021 43rd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_mendoza_superficial_2023.md b/_collections/_biblio/ginkgo/ginkgo_mendoza_superficial_2023.md deleted file mode 100644 index 33afe5a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_mendoza_superficial_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Cristobal Mendoza et al. -title: Superficial white matter shape characterization using hierarchical clustering and a multi-subject bundle atlas -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/2669738/Superficial-white-matter-shape-characterization-using-hierarchical-clustering-and-a/10.1117/12.2669738.full -doi: 10.1117/12.2669738 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_mohammadi_probastem_2023.md b/_collections/_biblio/ginkgo/ginkgo_mohammadi_probastem_2023.md deleted file mode 100644 index 8b9325e..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_mohammadi_probastem_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Mohammad Mohammadi et al. -title: ProbaStem, a pipeline towards the first high-resolution probabilistic atlas of the whole human brainstem -journal: Brain Structure and Function -year: 2023 -type: article -url: https -//link.springer.com/10.1007/s00429-023-02726-8 -doi: 10.1007/s00429-023-02726-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_molina_group-wise_2023.md b/_collections/_biblio/ginkgo/ginkgo_molina_group-wise_2023.md deleted file mode 100644 index 6df06ee..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_molina_group-wise_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Joaquín Molina et al. -title: Group-wise cortical parcellation based on structural connectivity and hierarchical clustering -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670L/Group-wise-cortical-parcellation-based-on-structural-connectivity-and-hierarchical/10.1117/12.2670138.full -doi: 10.1117/12.2670138 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_moulton_connectivity_2019.md b/_collections/_biblio/ginkgo/ginkgo_moulton_connectivity_2019.md deleted file mode 100644 index 410fbf9..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_moulton_connectivity_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Eric Moulton et al. -title: Connectivity between the visual word form area and the parietal lobe improves after the first year of reading instruction - a longitudinal MRI study in children -journal: Brain Structure and Function -year: 2019 -type: article -url: http -//link.springer.com/10.1007/s00429-019-01855-3 -doi: 10.1007/s00429-019-01855-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_nabulsi_aberrant_2022.md b/_collections/_biblio/ginkgo/ginkgo_nabulsi_aberrant_2022.md deleted file mode 100644 index b5ab3fe..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_nabulsi_aberrant_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Leila Nabulsi et al. -title: Aberrant Subnetwork and Hub Dysconnectivity in Adult Bipolar Disorder - A Multicenter Graph Theory Analysis -journal: Cerebral Cortex -year: 2022 -type: article -url: https -//academic.oup.com/cercor/article/32/10/2254/6380064 -doi: 10.1093/cercor/bhab356 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_nguyen_parameter_2015.md b/_collections/_biblio/ginkgo/ginkgo_nguyen_parameter_2015.md deleted file mode 100644 index a5e4090..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_nguyen_parameter_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Hang Nguyen et al. -title: Parameter estimation using macroscopic diffusion MRI signal models -journal: Physics in Medicine and Biology -year: 2015 -type: article -doi: 10.1088/0031-9155/60/8/3389 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_operto_cati:_2016.md b/_collections/_biblio/ginkgo/ginkgo_operto_cati:_2016.md deleted file mode 100644 index 3273167..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_operto_cati:_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Grégory Operto et al. -title: CATI - A Large Distributed Infrastructure for the Neuroimaging of Cohorts -journal: Neuroinformatics -year: 2016 -type: article -doi: 10.1007/s12021-016-9295-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_osorio_abrainvis_2021.md b/_collections/_biblio/ginkgo/ginkgo_osorio_abrainvis_2021.md deleted file mode 100644 index 4582eaf..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_osorio_abrainvis_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ignacio Osorio et al. -title: ABrainVis - an android brain image visualization tool -journal: BioMedical Engineering OnLine -year: 2021 -type: article -url: https -//biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-021-00909-0 -doi: 10.1186/s12938-021-00909-0 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pagnamenta_defective_2019.md b/_collections/_biblio/ginkgo/ginkgo_pagnamenta_defective_2019.md deleted file mode 100644 index 7edc2eb..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pagnamenta_defective_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Alistair Pagnamenta et al. -title: Defective tubulin detyrosination causes structural brain abnormalities with cognitive deficiency in humans and mice -journal: Human Molecular Genetics -year: 2019 -type: article -url: https -//academic.oup.com/hmg/article/28/20/3391/5540982 -doi: 10.1093/hmg/ddz186 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pardo_study_2013.md b/_collections/_biblio/ginkgo/ginkgo_pardo_study_2013.md deleted file mode 100644 index a199a68..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pardo_study_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Edison Pardo et al. -title: Study of the variability of short association bundles on a HARDI database -journal: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference -year: 2013 -type: article -doi: 10.1109/EMBC.2013.6609441 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pinel_functional_2019.md b/_collections/_biblio/ginkgo/ginkgo_pinel_functional_2019.md deleted file mode 100644 index 9048fb9..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pinel_functional_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Philippe Pinel et al. -title: The functional database of the ARCHI project - Potential and perspectives -journal: NeuroImage -year: 2019 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S1053811919303428 -doi: 10.1016/j.neuroimage.2019.04.056 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pinel_genetic_2015.md b/_collections/_biblio/ginkgo/ginkgo_pinel_genetic_2015.md deleted file mode 100644 index 98c1097..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pinel_genetic_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Philippe Pinel et al. -title: Genetic and Environmental Influences on the Visual Word Form and Fusiform Face Areas -journal: Cerebral Cortex -year: 2015 -type: article -doi: 10.1093/cercor/bhu048 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pinto_stringent_2018.md b/_collections/_biblio/ginkgo/ginkgo_pinto_stringent_2018.md deleted file mode 100644 index 986e86f..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pinto_stringent_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Daniela Pinto et al. -title: A stringent fiber distance measure for dMRI tractography clustering and segmentation -year: 2018 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8512333/ -doi: 10.1109/EMBC.2018.8512333 -booktitle: 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_poo_fiber_2023.md b/_collections/_biblio/ginkgo/ginkgo_poo_fiber_2023.md deleted file mode 100644 index e28e8fe..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_poo_fiber_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Elida Poo et al. -title: Fiber bundles simulator using exponential curves to validate fiber clustering algorithms -year: 2023 -type: inproceedings -url: https -//www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670J/Fiber-bundles-simulator-using-exponential-curves-to-validate-fiber-clustering/10.1117/12.2669811.full -doi: 10.1117/12.2669811 -booktitle: 18th International Symposium on Medical Information Processing and Analysis ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_popov_length-dependent_nodate.md b/_collections/_biblio/ginkgo/ginkgo_popov_length-dependent_nodate.md deleted file mode 100644 index e0a51e3..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_popov_length-dependent_nodate.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Alexandros Popov et al. -title: Length-dependent spatial distribution of short fiber bundles revealed with the mesoscopic Chenonceau dataset -type: inproceedings -url: https -//archive.ismrm.org/2022/0657.html -doi: 10.58530/2022/0657 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_comparative_2018.md b/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_comparative_2018.md deleted file mode 100644 index ca30fb4..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_comparative_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: N. Pyatigorskaya et al. -title: Comparative Study of MRI Biomarkers in the Substantia Nigra to Discriminate Idiopathic Parkinson Disease -journal: AJNR. American journal of neuroradiology -year: 2018 -type: article -doi: 10.3174/ajnr.A5702 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_medulla_2016.md b/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_medulla_2016.md deleted file mode 100644 index 248bd9a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_medulla_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nadya Pyatigorskaya et al. -title: Medulla oblongata damage and cardiac autonomic dysfunction in Parkinson disease -journal: Neurology -year: 2016 -type: article -doi: 10.1212/WNL.0000000000003426 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_multimodal_2020.md b/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_multimodal_2020.md deleted file mode 100644 index b75f994..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_pyatigorskaya_multimodal_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Nadya Pyatigorskaya et al. -title: Multimodal Magnetic Resonance Imaging Quantification of Brain Changes in Progressive Supranuclear Palsy -journal: Movement Disorders -year: 2020 -type: article -url: https -//movementdisorders.onlinelibrary.wiley.com/doi/10.1002/mds.27877 -doi: 10.1002/mds.27877 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_reuter_faconstructor_2019.md b/_collections/_biblio/ginkgo/ginkgo_reuter_faconstructor_2019.md deleted file mode 100644 index cff5be3..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_reuter_faconstructor_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Jan Reuter et al. -title: FAConstructor - an interactive tool for geometric modeling of nerve fiber architectures in the brain -journal: International Journal of Computer Assisted Radiology and Surgery -year: 2019 -type: article -url: http -//link.springer.com/10.1007/s11548-019-02053-6 -doi: 10.1007/s11548-019-02053-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_rolland_exploring_2019.md b/_collections/_biblio/ginkgo/ginkgo_rolland_exploring_2019.md deleted file mode 100644 index 76091dd..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_rolland_exploring_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Rolland et al. -title: Exploring Microstructure Asymmetries in the Infant Brain Cortex - A Methodological Framework Combining Structural and Diffusion Mri -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/8759421 -doi: 10.1109/ISBI.2019.8759421 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_roman_effect_2019.md b/_collections/_biblio/ginkgo/ginkgo_roman_effect_2019.md deleted file mode 100644 index 527eeb1..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_roman_effect_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Roman et al. -title: The effect of the number of fibers in tractography reconstruction of white matter bundles -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8856379/ -doi: 10.1109/EMBC.2019.8856379 -booktitle: 2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_roman_short_2016.md b/_collections/_biblio/ginkgo/ginkgo_roman_short_2016.md deleted file mode 100644 index c16a4e7..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_roman_short_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Roman et al. -title: Short association bundle atlas based on inter-subject clustering from HARDI data -year: 2016 -type: inproceedings -doi: 10.1109/EMBC.2016.7591983 -booktitle: Conference proceedings - ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_roman_study_2021.md b/_collections/_biblio/ginkgo/ginkgo_roman_study_2021.md deleted file mode 100644 index a5c8a90..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_roman_study_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: C. Román et al. -title: Study Of Precentral-Postcentral Connections On Hcp Data Using Probabilistic Tractography And Fiber Clustering -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9434093 -doi: 10.1109/ISBI48211.2021.9434093 -booktitle: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_roman_superficial_2022.md b/_collections/_biblio/ginkgo/ginkgo_roman_superficial_2022.md deleted file mode 100644 index 5277272..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_roman_superficial_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Claudio Román et al. -title: Superficial white matter bundle atlas based on hierarchical fiber clustering over probabilistic tractography data -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922006656 -doi: 10.1016/j.neuroimage.2022.119550 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sarrazin_corpus_2015.md b/_collections/_biblio/ginkgo/ginkgo_sarrazin_corpus_2015.md deleted file mode 100644 index ffb95d6..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sarrazin_corpus_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Samuel Sarrazin et al. -title: Corpus callosum area in patients with bipolar disorder with and without psychotic features - an international multicentre study -journal: JOURNAL OF PSYCHIATRY \& NEUROSCIENCE -year: 2015 -type: article -doi: 10.1503/jpn.140262 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sarrazin_higher_2019.md b/_collections/_biblio/ginkgo/ginkgo_sarrazin_higher_2019.md deleted file mode 100644 index 05f2cec..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sarrazin_higher_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Samuel Sarrazin et al. -title: Higher in vivo Cortical Intracellular Volume Fraction Associated with Lithium Therapy in Bipolar Disorder - A Multicenter NODDI Study -journal: Psychotherapy and Psychosomatics -year: 2019 -type: article -url: https -//doi.org/10.1159/000498854 -doi: 10.1159/000498854 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicenter_2014.md b/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicenter_2014.md deleted file mode 100644 index 6bc363c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicenter_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Samuel Sarrazin et al. -title: A multicenter tractography study of deep white matter tracts in bipolar I disorder - psychotic features and interhemispheric disconnectivity -journal: JAMA psychiatry -year: 2014 -type: article -doi: 10.1001/jamapsychiatry.2013.4513 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicentric_2022.md b/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicentric_2022.md deleted file mode 100644 index 571e10d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sarrazin_multicentric_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: S. Sarrazin et al. -title: A multicentric multimodal in vivo microscopy MRI study of bipolar disorder reveals axonal loss and demyelination -journal: European Psychiatry -year: 2022 -type: article -url: https -//www.cambridge.org/core/product/identifier/S0924933822004291/type/journal_article -doi: 10.1192/j.eurpsy.2022.429 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sarrazin_neuroimaging_2020.md b/_collections/_biblio/ginkgo/ginkgo_sarrazin_neuroimaging_2020.md deleted file mode 100644 index d7551fe..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sarrazin_neuroimaging_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Samuel Sarrazin et al. -title: Neuroimaging Evidence for Increased Neurite Density in Patients Taking Lithium - A Replication Study -journal: Psychotherapy and Psychosomatics -year: 2020 -type: article -url: https -//doi.org/10.1159/000507556 -doi: 10.1159/000507556 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_schilling_challenges_2019.md b/_collections/_biblio/ginkgo/ginkgo_schilling_challenges_2019.md deleted file mode 100644 index 173be6e..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_schilling_challenges_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Kurt Schilling et al. -title: Challenges in diffusion MRI tractography – Lessons learned from international benchmark competitions -journal: Magnetic Resonance Imaging -year: 2019 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0730725X18305162 -doi: 10.1016/j.mri.2018.11.014 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_schilling_tractography_2021.md b/_collections/_biblio/ginkgo/ginkgo_schilling_tractography_2021.md deleted file mode 100644 index cd5f9b4..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_schilling_tractography_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Kurt Schilling et al. -title: Tractography dissection variability - What happens when 42 groups dissect 14 white matter bundles on the same dataset? -journal: NeuroImage -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921007758 -doi: 10.1016/j.neuroimage.2021.118502 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_scholz_dysfunctional_2016.md b/_collections/_biblio/ginkgo/ginkgo_scholz_dysfunctional_2016.md deleted file mode 100644 index ab94871..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_scholz_dysfunctional_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Vanessa Scholz et al. -title: Dysfunctional decision-making related to white matter alterations in bipolar I disorder -journal: Journal of Affective Disorders -year: 2016 -type: article -doi: 10.1016/j.jad.2015.12.019 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_senova_optogenetic_2018.md b/_collections/_biblio/ginkgo/ginkgo_senova_optogenetic_2018.md deleted file mode 100644 index dda2ecc..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_senova_optogenetic_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: S. Senova et al. -title: Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates -journal: Scientific Reports -year: 2018 -type: article -doi: 10.1038/s41598-018-21486-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_silva_cortical_2019.md b/_collections/_biblio/ginkgo/ginkgo_silva_cortical_2019.md deleted file mode 100644 index d07a05d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_silva_cortical_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Felipe Silva et al. -title: Cortical Surface Parcellation Based on Graph Representation of Short Fiber Bundle Connections -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8759580/ -doi: 10.1109/ISBI.2019.8759580 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_souza-queiroz_childhood_2016.md b/_collections/_biblio/ginkgo/ginkgo_souza-queiroz_childhood_2016.md deleted file mode 100644 index 645b35a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_souza-queiroz_childhood_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Julia Souza-Queiroz et al. -title: Childhood trauma and the limbic network - a multimodal MRI study in patients with bipolar disorder and controls -journal: Journal of Affective Disorders -year: 2016 -type: article -doi: 10.1016/j.jad.2016.04.038 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_sun_shape_2017.md b/_collections/_biblio/ginkgo/ginkgo_sun_shape_2017.md deleted file mode 100644 index 650e1ac..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_sun_shape_2017.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Zhong Sun et al. -title: Shape analysis of the cingulum, uncinate and arcuate fasciculi in patients with bipolar disorder -journal: Journal of psychiatry \& neuroscience - JPN -year: 2017 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_thirion_principal_2014.md b/_collections/_biblio/ginkgo/ginkgo_thirion_principal_2014.md deleted file mode 100644 index aa4eeae..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_thirion_principal_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Bertrand Thirion et al. -title: Principal component regression predicts functional responses across individuals -journal: Medical image computing and computer-assisted intervention - MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention -year: 2014 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_uszynski_towards_nodate.md b/_collections/_biblio/ginkgo/ginkgo_uszynski_towards_nodate.md deleted file mode 100644 index d3eadd8..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_uszynski_towards_nodate.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Ivy Uszynski et al. -title: Towards an ultra-high resolution structural connectivity atlas of the parrot brain using extreme high-field 17.2T diffusion MRI -type: inproceedings -url: https -//archive.ismrm.org/2022/0423.html -doi: 10.58530/2022/0423 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_vazquez_automatic_2020.md b/_collections/_biblio/ginkgo/ginkgo_vazquez_automatic_2020.md deleted file mode 100644 index 1150ef6..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_vazquez_automatic_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Andrea Vázquez et al. -title: Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information -journal: BioMedical Engineering OnLine -year: 2020 -type: article -url: https -//biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-020-00786-z -doi: 10.1186/s12938-020-00786-z ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_vazquez_ffclust_2020.md b/_collections/_biblio/ginkgo/ginkgo_vazquez_ffclust_2020.md deleted file mode 100644 index b696c51..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_vazquez_ffclust_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Andrea Vázquez et al. -title: FFClust - Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity -journal: NeuroImage -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811920305565 -doi: 10.1016/j.neuroimage.2020.117070 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_vazquez_parallel_2019.md b/_collections/_biblio/ginkgo/ginkgo_vazquez_parallel_2019.md deleted file mode 100644 index bce7f6a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_vazquez_parallel_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Andrea Vazquez et al. -title: Parallel Optimization of Fiber Bundle Segmentation for Massive Tractography Datasets -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8759208/ -doi: 10.1109/ISBI.2019.8759208 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_vergara_group-wise_2021.md b/_collections/_biblio/ginkgo/ginkgo_vergara_group-wise_2021.md deleted file mode 100644 index 3048846..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_vergara_group-wise_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Christopher Vergara et al. -title: Group-Wise Cortical Surface Parcellation Based on Inter-Subject Fiber Clustering -year: 2021 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/9631099 -doi: 10.1109/EMBC46164.2021.9631099 -booktitle: 2021 43rd Annual International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC) ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_wessa_impaired_2016.md b/_collections/_biblio/ginkgo/ginkgo_wessa_impaired_2016.md deleted file mode 100644 index f53ee1a..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_wessa_impaired_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Michèle Wessa et al. -title: Impaired and preserved aspects of feedback learning in aMCI - contributions of structural connectivity -journal: Brain Structure \& Function -year: 2016 -type: article -doi: 10.1007/s00429-015-1075-y ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_worbe_altered_2015.md b/_collections/_biblio/ginkgo/ginkgo_worbe_altered_2015.md deleted file mode 100644 index dd00c2c..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_worbe_altered_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Yulia Worbe et al. -title: Altered structural connectivity of cortico-striato-pallido-thalamic networks in Gilles de la Tourette syndrome -journal: BRAIN -year: 2015 -type: article -doi: 10.1093/brain/awu311 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_yang_diffusion_2021.md b/_collections/_biblio/ginkgo/ginkgo_yang_diffusion_2021.md deleted file mode 100644 index a566a00..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_yang_diffusion_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Joseph Yang et al. -title: Diffusion MRI tractography for neurosurgery - the basics, current state, technical reliability and challenges -journal: Physics in Medicine \& Biology -year: 2021 -type: article -url: https -//iopscience.iop.org/article/10.1088/1361-6560/ac0d90 -doi: 10.1088/1361-6560/ac0d90 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_yebga_hot_novel_2022.md b/_collections/_biblio/ginkgo/ginkgo_yebga_hot_novel_2022.md deleted file mode 100644 index 1a757e8..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_yebga_hot_novel_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Raïssa Yebga Hot et al. -title: A novel male Japanese quail structural connectivity atlas using ultra-high field diffusion MRI at 11.7 T -journal: Brain Structure and Function -year: 2022 -type: article -url: https -//link.springer.com/10.1007/s00429-022-02457-2 -doi: 10.1007/s00429-022-02457-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/ginkgo/ginkgo_yeh_diffusion_2013.md b/_collections/_biblio/ginkgo/ginkgo_yeh_diffusion_2013.md deleted file mode 100644 index a0b941d..0000000 --- a/_collections/_biblio/ginkgo/ginkgo_yeh_diffusion_2013.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: ginkgo -bestof: false -author: Chun-Hung Yeh et al. -title: Diffusion microscopist simulator - a general Monte Carlo simulation system for diffusion magnetic resonance imaging -journal: PLoS One -year: 2013 -type: article -doi: 10.1371/journal.pone.0076626 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_albaugh_amygdalar_2019.md b/_collections/_biblio/platform/platform_albaugh_amygdalar_2019.md deleted file mode 100644 index 5dcce56..0000000 --- a/_collections/_biblio/platform/platform_albaugh_amygdalar_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Matthew Albaugh et al. -title: Amygdalar reactivity is associated with prefrontal cortical thickness in a large population-based sample of adolescents -journal: PLOS ONE -year: 2019 -type: article -url: https -//journals.plos.org/plosone/article?id=10.1371/journal.pone.0216152 -doi: 10.1371/journal.pone.0216152 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_albaugh_association_2021.md b/_collections/_biblio/platform/platform_albaugh_association_2021.md deleted file mode 100644 index c2a5759..0000000 --- a/_collections/_biblio/platform/platform_albaugh_association_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Matthew Albaugh et al. -title: Association of Cannabis Use During Adolescence With Neurodevelopment -journal: JAMA Psychiatry -year: 2021 -type: article -url: https -//doi.org/10.1001/jamapsychiatry.2021.1258 -doi: 10.1001/jamapsychiatry.2021.1258 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_albaugh_differential_2023.md b/_collections/_biblio/platform/platform_albaugh_differential_2023.md deleted file mode 100644 index 9e5b316..0000000 --- a/_collections/_biblio/platform/platform_albaugh_differential_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Matthew Albaugh et al. -title: Differential associations of adolescent versus young adult cannabis initiation with longitudinal brain change and behavior -journal: Molecular Psychiatry -year: 2023 -type: article -url: https -//www.nature.com/articles/s41380-023-02148-2 -doi: 10.1038/s41380-023-02148-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_alentorn_p0588_2018.md b/_collections/_biblio/platform/platform_alentorn_p0588_2018.md deleted file mode 100644 index 21ae6cc..0000000 --- a/_collections/_biblio/platform/platform_alentorn_p0588_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: A Alentorn et al. -title: P05.88 Radiomics analysis of brain metastases from non-small cell lung cancer brings relevant supplementary information to clinical scores -journal: Neuro-Oncology -year: 2018 -type: article -url: https -//www.ncbi.nlm.nih.gov/pmc/articles/PMC6144734/ -doi: 10.1093/neuonc/noy139.414 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ambroise_interpretable_2024.md b/_collections/_biblio/platform/platform_ambroise_interpretable_2024.md deleted file mode 100644 index 7ebfc84..0000000 --- a/_collections/_biblio/platform/platform_ambroise_interpretable_2024.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Corentin Ambroise et al. -title: Interpretable and integrative deep learning for discovering brain-behaviour associations with stability analysis -year: 2024 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ambroise_mixup_2023.md b/_collections/_biblio/platform/platform_ambroise_mixup_2023.md deleted file mode 100644 index 8589fe2..0000000 --- a/_collections/_biblio/platform/platform_ambroise_mixup_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Corentin Ambroise et al. -title: MixUp brain-cortical augmentations in self-supervised learning -year: 2023 -type: inproceedings -booktitle: International Workshop on Machine Learning in Clinical Neuroimaging ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ambroise_multi-modal_2021.md b/_collections/_biblio/platform/platform_ambroise_multi-modal_2021.md deleted file mode 100644 index 84d6928..0000000 --- a/_collections/_biblio/platform/platform_ambroise_multi-modal_2021.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: C Ambroise et al. -title: Multi-modal Latent Variable Model could help individuals stratification - application to HBN cohort -year: 2021 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ambroise_multi-view_2023.md b/_collections/_biblio/platform/platform_ambroise_multi-view_2023.md deleted file mode 100644 index a57bb7e..0000000 --- a/_collections/_biblio/platform/platform_ambroise_multi-view_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Corentin Ambroise et al. -title: Multi-View Variational Autoencoders Allow for Interpretability Leveraging Digital Avatars - Application to the HBN Cohort -year: 2023 -type: inproceedings -doi: 10.1109/ISBI53787.2023.10230552 -booktitle: IEEE 20th International Symposium on Biomedical Imaging (ISBI) 2023 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_artiges_quantifying_2019.md b/_collections/_biblio/platform/platform_artiges_quantifying_2019.md deleted file mode 100644 index 4b5e41a..0000000 --- a/_collections/_biblio/platform/platform_artiges_quantifying_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Eric Artiges et al. -title: Quantifying performance of machine learning methods for neuroimaging data -journal: NeuroImage -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_backhausen_adolescent_2024.md b/_collections/_biblio/platform/platform_backhausen_adolescent_2024.md deleted file mode 100644 index c0ffdfd..0000000 --- a/_collections/_biblio/platform/platform_backhausen_adolescent_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lea Backhausen et al. -title: Adolescent to young adult longitudinal development of subcortical volumes in two European sites with four waves -journal: Human Brain Mapping -year: 2024 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/hbm.26574 -doi: 10.1002/hbm.26574 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_backhausen_interplay_2023.md b/_collections/_biblio/platform/platform_backhausen_interplay_2023.md deleted file mode 100644 index 17f2c47..0000000 --- a/_collections/_biblio/platform/platform_backhausen_interplay_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lea Backhausen et al. -title: Interplay of early negative life events, development of orbitofrontal cortical thickness and depression in young adulthood -journal: JCPP Advances -year: 2023 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_bossier_empirical_2020.md b/_collections/_biblio/platform/platform_bossier_empirical_2020.md deleted file mode 100644 index 9e5f3c4..0000000 --- a/_collections/_biblio/platform/platform_bossier_empirical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Han Bossier et al. -title: The empirical replicability of task-based fMRI as a function of sample size -journal: NeuroImage -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811920300884 -doi: 10.1016/j.neuroimage.2020.116601 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_bottinger_orbitofrontal_2022.md b/_collections/_biblio/platform/platform_bottinger_orbitofrontal_2022.md deleted file mode 100644 index c147b62..0000000 --- a/_collections/_biblio/platform/platform_bottinger_orbitofrontal_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Boris Böttinger et al. -title: Orbitofrontal control of conduct problems? Evidence from healthy adolescents processing negative facial affect -journal: European Child \& Adolescent Psychiatry -year: 2022 -type: article -url: https -//doi.org/10.1007/s00787-021-01770-1 -doi: 10.1007/s00787-021-01770-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_brouwer_age-dependent_2020.md b/_collections/_biblio/platform/platform_brouwer_age-dependent_2020.md deleted file mode 100644 index 3df21d1..0000000 --- a/_collections/_biblio/platform/platform_brouwer_age-dependent_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Rachel Brouwer et al. -title: Age-dependent genetic variants associated with longitudinal changes in brain structure across the lifespan -journal: bioRxiv -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_brouwer_dynamics_2020.md b/_collections/_biblio/platform/platform_brouwer_dynamics_2020.md deleted file mode 100644 index 11f32f2..0000000 --- a/_collections/_biblio/platform/platform_brouwer_dynamics_2020.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Rachel Brouwer et al. -title: Dynamics of brain structure and its genetic architecture over the lifespan -year: 2020 -type: techreport ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_brouwer_genetic_2022.md b/_collections/_biblio/platform/platform_brouwer_genetic_2022.md deleted file mode 100644 index d2517b2..0000000 --- a/_collections/_biblio/platform/platform_brouwer_genetic_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Rachel Brouwer et al. -title: Genetic variants associated with longitudinal changes in brain structure across the lifespan -journal: Nature neuroscience -year: 2022 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_cao_characterizing_2021.md b/_collections/_biblio/platform/platform_cao_characterizing_2021.md deleted file mode 100644 index 970e7d3..0000000 --- a/_collections/_biblio/platform/platform_cao_characterizing_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zhipeng Cao et al. -title: Characterizing reward system neural trajectories from adolescence to young adulthood -journal: Developmental Cognitive Neuroscience -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1878929321001316 -doi: 10.1016/j.dcn.2021.101042 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_cao_cortical_2023.md b/_collections/_biblio/platform/platform_cao_cortical_2023.md deleted file mode 100644 index 5a826cd..0000000 --- a/_collections/_biblio/platform/platform_cao_cortical_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zhipeng Cao et al. -title: Cortical profiles of numerous psychiatric disorders and normal development share a common pattern -journal: Molecular Psychiatry -year: 2023 -type: article -url: https -//www.nature.com/articles/s41380-022-01855-6 -doi: 10.1038/s41380-022-01855-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_chavanne_anxiety_2023.md b/_collections/_biblio/platform/platform_chavanne_anxiety_2023.md deleted file mode 100644 index 5507cc9..0000000 --- a/_collections/_biblio/platform/platform_chavanne_anxiety_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Alice Chavanne et al. -title: Anxiety onset in adolescents - a machine-learning prediction -journal: Molecular Psychiatry -year: 2023 -type: article -url: https -//www.nature.com/articles/s41380-022-01840-z -doi: 10.1038/s41380-022-01840-z ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_chegraoui_object_2021.md b/_collections/_biblio/platform/platform_chegraoui_object_2021.md deleted file mode 100644 index b6f2ca5..0000000 --- a/_collections/_biblio/platform/platform_chegraoui_object_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Hamza Chegraoui et al. -title: Object Detection Improves Tumour Segmentation in MR Images of Rare Brain Tumours -journal: Cancers -year: 2021 -type: article -url: https -//www.mdpi.com/2072-6694/13/23/6113 -doi: 10.3390/cancers13236113 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_chen_brain_2022.md b/_collections/_biblio/platform/platform_chen_brain_2022.md deleted file mode 100644 index 7efd78f..0000000 --- a/_collections/_biblio/platform/platform_chen_brain_2022.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Di Chen et al. -title: Brain Signatures During Reward Anticipation Predict Persistent Attention-Deficit/Hyperactivity Disorder Symptoms -journal: Journal of the American Academy of Child and Adolescent Psychiatry -year: 2022 -type: article -doi: 10.1016/j.jaac.2021.11.030 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_chen_genetic_2024.md b/_collections/_biblio/platform/platform_chen_genetic_2024.md deleted file mode 100644 index dd6a597..0000000 --- a/_collections/_biblio/platform/platform_chen_genetic_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Shi-Dong Chen et al. -title: The genetic architecture of the human hypothalamus and its involvement in neuropsychiatric behaviours and disorders -journal: Nature Human Behaviour -year: 2024 -type: article -url: https -//www.nature.com/articles/s41562-023-01792-6 -doi: 10.1038/s41562-023-01792-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_cherkaoui_analysis_2018.md b/_collections/_biblio/platform/platform_cherkaoui_analysis_2018.md deleted file mode 100644 index f704202..0000000 --- a/_collections/_biblio/platform/platform_cherkaoui_analysis_2018.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Hamza Cherkaoui et al. -title: Analysis vs synthesis-based regularization for combined compressed sensing and parallel MRI reconstruction at 7 tesla -year: 2018 -type: inproceedings -booktitle: 2018 26th European Signal Processing Conference (EUSIPCO) ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_claude_identifying_2019.md b/_collections/_biblio/platform/platform_claude_identifying_2019.md deleted file mode 100644 index 51bc5e5..0000000 --- a/_collections/_biblio/platform/platform_claude_identifying_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: LA Claude et al. -title: Identifying a predictive neuroanatomical signature of bipolar disorders reliable across 13 international sites -journal: French Journal of Psychiatry -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_cury_genome_2020.md b/_collections/_biblio/platform/platform_cury_genome_2020.md deleted file mode 100644 index 38450b7..0000000 --- a/_collections/_biblio/platform/platform_cury_genome_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Claire Cury et al. -title: Genome wide association study of incomplete hippocampal inversion in adolescents -journal: PLoS One -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_daedelow_are_2021.md b/_collections/_biblio/platform/platform_daedelow_are_2021.md deleted file mode 100644 index 8de94c8..0000000 --- a/_collections/_biblio/platform/platform_daedelow_are_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Laura Daedelow et al. -title: Are psychotic-like experiences related to a discontinuation of cannabis consumption in young adults? -journal: Schizophrenia Research -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0920996421000220 -doi: 10.1016/j.schres.2021.01.002 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_de_matos_temporo-basal_2023.md b/_collections/_biblio/platform/platform_de_matos_temporo-basal_2023.md deleted file mode 100644 index 14ae0de..0000000 --- a/_collections/_biblio/platform/platform_de_matos_temporo-basal_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Kevin Matos et al. -title: Temporo-basal sulcal connections - a manual annotation protocol and an investigation of sexual dimorphism and heritability -journal: Brain Structure and Function -year: 2023 -type: article -url: https -//doi.org/10.1007/s00429-023-02663-6 -doi: 10.1007/s00429-023-02663-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_desrivieres_machine_2024.md b/_collections/_biblio/platform/platform_desrivieres_machine_2024.md deleted file mode 100644 index 05a60e4..0000000 --- a/_collections/_biblio/platform/platform_desrivieres_machine_2024.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Sylvane Desrivières et al. -title: Machine learning models for diagnosis and risk prediction in eating disorders, depression, and alcohol use disorder -year: 2024 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_doger_de_speville_relationships_2017.md b/_collections/_biblio/platform/platform_doger_de_speville_relationships_2017.md deleted file mode 100644 index 7e757b7..0000000 --- a/_collections/_biblio/platform/platform_doger_de_speville_relationships_2017.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Elodie Speville et al. -title: Relationships between regional radiation doses and cognitive decline in children treated with cranio-spinal irradiation for posterior fossa tumors -journal: Frontiers in oncology -year: 2017 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_duan_population_2024.md b/_collections/_biblio/platform/platform_duan_population_2024.md deleted file mode 100644 index c3ec220..0000000 --- a/_collections/_biblio/platform/platform_duan_population_2024.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Haojing Duan et al. -title: Population clustering of structural brain aging and its association with brain development -year: 2024 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_dufumier_benchmarking_2021.md b/_collections/_biblio/platform/platform_dufumier_benchmarking_2021.md deleted file mode 100644 index 2f96df4..0000000 --- a/_collections/_biblio/platform/platform_dufumier_benchmarking_2021.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Benoit Dufumier et al. -title: Benchmarking CNN on 3D Anatomical Brain MRI - Architectures, Data Augmentation and Deep Ensemble Learning -year: 2021 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_dufumier_conditional_2021.md b/_collections/_biblio/platform/platform_dufumier_conditional_2021.md deleted file mode 100644 index 350c72e..0000000 --- a/_collections/_biblio/platform/platform_dufumier_conditional_2021.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Benoit Dufumier et al. -title: Conditional Alignment and Uniformity for Contrastive Learning with Continuous Proxy Labels -year: 2021 -type: inproceedings -url: https -//hal.telecom-paris.fr/hal-03523114 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_dufumier_contrastive_2021.md b/_collections/_biblio/platform/platform_dufumier_contrastive_2021.md deleted file mode 100644 index 11039b4..0000000 --- a/_collections/_biblio/platform/platform_dufumier_contrastive_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Benoit Dufumier et al. -title: Contrastive Learning with Continuous Proxy Meta-Data for 3D MRI Classification -year: 2021 -type: inproceedings -url: https -//link.springer.com/chapter/10.1007%2F978-3-030-87196-3_6 -doi: 10.1007/978-3-030-87196-3_6 -booktitle: 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2021 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_dufumier_exploring_2024.md b/_collections/_biblio/platform/platform_dufumier_exploring_2024.md deleted file mode 100644 index bee2f25..0000000 --- a/_collections/_biblio/platform/platform_dufumier_exploring_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Benoit Dufumier et al. -title: Exploring the potential of representation and transfer learning for anatomical neuroimaging - Application to psychiatry -journal: NeuroImage -year: 2024 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811924001605 -doi: 10.1016/j.neuroimage.2024.120665 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_dufumier_openbhb_2022.md b/_collections/_biblio/platform/platform_dufumier_openbhb_2022.md deleted file mode 100644 index 37582af..0000000 --- a/_collections/_biblio/platform/platform_dufumier_openbhb_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: true -author: Benoit Dufumier et al. -title: OpenBHB - a Large-Scale Multi-Site Brain MRI Data-set for Age Prediction and Debiasing -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922007522 -doi: 10.1016/j.neuroimage.2022.119637 ---- diff --git a/_collections/_biblio/platform/platform_el_gueddari_pysap-mri_2020.md b/_collections/_biblio/platform/platform_el_gueddari_pysap-mri_2020.md deleted file mode 100644 index 450e801..0000000 --- a/_collections/_biblio/platform/platform_el_gueddari_pysap-mri_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Loubna El Gueddari et al. -title: PySAP-MRI - A Python package for MR image reconstruction -year: 2020 -type: inproceedings -booktitle: ISMRM workshop on Data Sampling and Image Reconstruction ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_elandaloussi_understanding_2023.md b/_collections/_biblio/platform/platform_elandaloussi_understanding_2023.md deleted file mode 100644 index 303c56f..0000000 --- a/_collections/_biblio/platform/platform_elandaloussi_understanding_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yannis Elandaloussi et al. -title: Understanding the relationship between cerebellar structure and social abilities -journal: Molecular Autism -year: 2023 -type: article -url: https -//doi.org/10.1186/s13229-023-00551-8 -doi: 10.1186/s13229-023-00551-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ernst_pubertal_2019.md b/_collections/_biblio/platform/platform_ernst_pubertal_2019.md deleted file mode 100644 index cf15d98..0000000 --- a/_collections/_biblio/platform/platform_ernst_pubertal_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Monique Ernst et al. -title: Pubertal maturation and sex effects on the default-mode network connectivity implicated in mood dysregulation -journal: Translational Psychiatry -year: 2019 -type: article -url: https -//www.nature.com/articles/s41398-019-0433-6 -doi: 10.1038/s41398-019-0433-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_farrens_pysap_2020-1.md b/_collections/_biblio/platform/platform_farrens_pysap_2020-1.md deleted file mode 100644 index f9a2a6e..0000000 --- a/_collections/_biblio/platform/platform_farrens_pysap_2020-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: S Farrens et al. -title: PySAP - Python Sparse Data Analysis Package for multidisciplinary image processing -journal: Astronomy and Computing -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_farrens_pysap_2020.md b/_collections/_biblio/platform/platform_farrens_pysap_2020.md deleted file mode 100644 index 026b087..0000000 --- a/_collections/_biblio/platform/platform_farrens_pysap_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: S Farrens et al. -title: PySAP - Python Sparse data Analysis Package -journal: Astrophysics Source Code Library -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_farrens_pysap_2022.md b/_collections/_biblio/platform/platform_farrens_pysap_2022.md deleted file mode 100644 index 4f92fb4..0000000 --- a/_collections/_biblio/platform/platform_farrens_pysap_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Samuel Farrens et al. -title: PySAP - From Galaxies to Brains and Beyond -year: 2022 -type: inproceedings -booktitle: Astronomical Society of the Pacific Conference Series ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_freichel_drinking_2023.md b/_collections/_biblio/platform/platform_freichel_drinking_2023.md deleted file mode 100644 index f457586..0000000 --- a/_collections/_biblio/platform/platform_freichel_drinking_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: René Freichel et al. -title: Drinking Motives, Personality Traits, Life Stressors-Identifying Pathways to Harmful Alcohol Use in Adolescence Using a Panel Network Approach -journal: Addiction -year: 2023 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_freichel_unravelling_2023.md b/_collections/_biblio/platform/platform_freichel_unravelling_2023.md deleted file mode 100644 index f3fabea..0000000 --- a/_collections/_biblio/platform/platform_freichel_unravelling_2023.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: René Freichel et al. -title: Unravelling Robust Brain-Behavior Links of Depressive Symptoms Through Granular Network Models - Understanding Heterogeneity and Clinical Implications -year: 2023 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_frohner_associations_2022.md b/_collections/_biblio/platform/platform_frohner_associations_2022.md deleted file mode 100644 index 15f3a8b..0000000 --- a/_collections/_biblio/platform/platform_frohner_associations_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Juliane Fröhner et al. -title: Associations of delay discounting and drinking trajectories from ages 14 to 22 -journal: Alcoholism - Clinical and Experimental Research -year: 2022 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/acer.14799 -doi: 10.1111/acer.14799 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_gay_cartographie_2015.md b/_collections/_biblio/platform/platform_gay_cartographie_2015.md deleted file mode 100644 index a725a3a..0000000 --- a/_collections/_biblio/platform/platform_gay_cartographie_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: David Gay et al. -title: Cartographie T2* sur cerveau entier pour les études multicentriques de recherche clinique -year: 2015 -type: inproceedings -booktitle: 2. SFRMBM ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_gazula_federated_2023.md b/_collections/_biblio/platform/platform_gazula_federated_2023.md deleted file mode 100644 index c871a2e..0000000 --- a/_collections/_biblio/platform/platform_gazula_federated_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Harshvardhan Gazula et al. -title: Federated Analysis in COINSTAC Reveals Functional Network Connectivity and Spectral Links to Smoking and Alcohol Consumption in Nearly 2,000 Adolescent Brains -journal: Neuroinformatics -year: 2023 -type: article -url: https -//doi.org/10.1007/s12021-022-09604-4 -doi: 10.1007/s12021-022-09604-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ge_genetic_2024.md b/_collections/_biblio/platform/platform_ge_genetic_2024.md deleted file mode 100644 index bd20ee2..0000000 --- a/_collections/_biblio/platform/platform_ge_genetic_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yi-Jun Ge et al. -title: Genetic architectures of cerebral ventricles and their overlap with neuropsychiatric traits -journal: Nature Human Behaviour -year: 2024 -type: article -url: https -//www.nature.com/articles/s41562-023-01722-6 -doi: 10.1038/s41562-023-01722-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_gomez_characterization_2022.md b/_collections/_biblio/platform/platform_gomez_characterization_2022.md deleted file mode 100644 index 938234a..0000000 --- a/_collections/_biblio/platform/platform_gomez_characterization_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Chloé Gomez et al. -title: Characterization of Brain Activity Patterns Across States of Consciousness Based on Variational Auto-Encoders -year: 2022 -type: inproceedings -booktitle: International Conference on Medical Image Computing and Computer-Assisted Intervention ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_gomez_exploration_2023.md b/_collections/_biblio/platform/platform_gomez_exploration_2023.md deleted file mode 100644 index fc47e44..0000000 --- a/_collections/_biblio/platform/platform_gomez_exploration_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: C Gomez et al. -title: Exploration of the Neural Correlates of Consciousness Using Linear Latent Model -year: 2023 -type: inproceedings -booktitle: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_goyard_brainomics_2015.md b/_collections/_biblio/platform/platform_goyard_brainomics_2015.md deleted file mode 100644 index b9973f3..0000000 --- a/_collections/_biblio/platform/platform_goyard_brainomics_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: David Goyard et al. -title: Brainomics - Harnessing the CubicWeb semantic framework to manage large neuromaging genetics shared resources -year: 2015 -type: inproceedings -booktitle: Journées RITS 2015 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_approches_2012.md b/_collections/_biblio/platform/platform_grigis_approches_2012.md deleted file mode 100644 index 5c63752..0000000 --- a/_collections/_biblio/platform/platform_grigis_approches_2012.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Approches statistiques pour la détection de changements en IRM de diffusion - application au suivi longitudinal de pathologies neuro-dégénératives -year: 2012 -type: PhD Thesis ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_change_2010.md b/_collections/_biblio/platform/platform_grigis_change_2010.md deleted file mode 100644 index cd1ba2f..0000000 --- a/_collections/_biblio/platform/platform_grigis_change_2010.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Change detection in diffusion MRI using multivariate statistical testing on tensors -year: 2010 -type: inproceedings -booktitle: Medical Image Computing and Computer-Assisted Intervention–MICCAI 2010 - 13th International Conference, Beijing, China, September 20-24, 2010, Proceedings, Part II 13 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_integration_2011.md b/_collections/_biblio/platform/platform_grigis_integration_2011.md deleted file mode 100644 index a78b230..0000000 --- a/_collections/_biblio/platform/platform_grigis_integration_2011.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: On the integration of spatial neighborhood information for detecting longitudinal changes in MRI sequences -year: 2011 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_interpretable_2022.md b/_collections/_biblio/platform/platform_grigis_interpretable_2022.md deleted file mode 100644 index ad70d81..0000000 --- a/_collections/_biblio/platform/platform_grigis_interpretable_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Interpretable Signature of Consciousness in Resting-State Functional Network Brain Activity -year: 2022 -type: inproceedings -booktitle: International Conference on Medical Image Computing and Computer-Assisted Intervention ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_learning_2020.md b/_collections/_biblio/platform/platform_grigis_learning_2020.md deleted file mode 100644 index 1b9af88..0000000 --- a/_collections/_biblio/platform/platform_grigis_learning_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: A Grigis et al. -title: Learning to leverage salient regions in neuro-oncology using Deap Learning -journal: bioRxiv -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_longitudinal_2011.md b/_collections/_biblio/platform/platform_grigis_longitudinal_2011.md deleted file mode 100644 index e87ffde..0000000 --- a/_collections/_biblio/platform/platform_grigis_longitudinal_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Longitudinal change detection - inference on the diffusion tensor along white-matter pathways -year: 2011 -type: inproceedings -booktitle: Medical Image Computing and Computer-Assisted Intervention–MICCAI 2011 - 14th International Conference, Toronto, Canada, September 18-22, 2011, Proceedings, Part II 14 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_longitudinal_2012.md b/_collections/_biblio/platform/platform_grigis_longitudinal_2012.md deleted file mode 100644 index 98b6586..0000000 --- a/_collections/_biblio/platform/platform_grigis_longitudinal_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Longitudinal change detection in diffusion MRI using multivariate statistical testing on tensors -journal: Neuroimage -year: 2012 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_longitudinal_2013.md b/_collections/_biblio/platform/platform_grigis_longitudinal_2013.md deleted file mode 100644 index f5e4bad..0000000 --- a/_collections/_biblio/platform/platform_grigis_longitudinal_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Longitudinal change detection - inference on the diffusion tensor along white matter pathways -journal: Medical image analysis -year: 2013 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_neuroimaging_2017.md b/_collections/_biblio/platform/platform_grigis_neuroimaging_2017.md deleted file mode 100644 index a6f2e1f..0000000 --- a/_collections/_biblio/platform/platform_grigis_neuroimaging_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework -journal: Frontiers in Neuroinformatics -year: 2017 -type: article -doi: 10.3389/fninf.2017.00018 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_new_2011.md b/_collections/_biblio/platform/platform_grigis_new_2011.md deleted file mode 100644 index 6a4e7b8..0000000 --- a/_collections/_biblio/platform/platform_grigis_new_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: A new high order tensor decomposition - Application to reorientation. -year: 2011 -type: inproceedings -booktitle: 2011 IEEE International Symposium on Biomedical Imaging - From Nano to Macro ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_predicting_2020.md b/_collections/_biblio/platform/platform_grigis_predicting_2020.md deleted file mode 100644 index 8f3e871..0000000 --- a/_collections/_biblio/platform/platform_grigis_predicting_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Predicting cortical signatures of consciousness using dynamic functional connectivity graph-convolutional neural networks -journal: bioRxiv -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_grigis_statistical_2012.md b/_collections/_biblio/platform/platform_grigis_statistical_2012.md deleted file mode 100644 index f928f2a..0000000 --- a/_collections/_biblio/platform/platform_grigis_statistical_2012.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Antoine Grigis et al. -title: Statistical approaches for change detection in diffusion MRI (application to the longitudinal follow-up of neuro-degenerative pathologies) -year: 2012 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_gros_whole-brain_2024.md b/_collections/_biblio/platform/platform_gros_whole-brain_2024.md deleted file mode 100644 index dfdb5b6..0000000 --- a/_collections/_biblio/platform/platform_gros_whole-brain_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Guillaume Gros et al. -title: Whole-brain gray matter maturation trajectories associated with autistic traits from adolescence to early adulthood -journal: Brain Structure and Function -year: 2024 -type: article -url: https -//doi.org/10.1007/s00429-023-02710-2 -doi: 10.1007/s00429-023-02710-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_guevara_disentangling_2022.md b/_collections/_biblio/platform/platform_guevara_disentangling_2022.md deleted file mode 100644 index fa7ec8a..0000000 --- a/_collections/_biblio/platform/platform_guevara_disentangling_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Miguel Guevara et al. -title: Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922003214 -doi: 10.1016/j.neuroimage.2022.119197 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_haeger_imaging_2020.md b/_collections/_biblio/platform/platform_haeger_imaging_2020.md deleted file mode 100644 index f71db62..0000000 --- a/_collections/_biblio/platform/platform_haeger_imaging_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Alexa Haeger et al. -title: Imaging the aging brain - study design and baseline findings of the SENIOR cohort -journal: Alzheimer's Research \& Therapy -year: 2020 -type: article -url: https -//alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1 -doi: 10.1186/s13195-020-00642-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_hemforth_interpretable_2023.md b/_collections/_biblio/platform/platform_hemforth_interpretable_2023.md deleted file mode 100644 index 5a3df50..0000000 --- a/_collections/_biblio/platform/platform_hemforth_interpretable_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lisa Hemforth et al. -title: Interpretable automatic detection of incomplete hippocampal inversions using anatomical criteria -year: 2023 -type: inproceedings -booktitle: Medical Imaging 2023 - Image Processing ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_heukamp_adolescents_2024.md b/_collections/_biblio/platform/platform_heukamp_adolescents_2024.md deleted file mode 100644 index 50aadf6..0000000 --- a/_collections/_biblio/platform/platform_heukamp_adolescents_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Nils Heukamp et al. -title: Adolescents’ pain-related ontogeny shares a neural basis with adults’ chronic pain in basothalamo-cortical organization -journal: iScience -year: 2024 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S2589004224001755 -doi: 10.1016/j.isci.2024.108954 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_holz_stable_2023.md b/_collections/_biblio/platform/platform_holz_stable_2023.md deleted file mode 100644 index 7c8a498..0000000 --- a/_collections/_biblio/platform/platform_holz_stable_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Nathalie Holz et al. -title: A stable and replicable neural signature of lifespan adversity in the adult brain -journal: Nature Neuroscience -year: 2023 -type: article -url: https -//www.nature.com/articles/s41593-023-01410-8 -doi: 10.1038/s41593-023-01410-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_iftimovici_asynchronous_2023.md b/_collections/_biblio/platform/platform_iftimovici_asynchronous_2023.md deleted file mode 100644 index 8fbcdf6..0000000 --- a/_collections/_biblio/platform/platform_iftimovici_asynchronous_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Anton Iftimovici et al. -title: Asynchronous neural maturation predicts transition to psychosis -journal: Psychiatry and Clinical Neurosciences -year: 2023 -type: article -doi: 10.1111/pcn.13612 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ivanov_substance_2019.md b/_collections/_biblio/platform/platform_ivanov_substance_2019.md deleted file mode 100644 index 0481f82..0000000 --- a/_collections/_biblio/platform/platform_ivanov_substance_2019.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Iliyan Ivanov et al. -title: Substance Use Initiation in Drug Naïve Adolescents-Possible Predictors and Consequences From a Large Cohort Naturalistic Study -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ivanov_substance_2021.md b/_collections/_biblio/platform/platform_ivanov_substance_2021.md deleted file mode 100644 index e1ac683..0000000 --- a/_collections/_biblio/platform/platform_ivanov_substance_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Iliyan Ivanov et al. -title: Substance Use Initiation, Particularly Alcohol, in Drug-Naive Adolescents - Possible Predictors and Consequences From a Large Cohort Naturalistic Study -journal: Journal of the American Academy of Child and Adolescent Psychiatry -year: 2021 -type: article -doi: 10.1016/j.jaac.2020.08.443 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ji_alterations_2020.md b/_collections/_biblio/platform/platform_ji_alterations_2020.md deleted file mode 100644 index 44c2461..0000000 --- a/_collections/_biblio/platform/platform_ji_alterations_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Ellen Ji et al. -title: Alterations In Short-Range Structural Connectivity Across The Psychosis Spectrum - Findings From The B-Snip Study -journal: Schizophrenia Bulletin -year: 2020 -type: article -url: https -//academic.oup.com/schizophreniabulletin/article/46/Supplement_1/S97/5839281 -doi: 10.1093/schbul/sbaa031.226 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ji_increased_2019.md b/_collections/_biblio/platform/platform_ji_increased_2019.md deleted file mode 100644 index 1e96720..0000000 --- a/_collections/_biblio/platform/platform_ji_increased_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Ellen Ji et al. -title: Increased and Decreased Superficial White Matter Structural Connectivity in Schizophrenia and Bipolar Disorder -journal: Schizophrenia Bulletin -year: 2019 -type: article -url: https -//doi.org/10.1093/schbul/sbz015 -doi: 10.1093/schbul/sbz015 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ji_t240_2018.md b/_collections/_biblio/platform/platform_ji_t240_2018.md deleted file mode 100644 index 531b602..0000000 --- a/_collections/_biblio/platform/platform_ji_t240_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Ellen Ji et al. -title: T240. Relationship Between Cognitive Performance and Superficial White Matter Integrity in the Cingulate Cortex in Schizophrenia - A DWI Study Using a Novel Atlas -journal: Biological Psychiatry -year: 2018 -type: article -url: https -//linkinghub.elsevier.com/retrieve/pii/S0006322318306796 -doi: 10.1016/j.biopsych.2018.02.577 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_jia_neural_2021.md b/_collections/_biblio/platform/platform_jia_neural_2021.md deleted file mode 100644 index bcf0fac..0000000 --- a/_collections/_biblio/platform/platform_jia_neural_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Tianye Jia et al. -title: Neural network involving medial orbitofrontal cortex and dorsal periaqueductal gray regulation in human alcohol abuse -journal: Science Advances -year: 2021 -type: article -url: https -//www.science.org/doi/full/10.1126/sciadv.abd4074 -doi: 10.1126/sciadv.abd4074 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_jia_neurobehavioural_2020.md b/_collections/_biblio/platform/platform_jia_neurobehavioural_2020.md deleted file mode 100644 index 7fed167..0000000 --- a/_collections/_biblio/platform/platform_jia_neurobehavioural_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Tianye Jia et al. -title: Neurobehavioural characterisation and stratification of reinforcement-related behaviour -journal: Nature Human Behaviour -year: 2020 -type: article -url: https -//www.nature.com/articles/s41562-020-0846-5 -doi: 10.1038/s41562-020-0846-5 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_jollans_quantifying_2019.md b/_collections/_biblio/platform/platform_jollans_quantifying_2019.md deleted file mode 100644 index d09243a..0000000 --- a/_collections/_biblio/platform/platform_jollans_quantifying_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lee Jollans et al. -title: Quantifying performance of machine learning methods for neuroimaging data -journal: Neuroimage -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_judd_cognitive_2020.md b/_collections/_biblio/platform/platform_judd_cognitive_2020.md deleted file mode 100644 index bec8fe8..0000000 --- a/_collections/_biblio/platform/platform_judd_cognitive_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Nicholas Judd et al. -title: Cognitive and brain development is independently influenced by socioeconomic status and polygenic scores for educational attainment -journal: Proceedings of the National Academy of Sciences -year: 2020 -type: article -url: https -//www.pnas.org/doi/abs/10.1073/pnas.2001228117 -doi: 10.1073/pnas.2001228117 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_judd_independent_2019.md b/_collections/_biblio/platform/platform_judd_independent_2019.md deleted file mode 100644 index 28a963f..0000000 --- a/_collections/_biblio/platform/platform_judd_independent_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Nicholas Judd et al. -title: Independent effects of socioeconomic status and genetics on adolescent cognition and brain development -journal: bioRxiv -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kaiser_developmental_2022.md b/_collections/_biblio/platform/platform_kaiser_developmental_2022.md deleted file mode 100644 index 3b6d6d7..0000000 --- a/_collections/_biblio/platform/platform_kaiser_developmental_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Anna Kaiser et al. -title: A Developmental Perspective on Facets of Impulsivity and Brain Activity Correlates From Adolescence to Adulthood -journal: Biological Psychiatry - Cognitive Neuroscience and Neuroimaging -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2451902222000428 -doi: 10.1016/j.bpsc.2022.02.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_khalid_multimodal_2023.md b/_collections/_biblio/platform/platform_khalid_multimodal_2023.md deleted file mode 100644 index 60b7474..0000000 --- a/_collections/_biblio/platform/platform_khalid_multimodal_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Fahad Khalid et al. -title: Multimodal MRI radiomic models to predict genomic mutations in diffuse intrinsic pontine glioma with missing imaging modalities -journal: Frontiers in Medicine -year: 2023 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fmed.2023.1071447 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2021.md b/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2021.md deleted file mode 100644 index f00e75d..0000000 --- a/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2021.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Roxanna Korologou-Linden et al. -title: The bidirectional causal effects of brain morphology across the life course and risk of Alzheimer’s disease - A cross-cohort comparison and Mendelian randomization meta-analysis -year: 2021 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2023.md b/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2023.md deleted file mode 100644 index 3c7538e..0000000 --- a/_collections/_biblio/platform/platform_korologou-linden_bidirectional_2023.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Roxanna Korologou-Linden et al. -title: The bidirectional effects between cognitive ability and brain morphology - A life course Mendelian randomization analysis -year: 2023 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kuhn_brain_2020.md b/_collections/_biblio/platform/platform_kuhn_brain_2020.md deleted file mode 100644 index c81f7e6..0000000 --- a/_collections/_biblio/platform/platform_kuhn_brain_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Simone Kühn et al. -title: Brain structure and habitat - Do the brains of our children tell us where they have been brought up? -journal: NeuroImage -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811920307114 -doi: 10.1016/j.neuroimage.2020.117225 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kuhn_hierarchical_2020.md b/_collections/_biblio/platform/platform_kuhn_hierarchical_2020.md deleted file mode 100644 index e2b473e..0000000 --- a/_collections/_biblio/platform/platform_kuhn_hierarchical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Simone Kühn et al. -title: Hierarchical associations of alcohol use disorder symptoms in late adolescence with markers during early adolescence -journal: Addictive Behaviors -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0306460319303168 -doi: 10.1016/j.addbeh.2019.106130 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kuhn_predicting_2019.md b/_collections/_biblio/platform/platform_kuhn_predicting_2019.md deleted file mode 100644 index 917152e..0000000 --- a/_collections/_biblio/platform/platform_kuhn_predicting_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Simone Kühn et al. -title: Predicting development of adolescent drinking behaviour from whole brain structure at 14 years of age -journal: eLife -year: 2019 -type: article -url: https -//doi.org/10.7554/eLife.44056 -doi: 10.7554/eLife.44056 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kuhn_predicting_2020.md b/_collections/_biblio/platform/platform_kuhn_predicting_2020.md deleted file mode 100644 index 0f02843..0000000 --- a/_collections/_biblio/platform/platform_kuhn_predicting_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Simone Kühn et al. -title: Predicting change trajectories of neuroticism from baseline brain structure using whole brain analyses and latent growth curve models in adolescents -journal: Scientific Reports -year: 2020 -type: article -url: https -//www.nature.com/articles/s41598-020-58128-x -doi: 10.1038/s41598-020-58128-x ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_kuhn_trees_2023.md b/_collections/_biblio/platform/platform_kuhn_trees_2023.md deleted file mode 100644 index c9756f9..0000000 --- a/_collections/_biblio/platform/platform_kuhn_trees_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Simone Kühn et al. -title: Trees for brains - Current residential tree cover density and its association with brain structure in young adults -journal: Journal of Environmental Psychology -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0272494423000956 -doi: 10.1016/j.jenvp.2023.102047 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_laroche_drum_2017.md b/_collections/_biblio/platform/platform_laroche_drum_2017.md deleted file mode 100644 index 4a8a80f..0000000 --- a/_collections/_biblio/platform/platform_laroche_drum_2017.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: C. Laroche et al. -title: Drum extraction in single channel audio signals using multi-layer non negative matrix factor deconvolution -year: 2017 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_laroche_methode_2015.md b/_collections/_biblio/platform/platform_laroche_methode_2015.md deleted file mode 100644 index 0eed9bd..0000000 --- a/_collections/_biblio/platform/platform_laroche_methode_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: C. Laroche et al. -title: Méthode Structurée de décomposition en matrices non- négatives appliquéè a la séparation de sources audio -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_laroche_structured_2015.md b/_collections/_biblio/platform/platform_laroche_structured_2015.md deleted file mode 100644 index 77d409a..0000000 --- a/_collections/_biblio/platform/platform_laroche_structured_2015.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: C. Laroche et al. -title: A structured nonnegative matrix factorization for source separation -year: 2015 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_le_guen_chaotic_2018.md b/_collections/_biblio/platform/platform_le_guen_chaotic_2018.md deleted file mode 100644 index 07c464c..0000000 --- a/_collections/_biblio/platform/platform_le_guen_chaotic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yann Le Guen et al. -title: The chaotic morphology of the left superior temporal sulcus is genetically constrained -journal: NeuroImage -year: 2018 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811918302568 -doi: 10.1016/j.neuroimage.2018.03.046 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_le_guen_eqtl_2019.md b/_collections/_biblio/platform/platform_le_guen_eqtl_2019.md deleted file mode 100644 index 6e6df26..0000000 --- a/_collections/_biblio/platform/platform_le_guen_eqtl_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yann Le Guen et al. -title: eQTL of KCNK2 regionally influences the brain sulcal widening - evidence from 15,597 UK Biobank participants with neuroimaging data -journal: Brain Structure and Function -year: 2019 -type: article -url: https -//doi.org/10.1007/s00429-018-1808-9 -doi: 10.1007/s00429-018-1808-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_le_guen_heritability_2019.md b/_collections/_biblio/platform/platform_le_guen_heritability_2019.md deleted file mode 100644 index 204f7f0..0000000 --- a/_collections/_biblio/platform/platform_le_guen_heritability_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yann Le Guen et al. -title: Heritability of surface area and cortical thickness - a comparison between the Human Connectome Project and the UK Biobank dataset -year: 2019 -type: inproceedings -url: https -//ieeexplore.ieee.org/abstract/document/8759539 -doi: 10.1109/ISBI.2019.8759539 -booktitle: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_lett_f51_2019.md b/_collections/_biblio/platform/platform_lett_f51_2019.md deleted file mode 100644 index 6821ca9..0000000 --- a/_collections/_biblio/platform/platform_lett_f51_2019.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Tristram Lett et al. -title: F51. Putative Causal Relationship Among Polygenic Scores, Cortical Surfaces, and General Intelligence -journal: Biological Psychiatry -year: 2019 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_li_anatomical_2022.md b/_collections/_biblio/platform/platform_li_anatomical_2022.md deleted file mode 100644 index 7eb8452..0000000 --- a/_collections/_biblio/platform/platform_li_anatomical_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Wen Li et al. -title: Anatomical connectivity profile development constrains medial-lateral topography in the dorsal prefrontal cortex -journal: bioRxiv -year: 2022 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_liao_hemispheric_2023.md b/_collections/_biblio/platform/platform_liao_hemispheric_2023.md deleted file mode 100644 index 7ada9d0..0000000 --- a/_collections/_biblio/platform/platform_liao_hemispheric_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zhijie Liao et al. -title: Hemispheric asymmetry in cortical thinning reflects intrinsic organization of the neurotransmitter systems and homotopic functional connectivity -journal: Proceedings of the National Academy of Sciences -year: 2023 -type: article -url: https -//www.pnas.org/doi/abs/10.1073/pnas.2306990120 -doi: 10.1073/pnas.2306990120 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_liao_similarity_2021.md b/_collections/_biblio/platform/platform_liao_similarity_2021.md deleted file mode 100644 index 489cff4..0000000 --- a/_collections/_biblio/platform/platform_liao_similarity_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zhijie Liao et al. -title: Similarity and stability of face network across populations and throughout adolescence and adulthood -journal: NeuroImage -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811921008600 -doi: 10.1016/j.neuroimage.2021.118587 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_lotter_human_2023.md b/_collections/_biblio/platform/platform_lotter_human_2023.md deleted file mode 100644 index cbd57cb..0000000 --- a/_collections/_biblio/platform/platform_lotter_human_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Leon Lotter et al. -title: Human cortex development is shaped by molecular and cellular brain systems -journal: bioRxiv -year: 2023 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_louiset_separating_2024.md b/_collections/_biblio/platform/platform_louiset_separating_2024.md deleted file mode 100644 index 8717b2c..0000000 --- a/_collections/_biblio/platform/platform_louiset_separating_2024.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Robin Louiset et al. -title: Separating common from salient patterns with Contrastive Representation Learning -year: 2024 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_louiset_sepvae_2023.md b/_collections/_biblio/platform/platform_louiset_sepvae_2023.md deleted file mode 100644 index e93c2f7..0000000 --- a/_collections/_biblio/platform/platform_louiset_sepvae_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Robin Louiset et al. -title: SepVAE - a contrastive VAE to separate pathological patterns from healthy ones -year: 2023 -type: inproceedings -url: http -//arxiv.org/abs/2307.06206 -doi: 10.48550/arXiv.2307.06206 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_louiset_ucsl_2021.md b/_collections/_biblio/platform/platform_louiset_ucsl_2021.md deleted file mode 100644 index 1673b71..0000000 --- a/_collections/_biblio/platform/platform_louiset_ucsl_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Robin Louiset et al. -title: UCSL - A Machine Learning Expectation-Maximization framework for Unsupervised Clustering driven by Supervised Learning -year: 2021 -type: inproceedings -url: http -//arxiv.org/abs/2107.01988 -booktitle: Joint European Conference on Machine Learning and Knowledge Discovery in Databases (ECML/PKDD) 2021 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_maitra_psychotic_2023.md b/_collections/_biblio/platform/platform_maitra_psychotic_2023.md deleted file mode 100644 index 8ccc959..0000000 --- a/_collections/_biblio/platform/platform_maitra_psychotic_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Raka Maitra et al. -title: Psychotic Like Experiences in Healthy Adolescents are Underpinned by Lower Fronto-Temporal Cortical Gyrification - a Study from the IMAGEN Consortium -journal: Schizophrenia Bulletin -year: 2023 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_maltais_prospective_2020-1.md b/_collections/_biblio/platform/platform_maltais_prospective_2020-1.md deleted file mode 100644 index dfcae40..0000000 --- a/_collections/_biblio/platform/platform_maltais_prospective_2020-1.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Mathieu Maltais et al. -title: Prospective associations between physical activity levels and white matter integrity in older adults - results from the MAPT study -journal: Maturitas -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0378512220302425 -doi: 10.1016/j.maturitas.2020.04.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_maltais_prospective_2020.md b/_collections/_biblio/platform/platform_maltais_prospective_2020.md deleted file mode 100644 index e8c4312..0000000 --- a/_collections/_biblio/platform/platform_maltais_prospective_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Mathieu Maltais et al. -title: Prospective Associations Between Diffusion Tensor Imaging Parameters and Frailty in Older Adults -journal: Journal of the American Geriatrics Society -year: 2020 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16343 -doi: 10.1111/jgs.16343 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_mangin_plis_2019.md b/_collections/_biblio/platform/platform_mangin_plis_2019.md deleted file mode 100644 index 7cc40eb..0000000 --- a/_collections/_biblio/platform/platform_mangin_plis_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jean-François Mangin et al. -title: “Plis de passage” Deserve a Role in Models of the Cortical Folding Process -journal: Brain Topography -year: 2019 -type: article -url: https -//doi.org/10.1007/s10548-019-00734-8 -doi: 10.1007/s10548-019-00734-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_mihailov_cortical_2020.md b/_collections/_biblio/platform/platform_mihailov_cortical_2020.md deleted file mode 100644 index ab62a38..0000000 --- a/_collections/_biblio/platform/platform_mihailov_cortical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Angeline Mihailov et al. -title: Cortical signatures in behaviorally clustered autistic traits subgroups - a population-based study -journal: Translational Psychiatry -year: 2020 -type: article -url: https -//www.nature.com/articles/s41398-020-00894-3 -doi: 10.1038/s41398-020-00894-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_mihailov_multidimensional_2019.md b/_collections/_biblio/platform/platform_mihailov_multidimensional_2019.md deleted file mode 100644 index 3775ce6..0000000 --- a/_collections/_biblio/platform/platform_mihailov_multidimensional_2019.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Angeline Mihailov et al. -title: Multidimensional Approaches in the Study of Autistic Traits using Behavioral and Imaging Data -year: 2019 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_milham_accelerating_2020.md b/_collections/_biblio/platform/platform_milham_accelerating_2020.md deleted file mode 100644 index f8dd8ef..0000000 --- a/_collections/_biblio/platform/platform_milham_accelerating_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Michael Milham et al. -title: Accelerating the Evolution of Nonhuman Primate Neuroimaging -journal: Neuron -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_modabbernia_linked_2021.md b/_collections/_biblio/platform/platform_modabbernia_linked_2021.md deleted file mode 100644 index d9281e3..0000000 --- a/_collections/_biblio/platform/platform_modabbernia_linked_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Amirhossein Modabbernia et al. -title: Linked patterns of biological and environmental covariation with brain structure in adolescence - a population-based longitudinal study -journal: Molecular Psychiatry -year: 2021 -type: article -url: https -//www.nature.com/articles/s41380-020-0757-x -doi: 10.1038/s41380-020-0757-x ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_navarri_biologically_2023.md b/_collections/_biblio/platform/platform_navarri_biologically_2023.md deleted file mode 100644 index b77b1a6..0000000 --- a/_collections/_biblio/platform/platform_navarri_biologically_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Xavier Navarri et al. -title: A biologically informed polygenic score of neuronal plasticity moderates the association between cognitive aptitudes and cortical thickness in adolescents -journal: Developmental Cognitive Neuroscience -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1878929323000373 -doi: 10.1016/j.dcn.2023.101232 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_nees_global_2022.md b/_collections/_biblio/platform/platform_nees_global_2022.md deleted file mode 100644 index d4f6fa8..0000000 --- a/_collections/_biblio/platform/platform_nees_global_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Frauke Nees et al. -title: Global and Regional Structural Differences and Prediction of Autistic Traits during Adolescence -journal: Brain Sciences -year: 2022 -type: article -url: https -//www.mdpi.com/2076-3425/12/9/1187 -doi: 10.3390/brainsci12091187 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_nweze_trajectories_2023.md b/_collections/_biblio/platform/platform_nweze_trajectories_2023.md deleted file mode 100644 index fab44c1..0000000 --- a/_collections/_biblio/platform/platform_nweze_trajectories_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Tochukwu Nweze et al. -title: Trajectories of cortical structures associated with stress across adolescence - a bivariate latent change score approach -journal: Journal of Child Psychology and Psychiatry -year: 2023 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/jcpp.13793 -doi: 10.1111/jcpp.13793 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_operto_cati:_2016.md b/_collections/_biblio/platform/platform_operto_cati:_2016.md deleted file mode 100644 index ba5da0b..0000000 --- a/_collections/_biblio/platform/platform_operto_cati:_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Grégory Operto et al. -title: CATI - A Large Distributed Infrastructure for the Neuroimaging of Cohorts -journal: Neuroinformatics -year: 2016 -type: article -doi: 10.1007/s12021-016-9295-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ortuno-sierra_new_2015.md b/_collections/_biblio/platform/platform_ortuno-sierra_new_2015.md deleted file mode 100644 index 1d488b0..0000000 --- a/_collections/_biblio/platform/platform_ortuno-sierra_new_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Javier Ortuno-Sierra et al. -title: New evidence of factor structure and measurement invariance of the SDQ across five European nations -journal: EUROPEAN CHILD \& ADOLESCENT PSYCHIATRY -year: 2015 -type: article -doi: 10.1007/s00787-015-0729-x ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_ottino-gonzalez_brain_2022.md b/_collections/_biblio/platform/platform_ottino-gonzalez_brain_2022.md deleted file mode 100644 index 55eac2b..0000000 --- a/_collections/_biblio/platform/platform_ottino-gonzalez_brain_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jonatan Ottino-González et al. -title: Brain structural covariance network differences in adults with alcohol dependence and heavy-drinking adolescents -journal: Addiction -year: 2022 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/add.15772 -doi: 10.1111/add.15772 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_owens_bayesian_2021.md b/_collections/_biblio/platform/platform_owens_bayesian_2021.md deleted file mode 100644 index dd333d7..0000000 --- a/_collections/_biblio/platform/platform_owens_bayesian_2021.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Max Owens et al. -title: Bayesian Causal Network Modeling Suggests Adolescent Cannabis Use Promotes Accelerated Prefrontal Cortical Thinning -year: 2021 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_owens_bayesian_2022.md b/_collections/_biblio/platform/platform_owens_bayesian_2022.md deleted file mode 100644 index 0392fe9..0000000 --- a/_collections/_biblio/platform/platform_owens_bayesian_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Max Owens et al. -title: Bayesian causal network modeling suggests adolescent cannabis use accelerates prefrontal cortical thinning -journal: Translational Psychiatry -year: 2022 -type: article -url: https -//www.nature.com/articles/s41398-022-01956-4 -doi: 10.1038/s41398-022-01956-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_pagano_arc_2023.md b/_collections/_biblio/platform/platform_pagano_arc_2023.md deleted file mode 100644 index 428ffd3..0000000 --- a/_collections/_biblio/platform/platform_pagano_arc_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Roberto Pagano et al. -title: Arc controls alcohol cue relapse by a central amygdala mechanism -journal: Molecular Psychiatry -year: 2023 -type: article -url: https -//www.nature.com/articles/s41380-022-01849-4 -doi: 10.1038/s41380-022-01849-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_papanastasiou_examination_2020-1.md b/_collections/_biblio/platform/platform_papanastasiou_examination_2020-1.md deleted file mode 100644 index 5dbc6b0..0000000 --- a/_collections/_biblio/platform/platform_papanastasiou_examination_2020-1.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Evangelos Papanastasiou et al. -title: Examination of the neural basis of psychotic-like experiences in adolescence during processing of emotional faces -journal: Scientific Reports -year: 2020 -type: article -url: https -//www.nature.com/articles/s41598-020-62026-7 -doi: 10.1038/s41598-020-62026-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_papanastasiou_examination_2020.md b/_collections/_biblio/platform/platform_papanastasiou_examination_2020.md deleted file mode 100644 index 476e26c..0000000 --- a/_collections/_biblio/platform/platform_papanastasiou_examination_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Evangelos Papanastasiou et al. -title: Examination of the neural basis of psychotic-like experiences in adolescenceduring processing of emotional faces -journal: Scientific Reports -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_penninck_immune-related_2021.md b/_collections/_biblio/platform/platform_penninck_immune-related_2021.md deleted file mode 100644 index 92ab400..0000000 --- a/_collections/_biblio/platform/platform_penninck_immune-related_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lukas Penninck et al. -title: Immune-Related Genetic Overlap Between Regional Gray Matter Reductions and Psychiatric Symptoms in Adolescents, and Gene-Set Validation in a Translational Model -journal: Frontiers in Systems Neuroscience -year: 2021 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fnsys.2021.725413 -doi: 10.3389/fnsys.2021.725413 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_peres_diffusion-weighted_2016.md b/_collections/_biblio/platform/platform_peres_diffusion-weighted_2016.md deleted file mode 100644 index e7d06dc..0000000 --- a/_collections/_biblio/platform/platform_peres_diffusion-weighted_2016.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Elodie Pérès et al. -title: Diffusion-weighted MR Imaging and Spectroscopy reveal brain tissue alterations induced by ionizing radiation in the mouse brain -year: 2016 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_peres_longitudinal_2018.md b/_collections/_biblio/platform/platform_peres_longitudinal_2018.md deleted file mode 100644 index 4bd412c..0000000 --- a/_collections/_biblio/platform/platform_peres_longitudinal_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Elodie Pérès et al. -title: Longitudinal Study of Irradiation-Induced Brain Microstructural Alterations With S-Index, a Diffusion MRI Biomarker, and MR Spectroscopy -journal: International Journal of Radiation Oncology, Biology, Physics -year: 2018 -type: article -doi: 10.1016/j.ijrobp.2018.01.070 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_perkins_assessing_2022.md b/_collections/_biblio/platform/platform_perkins_assessing_2022.md deleted file mode 100644 index 092e027..0000000 --- a/_collections/_biblio/platform/platform_perkins_assessing_2022.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Emily Perkins et al. -title: Assessing general versus specific liability for externalizing problems in adolescence - Concurrent and prospective prediction of symptoms of conduct disorder, ADHD, and substance use -journal: Journal of Psychopathology and Clinical Science -year: 2022 -type: article -doi: 10.1037/abn0000743 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_piguet_irritability_2021.md b/_collections/_biblio/platform/platform_piguet_irritability_2021.md deleted file mode 100644 index 2367136..0000000 --- a/_collections/_biblio/platform/platform_piguet_irritability_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Camille Piguet et al. -title: Irritability Is Associated With Decreased Cortical Surface Area and Anxiety With Decreased Gyrification During Brain Development -journal: Frontiers in Psychiatry -year: 2021 -type: article -doi: 10.3389/fpsyt.2021.744419 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_pijnenburg_autistic_2023.md b/_collections/_biblio/platform/platform_pijnenburg_autistic_2023.md deleted file mode 100644 index 45d7423..0000000 --- a/_collections/_biblio/platform/platform_pijnenburg_autistic_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lisa Pijnenburg et al. -title: Autistic traits and alcohol use in adolescents within the general population -journal: European Child \& Adolescent Psychiatry -year: 2023 -type: article -url: https -//doi.org/10.1007/s00787-022-01970-3 -doi: 10.1007/s00787-022-01970-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_poiret_attention-gated_2024.md b/_collections/_biblio/platform/platform_poiret_attention-gated_2024.md deleted file mode 100644 index a98be66..0000000 --- a/_collections/_biblio/platform/platform_poiret_attention-gated_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Clement Poiret et al. -title: Attention-gated 3D CapsNet for robust hippocampal segmentation -journal: Journal of Medical Imaging (Bellingham, Wash.) -year: 2024 -type: article -doi: 10.1117/1.JMI.11.1.014003 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_poiret_can_2023.md b/_collections/_biblio/platform/platform_poiret_can_2023.md deleted file mode 100644 index dd5c50a..0000000 --- a/_collections/_biblio/platform/platform_poiret_can_2023.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Clement Poiret et al. -title: Can we Agree? On the Rashomon Effect and the Reliability of Post-Hoc Explainable AI -year: 2023 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_poiret_fast_2023.md b/_collections/_biblio/platform/platform_poiret_fast_2023.md deleted file mode 100644 index ea4cb51..0000000 --- a/_collections/_biblio/platform/platform_poiret_fast_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Clement Poiret et al. -title: A fast and robust hippocampal subfields segmentation - HSF revealing lifespan volumetric dynamics -journal: Frontiers in Neuroinformatics -year: 2023 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2023.1130845 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_price_examination_2021.md b/_collections/_biblio/platform/platform_price_examination_2021.md deleted file mode 100644 index 708e3a0..0000000 --- a/_collections/_biblio/platform/platform_price_examination_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Matthew Price et al. -title: Examination of the association between exposure to childhood maltreatment and brain structure in young adults - a machine learning analysis -journal: Neuropsychopharmacology -year: 2021 -type: article -url: https -//www.nature.com/articles/s41386-021-00987-7 -doi: 10.1038/s41386-021-00987-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_prignitz_role_2023.md b/_collections/_biblio/platform/platform_prignitz_role_2023.md deleted file mode 100644 index 2b38be5..0000000 --- a/_collections/_biblio/platform/platform_prignitz_role_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Maren Prignitz et al. -title: The Role of Empathy in Alcohol Use of Bullying Perpetrators and Victims - Lower Personal Empathic Distress Makes Male Perpetrators of Bullying More Vulnerable to Alcohol Use -journal: International Journal of Environmental Research and Public Health -year: 2023 -type: article -url: https -//www.mdpi.com/1660-4601/20/13/6286 -doi: 10.3390/ijerph20136286 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_qi_differing_2023.md b/_collections/_biblio/platform/platform_qi_differing_2023.md deleted file mode 100644 index cb6378d..0000000 --- a/_collections/_biblio/platform/platform_qi_differing_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lu Qi et al. -title: Differing impact of the COVID-19 pandemic on youth mental health - combined population and clinical study -journal: BJPsych Open -year: 2023 -type: article -url: https -//www.cambridge.org/core/journals/bjpsych-open/article/differing-impact-of-the-covid19-pandemic-on-youth-mental-health-combined-population-and-clinical-study/939EDB00D962E84F86DC362C16B82A14# -doi: 10.1192/bjo.2023.601 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_qi_reward_2021.md b/_collections/_biblio/platform/platform_qi_reward_2021.md deleted file mode 100644 index 213dbbf..0000000 --- a/_collections/_biblio/platform/platform_qi_reward_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Shile Qi et al. -title: Reward Processing in Novelty Seekers - A Transdiagnostic Psychiatric Imaging Biomarker -journal: Biological Psychiatry -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0006322321000780 -doi: 10.1016/j.biopsych.2021.01.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_rane_structural_2022.md b/_collections/_biblio/platform/platform_rane_structural_2022.md deleted file mode 100644 index f77fcec..0000000 --- a/_collections/_biblio/platform/platform_rane_structural_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Roshan Rane et al. -title: Structural differences in adolescent brains can predict alcohol misuse -journal: eLife -year: 2022 -type: article -url: https -//doi.org/10.7554/eLife.77545 -doi: 10.7554/eLife.77545 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_renard_comparison_2010.md b/_collections/_biblio/platform/platform_renard_comparison_2010.md deleted file mode 100644 index 3280d2c..0000000 --- a/_collections/_biblio/platform/platform_renard_comparison_2010.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Félix Renard et al. -title: Comparison of interpolation methods for angular resampling of diffusion weighted images -year: 2010 -type: inproceedings -booktitle: 2010 2nd International Conference on Image Processing Theory, Tools and Applications ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_robinson_association_2020.md b/_collections/_biblio/platform/platform_robinson_association_2020.md deleted file mode 100644 index 700d366..0000000 --- a/_collections/_biblio/platform/platform_robinson_association_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lauren Robinson et al. -title: Association of Genetic and Phenotypic Assessments With Onset of Disordered Eating Behaviors and Comorbid Mental Health Problems Among Adolescents -journal: JAMA Network Open -year: 2020 -type: article -url: https -//doi.org/10.1001/jamanetworkopen.2020.26874 -doi: 10.1001/jamanetworkopen.2020.26874 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_rosenthal_relationship_2020.md b/_collections/_biblio/platform/platform_rosenthal_relationship_2020.md deleted file mode 100644 index f9ad3ff..0000000 --- a/_collections/_biblio/platform/platform_rosenthal_relationship_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: A Rosenthal et al. -title: THE RELATIONSHIP BETWEEN AMYGDALA NEURAL ACTIVATION IN RESPONSE TO EMOTIONAL STIMULI WITH DEPRESSIVE SYMPTOMS AND PROBLEMATIC DRINKING -year: 2020 -type: inproceedings -booktitle: Alcoholism-clinical and experimental research ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_roser_188_2023.md b/_collections/_biblio/platform/platform_roser_188_2023.md deleted file mode 100644 index 7b18ce2..0000000 --- a/_collections/_biblio/platform/platform_roser_188_2023.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Mathilde Roser et al. -title: 188. Cerebellar Vermis and Depressive Symptoms in Bipolar Disorder -journal: Biological Psychiatry -year: 2023 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_schumann_satellite_2021.md b/_collections/_biblio/platform/platform_schumann_satellite_2021.md deleted file mode 100644 index 8f258df..0000000 --- a/_collections/_biblio/platform/platform_schumann_satellite_2021.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Gunter Schumann et al. -title: Satellite Imaging of Global Urbanicity relates to Brain and Behavior in Young People -year: 2021 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_scott_prospective_2019.md b/_collections/_biblio/platform/platform_scott_prospective_2019.md deleted file mode 100644 index bfa8a50..0000000 --- a/_collections/_biblio/platform/platform_scott_prospective_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jan Scott et al. -title: Prospective cohort study of early biosignatures of response to lithium in bipolar-I-disorders - overview of the H2020-funded R-LiNK initiative -journal: International Journal of Bipolar Disorders -year: 2019 -type: article -url: https -//journalbipolardisorders.springeropen.com/articles/10.1186/s40345-019-0156-x -doi: 10.1186/s40345-019-0156-x ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_sibilia_relationship_2024.md b/_collections/_biblio/platform/platform_sibilia_relationship_2024.md deleted file mode 100644 index 320e448..0000000 --- a/_collections/_biblio/platform/platform_sibilia_relationship_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Francesca Sibilia et al. -title: The relationship between negative life events and cortical structural connectivity in adolescents -journal: IBRO Neuroscience Reports -year: 2024 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2667242124000101 -doi: 10.1016/j.ibneur.2024.01.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_spechler_cannabis_2015.md b/_collections/_biblio/platform/platform_spechler_cannabis_2015.md deleted file mode 100644 index 091b8e6..0000000 --- a/_collections/_biblio/platform/platform_spechler_cannabis_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Philip Spechler et al. -title: Cannabis use in early adolescence - Evidence of amygdala hypersensitivity to signals of threat -journal: DEVELOPMENTAL COGNITIVE NEUROSCIENCE -year: 2015 -type: article -doi: 10.1016/j.dcn.2015.08.007 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_spechler_longitudinal_2020.md b/_collections/_biblio/platform/platform_spechler_longitudinal_2020.md deleted file mode 100644 index 1ae50e0..0000000 --- a/_collections/_biblio/platform/platform_spechler_longitudinal_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Philip Spechler et al. -title: Longitudinal associations between amygdala reactivity and cannabis use in a large sample of adolescents -journal: Psychopharmacology -year: 2020 -type: article -url: https -//doi.org/10.1007/s00213-020-05624-7 -doi: 10.1007/s00213-020-05624-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_stringaris_brains_2015.md b/_collections/_biblio/platform/platform_stringaris_brains_2015.md deleted file mode 100644 index 56ab978..0000000 --- a/_collections/_biblio/platform/platform_stringaris_brains_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Argyris Stringaris et al. -title: The Brain's Response to Reward Anticipation and Depression in Adolescence - Dimensionality, Specificity, and Longitudinal Predictions in a Community-Based Sample -journal: AMERICAN JOURNAL OF PSYCHIATRY -year: 2015 -type: article -doi: 10.1176/appi.ajp.2015.14101298 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_sun_associations_2023.md b/_collections/_biblio/platform/platform_sun_associations_2023.md deleted file mode 100644 index b32bdbb..0000000 --- a/_collections/_biblio/platform/platform_sun_associations_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yan Sun et al. -title: Associations of DNA Methylation With Behavioral Problems, Gray Matter Volumes, and Negative Life Events Across Adolescence - Evidence From the Longitudinal IMAGEN Study -journal: Biological Psychiatry -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0006322322013567 -doi: 10.1016/j.biopsych.2022.06.012 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_sun_manifold-based_2019.md b/_collections/_biblio/platform/platform_sun_manifold-based_2019.md deleted file mode 100644 index 36f7178..0000000 --- a/_collections/_biblio/platform/platform_sun_manifold-based_2019.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zhong Sun et al. -title: Manifold-based exploration of the links between cortical morphology and functional architecture -year: 2019 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_sun_manifold-based_2020.md b/_collections/_biblio/platform/platform_sun_manifold-based_2020.md deleted file mode 100644 index 878986d..0000000 --- a/_collections/_biblio/platform/platform_sun_manifold-based_2020.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: ZY Sun et al. -title: Manifold-based exploration of the links between precentral sulcus interruptions and language-associated area 55b -year: 2020 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_tasserie_pypreclin_2020.md b/_collections/_biblio/platform/platform_tasserie_pypreclin_2020.md deleted file mode 100644 index 459c9dd..0000000 --- a/_collections/_biblio/platform/platform_tasserie_pypreclin_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jordy Tasserie et al. -title: Pypreclin - An automatic pipeline for macaque functional MRI preprocessing -journal: NeuroImage -year: 2020 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_toenders_predicting_2022.md b/_collections/_biblio/platform/platform_toenders_predicting_2022.md deleted file mode 100644 index b1b2b10..0000000 --- a/_collections/_biblio/platform/platform_toenders_predicting_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Yara Toenders et al. -title: Predicting Depression Onset in Young People Based on Clinical, Cognitive, Environmental, and Neurobiological Data -journal: Biological Psychiatry - Cognitive Neuroscience and Neuroimaging -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2451902221000823 -doi: 10.1016/j.bpsc.2021.03.005 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_tschorn_differential_2021.md b/_collections/_biblio/platform/platform_tschorn_differential_2021.md deleted file mode 100644 index 85e2374..0000000 --- a/_collections/_biblio/platform/platform_tschorn_differential_2021.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Mira Tschorn et al. -title: Differential predictors for alcohol use in adolescents as a function of familial risk -journal: Translational psychiatry -year: 2021 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_vulser_chronotype_2023.md b/_collections/_biblio/platform/platform_vulser_chronotype_2023.md deleted file mode 100644 index ccc9b04..0000000 --- a/_collections/_biblio/platform/platform_vulser_chronotype_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Hélène Vulser et al. -title: Chronotype, Longitudinal Volumetric Brain Variations Throughout Adolescence, and Depressive Symptom Development -journal: Journal of the American Academy of Child \& Adolescent Psychiatry -year: 2023 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0890856722002982 -doi: 10.1016/j.jaac.2022.06.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_wang_functional_2021.md b/_collections/_biblio/platform/platform_wang_functional_2021.md deleted file mode 100644 index 9dc13de..0000000 --- a/_collections/_biblio/platform/platform_wang_functional_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Haiyan Wang et al. -title: Functional Connectivity Predicts Individual Development of Inhibitory Control during Adolescence -journal: Cerebral Cortex -year: 2021 -type: article -url: https -//doi.org/10.1093/cercor/bhaa383 -doi: 10.1093/cercor/bhaa383 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_wendel_residual_2021.md b/_collections/_biblio/platform/platform_wendel_residual_2021.md deleted file mode 100644 index f4e3a2b..0000000 --- a/_collections/_biblio/platform/platform_wendel_residual_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Lena Wendel et al. -title: Residual effects of cannabis-use on neuropsychological functioning -journal: Cognitive Development -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0885201421000678 -doi: 10.1016/j.cogdev.2021.101072 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_wesarg_interaction_2021.md b/_collections/_biblio/platform/platform_wesarg_interaction_2021.md deleted file mode 100644 index bae9cea..0000000 --- a/_collections/_biblio/platform/platform_wesarg_interaction_2021.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Christiane Wesarg et al. -title: The interaction of child abuse and rs1360780 of the FKBP5 gene is associated with amygdala resting-state functional connectivity in young adults -journal: Human brain mapping -year: 2021 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xiang_association_2023.md b/_collections/_biblio/platform/platform_xiang_association_2023.md deleted file mode 100644 index ffa5677..0000000 --- a/_collections/_biblio/platform/platform_xiang_association_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Shitong Xiang et al. -title: Association between vmPFC gray matter volume and smoking initiation in adolescents -journal: Nature Communications -year: 2023 -type: article -url: https -//www.nature.com/articles/s41467-023-40079-2 -doi: 10.1038/s41467-023-40079-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xie_reward_2021.md b/_collections/_biblio/platform/platform_xie_reward_2021.md deleted file mode 100644 index 609bad5..0000000 --- a/_collections/_biblio/platform/platform_xie_reward_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Chao Xie et al. -title: Reward Versus Nonreward Sensitivity of the Medial Versus Lateral Orbitofrontal Cortex Relates to the Severity of Depressive Symptoms -journal: Biological Psychiatry - Cognitive Neuroscience and Neuroimaging -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2451902220302548 -doi: 10.1016/j.bpsc.2020.08.017 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xie_shared_2023.md b/_collections/_biblio/platform/platform_xie_shared_2023.md deleted file mode 100644 index d85e751..0000000 --- a/_collections/_biblio/platform/platform_xie_shared_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Chao Xie et al. -title: A shared neural basis underlying psychiatric comorbidity -journal: Nature Medicine -year: 2023 -type: article -url: https -//www.nature.com/articles/s41591-023-02317-4 -doi: 10.1038/s41591-023-02317-4 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xu_causal_2022.md b/_collections/_biblio/platform/platform_xu_causal_2022.md deleted file mode 100644 index 8e6c84f..0000000 --- a/_collections/_biblio/platform/platform_xu_causal_2022.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jiayuan Xu et al. -title: A causal association of ANKRD37 with human hippocampal volume -journal: Molecular Psychiatry -year: 2022 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xu_global_2022.md b/_collections/_biblio/platform/platform_xu_global_2022.md deleted file mode 100644 index 00536aa..0000000 --- a/_collections/_biblio/platform/platform_xu_global_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Jiayuan Xu et al. -title: Global urbanicity is associated with brain and behaviour in young people -journal: Nature Human Behaviour -year: 2022 -type: article -url: https -//www.nature.com/articles/s41562-021-01204-7 -doi: 10.1038/s41562-021-01204-7 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_xue_covariation_2023.md b/_collections/_biblio/platform/platform_xue_covariation_2023.md deleted file mode 100644 index 5656878..0000000 --- a/_collections/_biblio/platform/platform_xue_covariation_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Kaizhong Xue et al. -title: Covariation of preadult environmental exposures, adult brain imaging phenotypes, and adult personality traits -journal: Molecular Psychiatry -year: 2023 -type: article -url: https -//www.nature.com/articles/s41380-023-02261-2 -doi: 10.1038/s41380-023-02261-2 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_yip_brain_2023.md b/_collections/_biblio/platform/platform_yip_brain_2023.md deleted file mode 100644 index 38ac0ee..0000000 --- a/_collections/_biblio/platform/platform_yip_brain_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Sarah Yip et al. -title: Brain Networks and Adolescent Alcohol Use -journal: JAMA Psychiatry -year: 2023 -type: article -url: https -//doi.org/10.1001/jamapsychiatry.2023.2949 -doi: 10.1001/jamapsychiatry.2023.2949 ---- \ No newline at end of file diff --git a/_collections/_biblio/platform/platform_zhang_development_2021.md b/_collections/_biblio/platform/platform_zhang_development_2021.md deleted file mode 100644 index 0baeca1..0000000 --- a/_collections/_biblio/platform/platform_zhang_development_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: platform -bestof: false -author: Zuo Zhang et al. -title: Development of Disordered Eating Behaviors and Comorbid Depressive Symptoms in Adolescence - Neural and Psychopathological Predictors -journal: Biological Psychiatry -year: 2021 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0006322320316723 -doi: 10.1016/j.biopsych.2020.06.003 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_ambroise_multi-view_2023.md b/_collections/_biblio/signature/signature_ambroise_multi-view_2023.md deleted file mode 100644 index 0cd71cd..0000000 --- a/_collections/_biblio/signature/signature_ambroise_multi-view_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Corentin Ambroise et al. -title: Multi-View Variational Autoencoders Allow for Interpretability Leveraging Digital Avatars - Application to the HBN Cohort -year: 2023 -type: inproceedings -doi: 10.1109/ISBI53787.2023.10230552 -booktitle: IEEE 20th International Symposium on Biomedical Imaging (ISBI) 2023 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_auriau_supervised_2024.md b/_collections/_biblio/signature/signature_auriau_supervised_2024.md deleted file mode 100644 index 73ce570..0000000 --- a/_collections/_biblio/signature/signature_auriau_supervised_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Pierre Auriau et al. -title: Supervised Diagnosis Prediction from Cortical Sulci - Toward the Discovery of Eurodevelopmental Biomarkers in Mental Disorders -year: 2024 -type: inproceedings -url: https -//hal.science/hal-04494994 -booktitle: 21st IEEE International Symposium on Biomedical Imaging (ISBI 2024) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_barbano_contrastive_2023.md b/_collections/_biblio/signature/signature_barbano_contrastive_2023.md deleted file mode 100644 index dddffb2..0000000 --- a/_collections/_biblio/signature/signature_barbano_contrastive_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Carlo Barbano et al. -title: Contrastive learning for regression in multi-site brain age prediction -year: 2023 -type: inproceedings -url: http -//arxiv.org/abs/2211.08326 -doi: 10.48550/arXiv.2211.08326 -booktitle: IEEE 20th International Symposium on Biomedical Imaging (ISBI) 2023 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_bourgin_hyper-responsivity_2015.md b/_collections/_biblio/signature/signature_bourgin_hyper-responsivity_2015.md deleted file mode 100644 index 6ded06d..0000000 --- a/_collections/_biblio/signature/signature_bourgin_hyper-responsivity_2015.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J. Bourgin et al. -title: Hyper-responsivity to stress in rats is associated with a large increase in amygdala volume. A 7T MRI study -journal: European Neuropsychopharmacology - The Journal of the European College of Neuropsychopharmacology -year: 2015 -type: article -doi: 10.1016/j.euroneuro.2015.02.010 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_bourgin_phenotypes_2014.md b/_collections/_biblio/signature/signature_bourgin_phenotypes_2014.md deleted file mode 100644 index 50e1d0a..0000000 --- a/_collections/_biblio/signature/signature_bourgin_phenotypes_2014.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Julie Bourgin et al. -title: Phénotypes cliniques précoces et recherche de biomarqueurs stratégiques - les fondements d'une psychiatrie personnalisée -journal: L'information psychiatrique -year: 2014 -type: article -url: http -//www.cairn.info/article.php?ID_ARTICLE=INPSY_8910_0781 -doi: 10.1684/ipe.2013.1128 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_bourgin_predicting_2019.md b/_collections/_biblio/signature/signature_bourgin_predicting_2019.md deleted file mode 100644 index 44a0274..0000000 --- a/_collections/_biblio/signature/signature_bourgin_predicting_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Julie Bourgin et al. -title: Predicting the individual risk of psychosis conversion in at-risk mental state (ARMS) - a multivariate model reveals the influence of nonpsychotic prodromal symptoms -journal: European Child \& Adolescent Psychiatry -year: 2019 -type: article -doi: 10.1007/s00787-019-01461-y ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_cachia_cortical_2008.md b/_collections/_biblio/signature/signature_cachia_cortical_2008.md deleted file mode 100644 index 8c1c4f4..0000000 --- a/_collections/_biblio/signature/signature_cachia_cortical_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Arnaud Cachia et al. -title: Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations -journal: NeuroImage -year: 2008 -type: article -doi: 10.1016/j.neuroimage.2007.08.049 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_cachia_sulcus-based_2005.md b/_collections/_biblio/signature/signature_cachia_sulcus-based_2005.md deleted file mode 100644 index 3c0790b..0000000 --- a/_collections/_biblio/signature/signature_cachia_sulcus-based_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: A. Cachia et al. -title: Sulcus-based morphometry of heteromodal cortex in schizophrenia patients with resistant auditory hallucinations. -year: 2005 -type: inproceedings -booktitle: Proc. 11th HBM CD-Rom Neuroimage vol 26 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_ching_what_2020.md b/_collections/_biblio/signature/signature_ching_what_2020.md deleted file mode 100644 index 30cfd2e..0000000 --- a/_collections/_biblio/signature/signature_ching_what_2020.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Christopher Ching et al. -title: What we learn about bipolar disorder from large-scale neuroimaging - Findings and future directions from the ENIGMA Bipolar Disorder Working Group -journal: Human Brain Mapping -year: 2020 -type: article -doi: 10.1002/hbm.25098 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_claude_will_2020.md b/_collections/_biblio/signature/signature_claude_will_2020.md deleted file mode 100644 index eee644f..0000000 --- a/_collections/_biblio/signature/signature_claude_will_2020.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Laurie-Anne Claude et al. -title: Will machine learning applied to neuroimaging in bipolar disorder help the clinician? A critical review and methodological suggestions -journal: Bipolar Disorders -year: 2020 -type: article -doi: 10.1111/bdi.12895 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_da_mota_calcul_2014.md b/_collections/_biblio/signature/signature_da_mota_calcul_2014.md deleted file mode 100644 index 996d10e..0000000 --- a/_collections/_biblio/signature/signature_da_mota_calcul_2014.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Da Mota et al. -title: Le calcul haute performance pour l'analyse de données de neuroimagerie-génétique en grandes dimensions -year: 2014 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_da_mota_permuted_2014.md b/_collections/_biblio/signature/signature_da_mota_permuted_2014.md deleted file mode 100644 index cfdfccd..0000000 --- a/_collections/_biblio/signature/signature_da_mota_permuted_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Da Mota et al. -title: Permuted Voxelwise Genome-Wide Association -year: 2014 -type: inproceedings -booktitle: Human Brain Mapping ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_damon_discriminating_2008.md b/_collections/_biblio/signature/signature_damon_discriminating_2008.md deleted file mode 100644 index 6f6fe38..0000000 --- a/_collections/_biblio/signature/signature_damon_discriminating_2008.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Cécilia Damon et al. -title: Discriminating between populations of subjects based on FMRI data using sparse features selection and SRDA classifier -year: 2008 -type: inproceedings -booktitle: MICCAI Analysis of Functional Medical Images Workshop ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_damon_structured_2011.md b/_collections/_biblio/signature/signature_damon_structured_2011.md deleted file mode 100644 index 6b1bbd6..0000000 --- a/_collections/_biblio/signature/signature_damon_structured_2011.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: C. Damon et al. -title: Structured Multivariate Pattern Classification to Detect MRI Markers for an Early Diagnosis of Alzheimer's Disease -year: 2011 -type: inproceedings -url: http -//dl.acm.org/citation.cfm?id=2353108.2353268 -doi: 10.1109/ICMLA.2011.185 -booktitle: 2011 10th International Conference on Machine Learning and Applications and Workshops ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_guio_loss_2014.md b/_collections/_biblio/signature/signature_de_guio_loss_2014.md deleted file mode 100644 index 5ab6090..0000000 --- a/_collections/_biblio/signature/signature_de_guio_loss_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: François De Guio et al. -title: Loss of Venous Integrity in Cerebral Small Vessel Disease - A 7-T MRI Study in Cerebral Autosomal-Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy (CADASIL) -journal: Stroke; a Journal of Cerebral Circulation -year: 2014 -type: article -doi: 10.1161/STROKEAHA.114.005726 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_guio_vivo_2014.md b/_collections/_biblio/signature/signature_de_guio_vivo_2014.md deleted file mode 100644 index 27c25aa..0000000 --- a/_collections/_biblio/signature/signature_de_guio_vivo_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: François De Guio et al. -title: In Vivo High-Resolution 7 Tesla MRI Shows Early and Diffuse Cortical Alterations in CADASIL -journal: PloS One -year: 2014 -type: article -doi: 10.1371/journal.pone.0106311 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_pierrefeu_identifying_2018.md b/_collections/_biblio/signature/signature_de_pierrefeu_identifying_2018.md deleted file mode 100644 index a006038..0000000 --- a/_collections/_biblio/signature/signature_de_pierrefeu_identifying_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: A. Pierrefeu et al. -title: Identifying a neuroanatomical signature of schizophrenia, reproducible across sites and stages, using machine learning with structured sparsity -journal: Acta Psychiatrica Scandinavica -year: 2018 -type: article -doi: 10.1111/acps.12964 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_pierrefeu_interpretable_2018.md b/_collections/_biblio/signature/signature_de_pierrefeu_interpretable_2018.md deleted file mode 100644 index 4d73317..0000000 --- a/_collections/_biblio/signature/signature_de_pierrefeu_interpretable_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Amicie Pierrefeu et al. -title: Interpretable and stable prediction of schizophrenia on a large multisite dataset using machine learning with structured sparsity -year: 2018 -type: inproceedings -url: https -//ieeexplore.ieee.org/document/8423946/ -doi: 10.1109/PRNI.2018.8423946 -booktitle: 2018 International Workshop on Pattern Recognition in Neuroimaging (PRNI) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_pierrefeu_prediction_2018.md b/_collections/_biblio/signature/signature_de_pierrefeu_prediction_2018.md deleted file mode 100644 index 4ff42eb..0000000 --- a/_collections/_biblio/signature/signature_de_pierrefeu_prediction_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Amicie Pierrefeu et al. -title: Prediction of activation patterns preceding hallucinations in patients with schizophrenia using machine learning with structured sparsity -journal: Human Brain Mapping -year: 2018 -type: article -url: http -//onlinelibrary.wiley.com/doi/10.1002/hbm.23953/abstract -doi: 10.1002/hbm.23953 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_de_pierrefeu_structured_2018.md b/_collections/_biblio/signature/signature_de_pierrefeu_structured_2018.md deleted file mode 100644 index df6e817..0000000 --- a/_collections/_biblio/signature/signature_de_pierrefeu_structured_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Amicie Pierrefeu et al. -title: Structured Sparse Principal Components Analysis With the TV-Elastic Net Penalty -journal: IEEE Transactions on Medical Imaging -year: 2018 -type: article -doi: 10.1109/TMI.2017.2749140 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dubois_asynchrony_2008.md b/_collections/_biblio/signature/signature_dubois_asynchrony_2008.md deleted file mode 100644 index 3a7d650..0000000 --- a/_collections/_biblio/signature/signature_dubois_asynchrony_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jessica Dubois et al. -title: Asynchrony of the early maturation of white matter bundles in healthy infants - quantitative landmarks revealed noninvasively by diffusion tensor imaging -journal: Human Brain Mapping -year: 2008 -type: article -doi: 10.1002/hbm.20363 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dubois_automated_2007.md b/_collections/_biblio/signature/signature_dubois_automated_2007.md deleted file mode 100644 index b09ba9c..0000000 --- a/_collections/_biblio/signature/signature_dubois_automated_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Albertine Dubois et al. -title: Automated three-dimensional analysis of histological and autoradiographic rat brain sections - application to an activation study -journal: Journal of Cerebral Blood Flow and Metabolism - Official Journal of the International Society of Cerebral Blood Flow and Metabolism -year: 2007 -type: article -doi: 10.1038/sj.jcbfm.9600470 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dubois_predictive_2014.md b/_collections/_biblio/signature/signature_dubois_predictive_2014.md deleted file mode 100644 index 442cd2a..0000000 --- a/_collections/_biblio/signature/signature_dubois_predictive_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: M. Dubois et al. -title: Predictive support recovery with TV-Elastic Net penalty and logistic regression - An application to structural MRI -year: 2014 -type: inproceedings -doi: 10.1109/PRNI.2014.6858517 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dubois_quantitative_2008.md b/_collections/_biblio/signature/signature_dubois_quantitative_2008.md deleted file mode 100644 index 5d01562..0000000 --- a/_collections/_biblio/signature/signature_dubois_quantitative_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Albertine Dubois et al. -title: Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes - application to unilateral visual stimulation -journal: NeuroImage -year: 2008 -type: article -doi: 10.1016/j.neuroimage.2007.11.054 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_agent-based_2001.md b/_collections/_biblio/signature/signature_duchesnay_agent-based_2001.md deleted file mode 100644 index 6296e7e..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_agent-based_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: An agent-based implementation of irregular pyramid for distributed image segmentation -year: 2001 -type: inproceedings -booktitle: Emerging Technologies and Factory Automation, 2001. Proceedings. 2001 8th IEEE International Conference on ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_architecture_1999.md b/_collections/_biblio/signature/signature_duchesnay_architecture_1999.md deleted file mode 100644 index 2baa237..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_architecture_1999.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Architecture intelligente distribuée pour la vision artificielle -year: 1999 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_classification_2007.md b/_collections/_biblio/signature/signature_duchesnay_classification_2007.md deleted file mode 100644 index c73a96b..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_classification_2007.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Classification based on cortical folding patterns -journal: IEEE Transactions on Medical Imaging -year: 2007 -type: article -doi: 10.1109/TMI.2007.892501 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_cooperative_2003.md b/_collections/_biblio/signature/signature_duchesnay_cooperative_2003.md deleted file mode 100644 index 7495cab..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_cooperative_2003.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Cooperative agents society organized as an irregular pyramid - A mammography segmentation application -journal: Pattern Recognition Letters -year: 2003 -type: article -url: http -//www.sciencedirect.com/science/article/pii/S0167865503000771 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_different_2018.md b/_collections/_biblio/signature/signature_duchesnay_different_2018.md deleted file mode 100644 index d26cb73..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_different_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Different Types of White Matter Hyperintensities in CADASIL -journal: Frontiers in Neurology -year: 2018 -type: article -doi: 10.3389/fneur.2018.00526 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_feature_2011.md b/_collections/_biblio/signature/signature_duchesnay_feature_2011.md deleted file mode 100644 index 5f81c5f..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_feature_2011.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Feature selection and classification of imbalanced datasets - Application to PET images of children with autistic spectrum disorders -journal: NeuroImage -year: 2011 -type: article -url: http -//www.sciencedirect.com/science/article/pii/S105381191100499X -doi: 10.1016/j.neuroimage.2011.05.011 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_guessing_2004.md b/_collections/_biblio/signature/signature_duchesnay_guessing_2004.md deleted file mode 100644 index 83d3148..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_guessing_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Guessing the Sex from the Shapes of Cortical Folds -year: 2004 -type: inproceedings -booktitle: HBM, Budapest ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_irregular_2000.md b/_collections/_biblio/signature/signature_duchesnay_irregular_2000.md deleted file mode 100644 index 70abb62..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_irregular_2000.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: E. Duchesnay et al. -title: Irregular adaptative pyramid of agents for segmentation to interpretation of image -year: 2000 -type: inproceedings -doi: 10.1109/ICSMC.2000.886246 -booktitle: 2000 IEEE International Conference on Systems, Man, and Cybernetics ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_method_2010.md b/_collections/_biblio/signature/signature_duchesnay_method_2010.md deleted file mode 100644 index 83d459a..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_method_2010.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Method for Developing an Information Prediction Device, Use Thereof, and Corresponding Storage Medium and Apparatus -year: 2010 -type: patent -url: https -//patentscope.wipo.int/search/en/detail.jsf?docId=WO2010103248 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_method_nodate.md b/_collections/_biblio/signature/signature_duchesnay_method_nodate.md deleted file mode 100644 index aaa4191..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_method_nodate.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: E Duchesnay et al. -title: Method for Developing an Information Prediction Device, Use Thereof, and Corresponding Storage Medium and Apparatus -type: patent ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_methodes_2015-1.md b/_collections/_biblio/signature/signature_duchesnay_methodes_2015-1.md deleted file mode 100644 index ac58499..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_methodes_2015-1.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Méthodes de prédiction multivariées basées sur la neuroimagerie - application aux maladies psychiatriques -journal: Annales Médico-psychologiques, revue psychiatrique -year: 2015 -type: article -url: http -//www.sciencedirect.com/science/article/pii/S0003448715000621 -doi: 10.1016/j.amp.2015.03.002 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_methodes_2015.md b/_collections/_biblio/signature/signature_duchesnay_methodes_2015.md deleted file mode 100644 index 5c44966..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_methodes_2015.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Méthodes de prédiction multivariées basées sur la neuroimagerie - application aux maladies psychiatriques -journal: Annales Médico-psychologiques, revue psychiatrique -year: 2015 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_multiagent_2000.md b/_collections/_biblio/signature/signature_duchesnay_multiagent_2000.md deleted file mode 100644 index 6d816d2..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_multiagent_2000.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: A Multiagent System for a Cooperative and Distributed Vision System -year: 2000 -type: inproceedings -booktitle: Advances in Concurrent Engineering - CE2000 Proceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_neuroimaging_2020.md b/_collections/_biblio/signature/signature_duchesnay_neuroimaging_2020.md deleted file mode 100644 index e2b48bd..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_neuroimaging_2020.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Neuroimaging Signatures of Brain Disorders - Fighting Overfitting in Predictive Models -year: 2020 -type: thesis -url: https -//hal-cea.archives-ouvertes.fr/tel-03408786 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_population_2004.md b/_collections/_biblio/signature/signature_duchesnay_population_2004.md deleted file mode 100644 index 3199951..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_population_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edouard Duchesnay et al. -title: Population Classification Based on Structural Morphometry of Cortical Sulci -year: 2004 -type: inproceedings -booktitle: International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duchesnay_resolution_2000.md b/_collections/_biblio/signature/signature_duchesnay_resolution_2000.md deleted file mode 100644 index e066ca1..0000000 --- a/_collections/_biblio/signature/signature_duchesnay_resolution_2000.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: E. Duchesnay et al. -title: Résolution distribuée de conflits dans un réseau d'agents -year: 2000 -type: inproceedings -booktitle: 10ème Journées Neurosciences et Sciences de l'Ingénieur ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_duering_strategic_2014.md b/_collections/_biblio/signature/signature_duering_strategic_2014.md deleted file mode 100644 index 398842c..0000000 --- a/_collections/_biblio/signature/signature_duering_strategic_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Marco Duering et al. -title: Strategic white matter tracts for processing speed deficits in age-related small vessel disease -journal: Neurology -year: 2014 -type: article -doi: 10.1212/WNL.0000000000000475 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dufumier_conditional_2021.md b/_collections/_biblio/signature/signature_dufumier_conditional_2021.md deleted file mode 100644 index 525adb2..0000000 --- a/_collections/_biblio/signature/signature_dufumier_conditional_2021.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Dufumier et al. -title: Conditional Alignment and Uniformity for Contrastive Learning with Continuous Proxy Labels -year: 2021 -type: inproceedings -url: https -//hal.telecom-paris.fr/hal-03523114 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dufumier_contrastive_2021.md b/_collections/_biblio/signature/signature_dufumier_contrastive_2021.md deleted file mode 100644 index 1ed050d..0000000 --- a/_collections/_biblio/signature/signature_dufumier_contrastive_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Dufumier et al. -title: Contrastive Learning with Continuous Proxy Meta-Data for 3D MRI Classification -year: 2021 -type: inproceedings -url: https -//link.springer.com/chapter/10.1007%2F978-3-030-87196-3_6 -doi: 10.1007/978-3-030-87196-3_6 -booktitle: 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2021 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dufumier_exploring_2024.md b/_collections/_biblio/signature/signature_dufumier_exploring_2024.md deleted file mode 100644 index 00a991b..0000000 --- a/_collections/_biblio/signature/signature_dufumier_exploring_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: true -author: Benoit Dufumier et al. -title: Exploring the potential of representation and transfer learning for anatomical neuroimaging - Application to psychiatry -journal: NeuroImage -year: 2024 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811924001605 -doi: 10.1016/j.neuroimage.2024.120665 ---- diff --git a/_collections/_biblio/signature/signature_dufumier_integrating_2023.md b/_collections/_biblio/signature/signature_dufumier_integrating_2023.md deleted file mode 100644 index a1a0659..0000000 --- a/_collections/_biblio/signature/signature_dufumier_integrating_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Dufumier et al. -title: Integrating Prior Knowledge in Contrastive Learning with Kernel -year: 2023 -type: inproceedings -url: https -//telecom-paris.hal.science/hal-04111825 -booktitle: 40th International Conference on Machine Learning (ICML) 2023 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dufumier_openbhb_2022.md b/_collections/_biblio/signature/signature_dufumier_openbhb_2022.md deleted file mode 100644 index 581cfff..0000000 --- a/_collections/_biblio/signature/signature_dufumier_openbhb_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Dufumier et al. -title: OpenBHB - a Large-Scale Multi-Site Brain MRI Data-set for Age Prediction and Debiasing -journal: NeuroImage -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S1053811922007522 -doi: 10.1016/j.neuroimage.2022.119637 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dufumier_rethinking_2023.md b/_collections/_biblio/signature/signature_dufumier_rethinking_2023.md deleted file mode 100644 index 038808d..0000000 --- a/_collections/_biblio/signature/signature_dufumier_rethinking_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benoit Dufumier et al. -title: Rethinking Positive Sampling for Contrastive Learning with Kernel -year: 2023 -type: misc -url: http -//arxiv.org/abs/2206.01646 -doi: 10.48550/arXiv.2206.01646 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_dupont_prediction_2024.md b/_collections/_biblio/signature/signature_dupont_prediction_2024.md deleted file mode 100644 index 2031546..0000000 --- a/_collections/_biblio/signature/signature_dupont_prediction_2024.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Thibault Dupont et al. -title: Prediction of post-traumatic stress disorder in family members of ICU patients - a machine learning approach -journal: Intensive Care Medicine -year: 2024 -type: article -url: https -//doi.org/10.1007/s00134-023-07288-1 -doi: 10.1007/s00134-023-07288-1 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_elandaloussi_understanding_2023.md b/_collections/_biblio/signature/signature_elandaloussi_understanding_2023.md deleted file mode 100644 index 74abc3f..0000000 --- a/_collections/_biblio/signature/signature_elandaloussi_understanding_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Yannis Elandaloussi et al. -title: Understanding the relationship between cerebellar structure and social abilities -journal: Molecular Autism -year: 2023 -type: article -url: https -//doi.org/10.1186/s13229-023-00551-8 -doi: 10.1186/s13229-023-00551-8 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_favre_widespread_2019.md b/_collections/_biblio/signature/signature_favre_widespread_2019.md deleted file mode 100644 index fd2fb1d..0000000 --- a/_collections/_biblio/signature/signature_favre_widespread_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Pauline Favre et al. -title: Widespread white matter microstructural abnormalities in bipolar disorder - evidence from mega- and meta-analyses across 3033 individuals -journal: Neuropsychopharmacology -year: 2019 -type: article -url: https -//www.nature.com/articles/s41386-019-0485-6 -doi: 10.1038/s41386-019-0485-6 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_fouque_comparison_2013.md b/_collections/_biblio/signature/signature_fouque_comparison_2013.md deleted file mode 100644 index 4d31f6a..0000000 --- a/_collections/_biblio/signature/signature_fouque_comparison_2013.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Anne-Laure Fouque et al. -title: Comparison of Features for Voxel-Based Analysis and Classification of Anatomical Neuroimaging Data -year: 2013 -type: inproceedings -url: http -//dl.acm.org/citation.cfm?id=2552484.2552547 -doi: 10.1109/PRNI.2013.55 -booktitle: 2013 International Workshop on Pattern Recognition in Neuroimaging ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_fouque_voxelwise_2011.md b/_collections/_biblio/signature/signature_fouque_voxelwise_2011.md deleted file mode 100644 index 21b98f1..0000000 --- a/_collections/_biblio/signature/signature_fouque_voxelwise_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Anne-Laure Fouque et al. -title: Voxelwise multivariate statistics and brain-wide machine learning using the full diffusion tensor -year: 2011 -type: inproceedings -booktitle: MICCAI ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_fouquet_longitudinal_2009.md b/_collections/_biblio/signature/signature_fouquet_longitudinal_2009.md deleted file mode 100644 index 590e419..0000000 --- a/_collections/_biblio/signature/signature_fouquet_longitudinal_2009.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Marine Fouquet et al. -title: Longitudinal brain metabolic changes from amnestic mild cognitive impairment to Alzheimer's disease -journal: Brain - A Journal of Neurology -year: 2009 -type: article -doi: 10.1093/brain/awp132 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_fovet_decoding_2022.md b/_collections/_biblio/signature/signature_fovet_decoding_2022.md deleted file mode 100644 index 17ee1c8..0000000 --- a/_collections/_biblio/signature/signature_fovet_decoding_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Thomas Fovet et al. -title: Decoding Activity in Broca's Area Predicts the Occurrence of Auditory Hallucinations Across Subjects -journal: Biological Psychiatry -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0006322321015699 -doi: 10.1016/j.biopsych.2021.08.024 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_fraize_enhancing_2023.md b/_collections/_biblio/signature/signature_fraize_enhancing_2023.md deleted file mode 100644 index 17e0f05..0000000 --- a/_collections/_biblio/signature/signature_fraize_enhancing_2023.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Justine Fraize et al. -title: Enhancing fetal alcohol spectrum disorders diagnosis with a classifier based on the intracerebellar gradient of volumetric undersizing -journal: Human Brain Mapping -year: 2023 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1002/hbm.26348 -doi: 10.1002/hbm.26348 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_gesierich_features_2016.md b/_collections/_biblio/signature/signature_gesierich_features_2016.md deleted file mode 100644 index 2364050..0000000 --- a/_collections/_biblio/signature/signature_gesierich_features_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Benno Gesierich et al. -title: Features and Determinants of Lacune Shape - Relationship With Fiber Tracts and Perforating Arteries -journal: Stroke -year: 2016 -type: article -doi: 10.1161/STROKEAHA.116.012779 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_guen_regional_2017.md b/_collections/_biblio/signature/signature_guen_regional_2017.md deleted file mode 100644 index 55f71f9..0000000 --- a/_collections/_biblio/signature/signature_guen_regional_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Yann Guen et al. -title: Regional study of the genetic influence on the sulcal pits -year: 2017 -type: inproceedings -doi: 10.1109/ISBI.2017.7950472 -booktitle: 14th IEEE International Symposium on Biomedical Imaging, ISBI 2017, Melbourne, Australia, April 18-21, 2017 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_guillemot_multi-block_2013.md b/_collections/_biblio/signature/signature_guillemot_multi-block_2013.md deleted file mode 100644 index de49661..0000000 --- a/_collections/_biblio/signature/signature_guillemot_multi-block_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Vincent Guillemot et al. -title: A multi-block approach in imaging genetics -year: 2013 -type: inproceedings -booktitle: 9th International Imaging Genetics Conference ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_hadj-selem_continuation_2018.md b/_collections/_biblio/signature/signature_hadj-selem_continuation_2018.md deleted file mode 100644 index bf3ba50..0000000 --- a/_collections/_biblio/signature/signature_hadj-selem_continuation_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Fouad Hadj-Selem et al. -title: Continuation of Nesterov's Smoothing for Regression With Structured Sparsity in High-Dimensional Neuroimaging -journal: IEEE Transactions on Medical Imaging -year: 2018 -type: article -doi: 10.1109/TMI.2018.2829802 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_hadj-selem_supplementary_2018.md b/_collections/_biblio/signature/signature_hadj-selem_supplementary_2018.md deleted file mode 100644 index db23ed7..0000000 --- a/_collections/_biblio/signature/signature_hadj-selem_supplementary_2018.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Fouad Hadj-Selem et al. -title: Supplementary material - Continuation of Nesterov's Smoothing for Regression with Structured Sparsity in High-Dimensional Neuroimaging -year: 2018 -type: misc -url: https -//hal-cea.archives-ouvertes.fr/cea-01324021/document ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_hozer_lithium_2021.md b/_collections/_biblio/signature/signature_hozer_lithium_2021.md deleted file mode 100644 index b31444c..0000000 --- a/_collections/_biblio/signature/signature_hozer_lithium_2021.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Franz Hozer et al. -title: Lithium prevents grey matter atrophy in patients with bipolar disorder - an international multicenter study -journal: Psychological Medicine -year: 2021 -type: article -url: https -//www.cambridge.org/core/journals/psychological-medicine/article/abs/lithium-prevents-grey-matter-atrophy-in-patients-with-bipolar-disorder-an-international-multicenter-study/6267A7E11F17EFDF5857F06E4C233D4F -doi: 10.1017/S0033291719004112 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_iftimovici_asynchronous_2023.md b/_collections/_biblio/signature/signature_iftimovici_asynchronous_2023.md deleted file mode 100644 index c02781a..0000000 --- a/_collections/_biblio/signature/signature_iftimovici_asynchronous_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Anton Iftimovici et al. -title: Asynchronous neural maturation predicts transition to psychosis -journal: Psychiatry and Clinical Neurosciences -year: 2023 -type: article -doi: 10.1111/pcn.13612 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_iftimovici_brain_2022.md b/_collections/_biblio/signature/signature_iftimovici_brain_2022.md deleted file mode 100644 index 7627901..0000000 --- a/_collections/_biblio/signature/signature_iftimovici_brain_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Anton Iftimovici et al. -title: Brain anomalies in early psychosis - From secondary to primary psychosis -journal: Neuroscience \& Biobehavioral Reviews -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0149763422002056 -doi: 10.1016/j.neubiorev.2022.104716 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_iftimovici_longitudinal_2023.md b/_collections/_biblio/signature/signature_iftimovici_longitudinal_2023.md deleted file mode 100644 index 688b852..0000000 --- a/_collections/_biblio/signature/signature_iftimovici_longitudinal_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Anton Iftimovici et al. -title: Longitudinal MicroRNA Signature of Conversion to Psychosis -journal: Schizophrenia Bulletin -year: 2023 -type: article -doi: 10.1093/schbul/sbad080 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_jacquelet_architecture_2001.md b/_collections/_biblio/signature/signature_jacquelet_architecture_2001.md deleted file mode 100644 index 0fde1cb..0000000 --- a/_collections/_biblio/signature/signature_jacquelet_architecture_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Yann Jacquelet et al. -title: Architecture pyramidale agent pour la segmentation d'image - Application à l'extraction d'une zone lobulaire issue d'une mammographie -year: 2001 -type: inproceedings -booktitle: 18° Colloque sur le traitement du signal et des images, FRA, 2001 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_jacquelet_combinatorial_2002.md b/_collections/_biblio/signature/signature_jacquelet_combinatorial_2002.md deleted file mode 100644 index 5103f40..0000000 --- a/_collections/_biblio/signature/signature_jacquelet_combinatorial_2002.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Y Jacquelet et al. -title: Combinatorial pyramid transposed to behavioural space for object recognition process -year: 2002 -type: inproceedings -booktitle: Systems, Man and Cybernetics, 2002 IEEE International Conference on ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_jouvent_longitudinal_2012.md b/_collections/_biblio/signature/signature_jouvent_longitudinal_2012.md deleted file mode 100644 index 69edede..0000000 --- a/_collections/_biblio/signature/signature_jouvent_longitudinal_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Eric Jouvent et al. -title: Longitudinal changes of cortical morphology in CADASIL -journal: Neurobiology of Aging -year: 2012 -type: article -doi: 10.1016/j.neurobiolaging.2011.09.013 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_jouvent_prediction_2016.md b/_collections/_biblio/signature/signature_jouvent_prediction_2016.md deleted file mode 100644 index 3d2156c..0000000 --- a/_collections/_biblio/signature/signature_jouvent_prediction_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Eric Jouvent et al. -title: Prediction of 3-year clinical course in CADASIL -journal: Neurology -year: 2016 -type: article -doi: 10.1212/WNL.0000000000003252 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_jouvent_shape_2016.md b/_collections/_biblio/signature/signature_jouvent_shape_2016.md deleted file mode 100644 index 2d09ef9..0000000 --- a/_collections/_biblio/signature/signature_jouvent_shape_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Eric Jouvent et al. -title: Shape of the Central Sulcus and Disability After Subcortical Stroke - A Motor Reserve Hypothesis -journal: Stroke -year: 2016 -type: article -doi: 10.1161/STROKEAHA.115.012562 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_kinie_segmentation_2001.md b/_collections/_biblio/signature/signature_kinie_segmentation_2001.md deleted file mode 100644 index 40e4c8e..0000000 --- a/_collections/_biblio/signature/signature_kinie_segmentation_2001.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Abel Kinie et al. -title: Segmentation vectorielle des signaux épileptiques une approche expérimentale multi-agents -year: 2001 -type: inproceedings -booktitle: 18° Colloque sur le traitement du signal et des images, FRA, 2001 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_laidi_cerebellar_2019.md b/_collections/_biblio/signature/signature_laidi_cerebellar_2019.md deleted file mode 100644 index 653fd61..0000000 --- a/_collections/_biblio/signature/signature_laidi_cerebellar_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: C. Laidi et al. -title: Cerebellar parcellation in schizophrenia and bipolar disorder -journal: Acta Psychiatrica Scandinavica -year: 2019 -type: article -url: https -//onlinelibrary.wiley.com/doi/abs/10.1111/acps.13087 -doi: 10.1111/acps.13087 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_laidi_cerebellar_2022.md b/_collections/_biblio/signature/signature_laidi_cerebellar_2022.md deleted file mode 100644 index d2b5cc3..0000000 --- a/_collections/_biblio/signature/signature_laidi_cerebellar_2022.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Charles Laidi et al. -title: Cerebellar atypicalities in autism? -journal: Biological Psychiatry -year: 2022 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S0006322322012781 -doi: 10.1016/j.biopsych.2022.05.020 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_laidi_decreased_2019.md b/_collections/_biblio/signature/signature_laidi_decreased_2019.md deleted file mode 100644 index 40bead2..0000000 --- a/_collections/_biblio/signature/signature_laidi_decreased_2019.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Charles Laidi et al. -title: Decreased Cortical Thickness in the Anterior Cingulate Cortex in Adults with Autism -journal: Journal of Autism and Developmental Disorders -year: 2019 -type: article -doi: 10.1007/s10803-018-3807-3 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_bridging_2011.md b/_collections/_biblio/signature/signature_le_floch_bridging_2011.md deleted file mode 100644 index 33a93e6..0000000 --- a/_collections/_biblio/signature/signature_le_floch_bridging_2011.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edith Le Floch et al. -title: Bridging the gap between imaging and genetics - a multivariate statistical investigation -year: 2011 -type: inproceedings -booktitle: Human brain mapping ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_cluster-level_2010.md b/_collections/_biblio/signature/signature_le_floch_cluster-level_2010.md deleted file mode 100644 index 3362c2e..0000000 --- a/_collections/_biblio/signature/signature_le_floch_cluster-level_2010.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edith Le Floch et al. -title: Cluster-level Inference and Resampling-Based Multiple Testing applied to Imaging Genetics Studies -year: 2010 -type: inproceedings -booktitle: Human brain mapping ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_dimension_2012.md b/_collections/_biblio/signature/signature_le_floch_dimension_2012.md deleted file mode 100644 index aa837ff..0000000 --- a/_collections/_biblio/signature/signature_le_floch_dimension_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: E. Le Floch et al. -title: Dimension reduction and regularisation combined with Partial Least Squares in high dimensional imaging-genetics studies -year: 2012 -type: inproceedings -booktitle: Partial Least Squares ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_dimension_2013.md b/_collections/_biblio/signature/signature_le_floch_dimension_2013.md deleted file mode 100644 index c578cbb..0000000 --- a/_collections/_biblio/signature/signature_le_floch_dimension_2013.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edith Le Floch et al. -title: Dimension Reduction and Regularization Combined with Partial Least Squares in High Dimensional Imaging Genetics Studies -year: 2013 -type: inproceedings -booktitle: New Perspectives in Partial Least Squares and Related Methods ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_discovering_2012.md b/_collections/_biblio/signature/signature_le_floch_discovering_2012.md deleted file mode 100644 index 69d7554..0000000 --- a/_collections/_biblio/signature/signature_le_floch_discovering_2012.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edith Le Floch et al. -title: Discovering associations in high dimensional imaging-genetics data - A comparison study of dimension reduction and regularisation strategies combined with partial least squares -year: 2012 -type: inproceedings -booktitle: International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_floch_significant_2012.md b/_collections/_biblio/signature/signature_le_floch_significant_2012.md deleted file mode 100644 index 82a0224..0000000 --- a/_collections/_biblio/signature/signature_le_floch_significant_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Edith Le Floch et al. -title: Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse Partial Least Squares -journal: NeuroImage -year: 2012 -type: article -doi: 10.1016/j.neuroimage.2012.06.061 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_le_guen_genetic_2018.md b/_collections/_biblio/signature/signature_le_guen_genetic_2018.md deleted file mode 100644 index 4787bb8..0000000 --- a/_collections/_biblio/signature/signature_le_guen_genetic_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Yann Le Guen et al. -title: Genetic Influence on the Sulcal Pits - On the Origin of the First Cortical Folds -journal: Cerebral Cortex -year: 2018 -type: article -url: https -//doi.org/10.1093/cercor/bhx098 -doi: 10.1093/cercor/bhx098 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_lebenberg_framework_2018.md b/_collections/_biblio/signature/signature_lebenberg_framework_2018.md deleted file mode 100644 index 9caf203..0000000 --- a/_collections/_biblio/signature/signature_lebenberg_framework_2018.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J. Lebenberg et al. -title: A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem -journal: Brain Structure and Function -year: 2018 -type: article -url: https -//doi.org/10.1007/s00429-018-1735-9 -doi: 10.1007/s00429-018-1735-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_leroy_striatal_2012.md b/_collections/_biblio/signature/signature_leroy_striatal_2012.md deleted file mode 100644 index 5390ddb..0000000 --- a/_collections/_biblio/signature/signature_leroy_striatal_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Claire Leroy et al. -title: Striatal and extrastriatal dopamine transporter in cannabis and tobacco addiction - a high-resolution PET study -journal: Addiction Biology -year: 2012 -type: article -doi: 10.1111/j.1369-1600.2011.00356.x ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_li_embarrassingly_2013.md b/_collections/_biblio/signature/signature_li_embarrassingly_2013.md deleted file mode 100644 index 0db6816..0000000 --- a/_collections/_biblio/signature/signature_li_embarrassingly_2013.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jinpeng LI et al. -title: Embarrassingly Parallel Array Computing (EPAC) -year: 2013 -type: inproceedings ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_lofstedt_analysis_2014.md b/_collections/_biblio/signature/signature_lofstedt_analysis_2014.md deleted file mode 100644 index cb5247a..0000000 --- a/_collections/_biblio/signature/signature_lofstedt_analysis_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Tommy Lofstedt et al. -title: Analysis, Structured variable selection for generalized canonical correlation -year: 2014 -type: inproceedings -booktitle: International Conference on Partial Least Squares and Related Methods ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_lofstedt_simulated_2014.md b/_collections/_biblio/signature/signature_lofstedt_simulated_2014.md deleted file mode 100644 index 20e0425..0000000 --- a/_collections/_biblio/signature/signature_lofstedt_simulated_2014.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Tommy Lofstedt et al. -title: Simulated Data for Linear Regression with Structured and Sparse Penalties -year: 2014 -type: misc -url: https -//hal-cea.archives-ouvertes.fr/cea-00914960/document ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_lofstedt_structured_2016.md b/_collections/_biblio/signature/signature_lofstedt_structured_2016.md deleted file mode 100644 index 7f5d53d..0000000 --- a/_collections/_biblio/signature/signature_lofstedt_structured_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Tommy Lofstedt et al. -title: Structured Variable Selection for Regularized Generalized Canonical Correlation Analysis, The Multiple Facets of Partial Least Squares and Related Methods -year: 2016 -type: incollection -url: https -//hal-centralesupelec.archives-ouvertes.fr/hal-01396614 -booktitle: Springer Proceedings in Mathematics and Statistics ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_louiset_sepclr_2024.md b/_collections/_biblio/signature/signature_louiset_sepclr_2024.md deleted file mode 100644 index f6379d9..0000000 --- a/_collections/_biblio/signature/signature_louiset_sepclr_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Robin Louiset et al. -title: SepCLR - Separating common from salient patterns with Contrastive Representation Learning -year: 2024 -type: inproceedings -url: https -//openreview.net/forum?id=30N3bNAiw3 -booktitle: The Twelfth International Conference on Learning Representations (ICLR) 2024 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_louiset_sepvae_2023.md b/_collections/_biblio/signature/signature_louiset_sepvae_2023.md deleted file mode 100644 index e653c9b..0000000 --- a/_collections/_biblio/signature/signature_louiset_sepvae_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Robin Louiset et al. -title: SepVAE - a contrastive VAE to separate pathological patterns from healthy ones -year: 2023 -type: inproceedings -url: http -//arxiv.org/abs/2307.06206 -doi: 10.48550/arXiv.2307.06206 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_louiset_sepvae_2024.md b/_collections/_biblio/signature/signature_louiset_sepvae_2024.md deleted file mode 100644 index 3526ed3..0000000 --- a/_collections/_biblio/signature/signature_louiset_sepvae_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Robin Louiset et al. -title: SepVAE - a contrastive VAE to separate pathological patterns from healthy ones -year: 2024 -type: inproceedings -url: https -//openreview.net/forum?id=yLySzM5yxs -booktitle: Medical Imaging with Deep Learning (MIDL) 2024 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_louiset_ucsl_2021.md b/_collections/_biblio/signature/signature_louiset_ucsl_2021.md deleted file mode 100644 index 67ecc64..0000000 --- a/_collections/_biblio/signature/signature_louiset_ucsl_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Robin Louiset et al. -title: UCSL - A Machine Learning Expectation-Maximization framework for Unsupervised Clustering driven by Supervised Learning -year: 2021 -type: inproceedings -url: http -//arxiv.org/abs/2107.01988 -booktitle: Joint European Conference on Machine Learning and Knowledge Discovery in Databases (ECML/PKDD) 2021 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_magalhaes_white_2017.md b/_collections/_biblio/signature/signature_magalhaes_white_2017.md deleted file mode 100644 index a784e53..0000000 --- a/_collections/_biblio/signature/signature_magalhaes_white_2017.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: R. Magalhães et al. -title: White matter changes in microstructure associated with a maladaptive response to stress in rats -journal: Translational Psychiatry -year: 2017 -type: article -doi: 10.1038/tp.2016.283 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_mangin_brain_2004.md b/_collections/_biblio/signature/signature_mangin_brain_2004.md deleted file mode 100644 index 9ef6048..0000000 --- a/_collections/_biblio/signature/signature_mangin_brain_2004.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J.-F. Mangin et al. -title: Brain morphometry using 3D moment invariants -journal: Medical Image Analysis -year: 2004 -type: article -doi: 10.1016/j.media.2004.06.016 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_mangin_framework_2004.md b/_collections/_biblio/signature/signature_mangin_framework_2004.md deleted file mode 100644 index a028a0b..0000000 --- a/_collections/_biblio/signature/signature_mangin_framework_2004.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J.-F. Mangin et al. -title: A framework to study the cortical folding patterns -journal: NeuroImage -year: 2004 -type: article -doi: 10.1016/j.neuroimage.2004.07.019 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_mangin_neocortical_2020.md b/_collections/_biblio/signature/signature_mangin_neocortical_2020.md deleted file mode 100644 index 7e7b9c4..0000000 --- a/_collections/_biblio/signature/signature_mangin_neocortical_2020.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jean-Francois Mangin et al. -title: Neocortical morphometry in Huntington's disease - Indication of the coexistence of abnormal neurodevelopmental and neurodegenerative processes -journal: NeuroImage - Clinical -year: 2020 -type: article -url: https -//www.sciencedirect.com/science/article/pii/S2213158220300486 -doi: 10.1016/j.nicl.2020.102211 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_mangin_object-based_2004.md b/_collections/_biblio/signature/signature_mangin_object-based_2004.md deleted file mode 100644 index 08ce365..0000000 --- a/_collections/_biblio/signature/signature_mangin_object-based_2004.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J. Mangin et al. -title: Object-based morphometry of the cerebral cortex -journal: IEEE Transactions on Medical Imaging -year: 2004 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_maroy_segmentation_2008.md b/_collections/_biblio/signature/signature_maroy_segmentation_2008.md deleted file mode 100644 index 755041e..0000000 --- a/_collections/_biblio/signature/signature_maroy_segmentation_2008.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Renaud Maroy et al. -title: Segmentation of rodent whole-body dynamic PET images - an unsupervised method based on voxel dynamics -journal: IEEE Transactions on Medical Imaging -year: 2008 -type: article -doi: 10.1109/TMI.2007.905106 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_martinot_brain_2005-1.md b/_collections/_biblio/signature/signature_martinot_brain_2005-1.md deleted file mode 100644 index abec549..0000000 --- a/_collections/_biblio/signature/signature_martinot_brain_2005-1.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J.-L. Martinot et al. -title: Brain folding in schizophrenia -year: 2005 -type: inproceedings -booktitle: Proc. 8th World congress of biological psychiatry. The world journal of biological psychiatry vol 6 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_martinot_brain_2005-2.md b/_collections/_biblio/signature/signature_martinot_brain_2005-2.md deleted file mode 100644 index abec549..0000000 --- a/_collections/_biblio/signature/signature_martinot_brain_2005-2.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J.-L. Martinot et al. -title: Brain folding in schizophrenia -year: 2005 -type: inproceedings -booktitle: Proc. 8th World congress of biological psychiatry. The world journal of biological psychiatry vol 6 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_martinot_brain_2005.md b/_collections/_biblio/signature/signature_martinot_brain_2005.md deleted file mode 100644 index 2827009..0000000 --- a/_collections/_biblio/signature/signature_martinot_brain_2005.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J. Martinot et al. -title: Brain folding in schizophrenia -year: 2005 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_martinot_cortical_2006.md b/_collections/_biblio/signature/signature_martinot_cortical_2006.md deleted file mode 100644 index 6ef1abd..0000000 --- a/_collections/_biblio/signature/signature_martinot_cortical_2006.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: J. Martinot et al. -title: Cortical gyrification and (developmental) pathopsychology -year: 2006 -type: misc ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_nunes_using_2018.md b/_collections/_biblio/signature/signature_nunes_using_2018.md deleted file mode 100644 index ff3e730..0000000 --- a/_collections/_biblio/signature/signature_nunes_using_2018.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Abraham Nunes et al. -title: Using structural MRI to identify bipolar disorders - 13 site machine learning study in 3020 individuals from the ENIGMA Bipolar Disorders Working Group -journal: Molecular Psychiatry -year: 2018 -type: article -doi: 10.1038/s41380-018-0228-9 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_pauling_bipolar_2017.md b/_collections/_biblio/signature/signature_pauling_bipolar_2017.md deleted file mode 100644 index cbe57e9..0000000 --- a/_collections/_biblio/signature/signature_pauling_bipolar_2017.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: M. Pauling et al. -title: Bipolar disorder and white matter microstructure - ENIGMA bipolar disorder fractional anisotropy DTI results -year: 2017 -type: inproceedings -url: http -//www.sciencedirect.com/science/article/pii/S0924977X17315110 -doi: 10.1016/S0924-977X(17)31511-0 -booktitle: European Neuropsychopharmacology ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_pedregosa_scikit-learn:_2012.md b/_collections/_biblio/signature/signature_pedregosa_scikit-learn:_2012.md deleted file mode 100644 index 1dbd4b8..0000000 --- a/_collections/_biblio/signature/signature_pedregosa_scikit-learn:_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Fabian Pedregosa et al. -title: Scikit-learn - Machine Learning in Python -journal: Journal of Machine Learning Research -year: 2012 -type: article -url: http -//arxiv.org/abs/1201.0490 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_penttila_cortical_2009-1.md b/_collections/_biblio/signature/signature_penttila_cortical_2009-1.md deleted file mode 100644 index e234aa5..0000000 --- a/_collections/_biblio/signature/signature_penttila_cortical_2009-1.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jani Penttilä et al. -title: Cortical folding difference between patients with early-onset and patients with intermediate-onset bipolar disorder -journal: Bipolar Disorders -year: 2009 -type: article -doi: 10.1111/j.1399-5618.2009.00683.x ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_penttila_cortical_2009.md b/_collections/_biblio/signature/signature_penttila_cortical_2009.md deleted file mode 100644 index a137a69..0000000 --- a/_collections/_biblio/signature/signature_penttila_cortical_2009.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jani Penttilä et al. -title: Cortical folding in patients with bipolar disorder or unipolar depression -journal: Journal of psychiatry \& neuroscience - JPN -year: 2009 -type: article ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_petiton_sara_how_2024.md b/_collections/_biblio/signature/signature_petiton_sara_how_2024.md deleted file mode 100644 index 1bb74be..0000000 --- a/_collections/_biblio/signature/signature_petiton_sara_how_2024.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Sara Petiton et al. -title: How and why does deep ensemble coupled with transfer learning increase performance in bipolar disorder and schizophrenia classification -year: 2024 -type: inproceedings -booktitle: 21st IEEE International Symposium on Biomedical Imaging (ISBI 2024) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_piguet_irritability_2021.md b/_collections/_biblio/signature/signature_piguet_irritability_2021.md deleted file mode 100644 index c62b6b5..0000000 --- a/_collections/_biblio/signature/signature_piguet_irritability_2021.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Camille Piguet et al. -title: Irritability Is Associated With Decreased Cortical Surface Area and Anxiety With Decreased Gyrification During Brain Development -journal: Frontiers in Psychiatry -year: 2021 -type: article -doi: 10.3389/fpsyt.2021.744419 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_pirpamer_determinants_2016.md b/_collections/_biblio/signature/signature_pirpamer_determinants_2016.md deleted file mode 100644 index 3c41399..0000000 --- a/_collections/_biblio/signature/signature_pirpamer_determinants_2016.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Lukas Pirpamer et al. -title: Determinants of iron accumulation in the normal aging brain -journal: Neurobiology of Aging -year: 2016 -type: article -doi: 10.1016/j.neurobiolaging.2016.04.002 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_poiret_attention-gated_2024.md b/_collections/_biblio/signature/signature_poiret_attention-gated_2024.md deleted file mode 100644 index b1e29e7..0000000 --- a/_collections/_biblio/signature/signature_poiret_attention-gated_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Clement Poiret et al. -title: Attention-gated 3D CapsNet for robust hippocampal segmentation -journal: Journal of Medical Imaging (Bellingham, Wash.) -year: 2024 -type: article -doi: 10.1117/1.JMI.11.1.014003 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_poiret_fast_2023.md b/_collections/_biblio/signature/signature_poiret_fast_2023.md deleted file mode 100644 index 7d16aa6..0000000 --- a/_collections/_biblio/signature/signature_poiret_fast_2023.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Clement Poiret et al. -title: A fast and robust hippocampal subfields segmentation - HSF revealing lifespan volumetric dynamics -journal: Frontiers in Neuroinformatics -year: 2023 -type: article -url: https -//www.frontiersin.org/articles/10.3389/fninf.2023.1130845 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_poline_imaging_2010.md b/_collections/_biblio/signature/signature_poline_imaging_2010.md deleted file mode 100644 index ac91a1c..0000000 --- a/_collections/_biblio/signature/signature_poline_imaging_2010.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jean-Baptiste Poline et al. -title: Imaging Genetics - Bio-Informatics and Bio-Statistics Challenges -year: 2010 -type: inproceedings -url: http -//www.springerlink.com/index/10.1007/978-3-7908-2604-3 -doi: 10.1007/978-3-7908-2604-3 -booktitle: compstat ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_reiner_sulcal_2012.md b/_collections/_biblio/signature/signature_reiner_sulcal_2012.md deleted file mode 100644 index 3208a37..0000000 --- a/_collections/_biblio/signature/signature_reiner_sulcal_2012.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Peggy Reiner et al. -title: Sulcal span in Azheimer's disease, amnestic mild cognitive impairment, and healthy controls -journal: Journal of Alzheimer's disease - JAD -year: 2012 -type: article -doi: 10.3233/JAD-2012-111622 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_sarrazin_multicenter_2014.md b/_collections/_biblio/signature/signature_sarrazin_multicenter_2014.md deleted file mode 100644 index a5ba302..0000000 --- a/_collections/_biblio/signature/signature_sarrazin_multicenter_2014.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Samuel Sarrazin et al. -title: A multicenter tractography study of deep white matter tracts in bipolar I disorder - psychotic features and interhemispheric disconnectivity -journal: JAMA psychiatry -year: 2014 -type: article -doi: 10.1001/jamapsychiatry.2013.4513 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_scott_prospective_2019.md b/_collections/_biblio/signature/signature_scott_prospective_2019.md deleted file mode 100644 index ff2bf92..0000000 --- a/_collections/_biblio/signature/signature_scott_prospective_2019.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jan Scott et al. -title: Prospective cohort study of early biosignatures of response to lithium in bipolar-I-disorders - overview of the H2020-funded R-LiNK initiative -journal: International Journal of Bipolar Disorders -year: 2019 -type: article -url: https -//journalbipolardisorders.springeropen.com/articles/10.1186/s40345-019-0156-x -doi: 10.1186/s40345-019-0156-x ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_stout_accumulation_2020.md b/_collections/_biblio/signature/signature_stout_accumulation_2020.md deleted file mode 100644 index 15a768b..0000000 --- a/_collections/_biblio/signature/signature_stout_accumulation_2020.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Jacques Stout et al. -title: Accumulation of Lithium in the Hippocampus of Patients With Bipolar Disorder - A Lithium-7 Magnetic Resonance Imaging Study at 7 Tesla -journal: Biological Psychiatry -year: 2020 -type: article -doi: 10.1016/j.biopsych.2020.02.1181 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_sun_defining_2008.md b/_collections/_biblio/signature/signature_sun_defining_2008.md deleted file mode 100644 index 94d01c1..0000000 --- a/_collections/_biblio/signature/signature_sun_defining_2008.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Zhong Sun et al. -title: Defining cortical sulcus patterns using partial clustering based on bootstrap and bagging -year: 2008 -type: inproceedings -url: http -//ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4541325 -doi: 10.1109/ISBI.2008.4541325 -booktitle: 2008 5th IEEE International Symposium on Biomedical Imaging - From Nano to Macro ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_teillac_colocalization_2016.md b/_collections/_biblio/signature/signature_teillac_colocalization_2016.md deleted file mode 100644 index 18ab15f..0000000 --- a/_collections/_biblio/signature/signature_teillac_colocalization_2016.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Achille Teillac et al. -title: Colocalization of Functional Activity and Neurite Density Within Cortical Areas -year: 2016 -type: inproceedings -url: https -//link.springer.com/chapter/10.1007/978-3-319-54130-3_15 -doi: 10.1007/978-3-319-54130-3_15 -booktitle: Computational Diffusion MRI ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_thirion_inverse_2006.md b/_collections/_biblio/signature/signature_thirion_inverse_2006.md deleted file mode 100644 index 97be2c9..0000000 --- a/_collections/_biblio/signature/signature_thirion_inverse_2006.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Bertrand Thirion et al. -title: Inverse retinotopy - inferring the visual content of images from brain activation patterns -journal: NeuroImage -year: 2006 -type: article -doi: 10.1016/j.neuroimage.2006.06.062 ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_thirion_reading_2005.md b/_collections/_biblio/signature/signature_thirion_reading_2005.md deleted file mode 100644 index 04a4429..0000000 --- a/_collections/_biblio/signature/signature_thirion_reading_2005.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Bertrand Thirion et al. -title: Reading in the subject's mind - the case of low-level vision -year: 2005 -type: inproceedings -booktitle: Proc. 11th HBM CD-Rom Neuroimage vol 26 (1) ---- \ No newline at end of file diff --git a/_collections/_biblio/signature/signature_thirion_reading_2006.md b/_collections/_biblio/signature/signature_thirion_reading_2006.md deleted file mode 100644 index 3ec941d..0000000 --- a/_collections/_biblio/signature/signature_thirion_reading_2006.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -cat: gaia -subcat: signature -bestof: false -author: Bertrand Thirion et al. -title: Reading the brain visual system as an inverse problem -year: 2006 -type: inproceedings -booktitle: International Symposium on Biomedical Imaging (ISBI) ---- \ No newline at end of file diff --git a/_collections/_labs/ciel.md b/_collections/_labs/ciel.md new file mode 100644 index 0000000..f50e393 --- /dev/null +++ b/_collections/_labs/ciel.md @@ -0,0 +1,12 @@ +--- +layout: +title: CIEL +cat: ciel +subcat: lab +headline: Cerebral Imaging and Engineering Lab +teasing: Laboratory, directed by Sébastien Mériaux, develops innovative methodologies for understanding the biophysics of brain mechanisms such as metabolism, neuronal activity and molecules transport, both in normal and pathological conditions using ultra-high and extreme field MRI and MRS, ultrasounds, and histology, following a translational strategy from animals to humans. +site: https://neurospin.github.io/ciel +icon: +added: 2020 +permalink: labs/ciel.html +--- diff --git a/_collections/_labs/gaia.md b/_collections/_labs/gaia.md new file mode 100644 index 0000000..7e698aa --- /dev/null +++ b/_collections/_labs/gaia.md @@ -0,0 +1,12 @@ +--- +layout: +title: GAIA +cat: gaia +subcat: lab +headline: Brain Imaging and Data Science Lab +teasing: Laboratory, directed by Jean-François Mangin, develops new computer vision systems dedicated to the modeling of the inter-subject variability of complex brain phenotypes, is the algorithmic forefront of the exploitation of high field MRI, designs dedicated artificial intelligence methods and software environments to exploit brain phenotypes in a variety of contexts (biomarker research, genetics, cognitive neuroscience, etc). +site: https://neurospin.github.io/gaia +icon: +added: 2020 +permalink: labs/gaia.html +--- diff --git a/_collections/_labs/gaia_architecture.md b/_collections/_labs/gaia_architecture.md deleted file mode 100644 index 1ede35e..0000000 --- a/_collections/_labs/gaia_architecture.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -layout: page_team -title: ARCHITECTURE -cat: gaia -subcat: team -headline: Deciphering the variability of the cortical folding pattern -teasing: Develops innovative methods to decipher the cortical folding pattern and perform automatic sulcus recognition, based on the use of machine learning and artificial intelligence techniques to infer dictionaries of tractable local polymorphisms supposed to provide a good proxy to the architectural segregation of populations. -leader: Denis Rivière -icon: architecture.png -added: 2020 -permalink: teams/gaia-architecture.html ---- - - - - - - -
-For 30 years, we have been improvi​​ng our tools for automatic recognition of cortical sulci. The latest generation (L. Borne, B. Cagna, C. Fischer) relies on deep learning and distillation techniques to learn first a representation of the folding variability on a very large number of brains before exploiting a database of a few hundred brains whose sulci have been manually labeled. Sulcus morphometry is used in a multitude of collaborations to establish biomarkers, e.g., for pathologies of aging (WQ Shu-Quartier-Dit-Maire). But we are approaching the limits of the current anatomical nomenclature, which is not adapted to certain observed patterns. - -This is why for a few years we question the usual idea that an atlas can be adapted to any brain. We seek to infer with unsupervised deep learning approaches a dictionary of all the folding patterns (L. Guillon, A. Gaudin, J. Chavas). The goal is to be able to decompose any brain from this dictionary and potentially to highlight anomalies when an observed pattern is not listed. We use generative models and contrastive models to bias the dictionary towards folding patterns predictive of behavioral traits or developmental ​​​pathologies. - -We are also developing machine learning analyses to project the geometric variability of a sulcus or a pattern into a low-dimensional manifold, in order to quantify possible links with a pathology or a behavior (Z. Y. Sun, M. Pascucci). We have adapted these strategies to the analysis of the d​​evelopment of the folding of premature babies (H. de Vareille) and to the comparison of the folding of great apes with that of humans (O. Foubet). - -In the context of the Human Brain Project, we have established the first atlases of short-range connectivity through U-fibers (M. Guevara, N. Labra, N. Vindas) and new parcellations of the cortical surface integrating connectivity from diffusion MRI and cytoarchitectonicity (C. Langlet, XY Wang). Our ultimate goal is to link folding variability with connectivity and architectonics variability.​ - -Developed neuroimaging software platform: [BrainVisa](https://brainvisa.info/web) diff --git a/_collections/_labs/gaia_brainomics.md b/_collections/_labs/gaia_brainomics.md deleted file mode 100644 index c914601..0000000 --- a/_collections/_labs/gaia_brainomics.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: -title: BRAINOMICS -cat: gaia -subcat: team -headline: Imaging genetics for neuroscience -teasing: Develops innovative analysis methods to integrate brain imaging with genomics data, often combined to clinical or environmental data to determine how brain phenotypes variability originates in genetic and environmental variabilities. -site: https://brainomics.org -leader: Vincent Frouin -icon: brainomics.png -added: 2020 -permalink: teams/gaia-brainomics.html ---- diff --git a/_collections/_labs/gaia_cati.md b/_collections/_labs/gaia_cati.md deleted file mode 100644 index 26678f6..0000000 --- a/_collections/_labs/gaia_cati.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -layout: -title: CATI -cat: gaia -subcat: cell -teasing: Founded in 2010, CATI, or Centre d'acquisition et de traitement des images in french, is a national service platform supporting more than 30 muticenter neuroimaging studies in the fields of neurodegenerative diseases and psychiatry (AD, Parkinson, Huntington, ALS, Bipolar, etc.) including several therapeutic trials. -leader: Yann Cointepas -site: http://www.cati-neuroimaging.com -icon: cati.jpg -added: 2020 -permalink: cells/gaia-cati.html ---- - diff --git a/_collections/_labs/gaia_ginkgo.md b/_collections/_labs/gaia_ginkgo.md deleted file mode 100644 index a072c06..0000000 --- a/_collections/_labs/gaia_ginkgo.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -layout: page_team -title: GINKGO -cat: gaia -subcat: team -headline: Mapping the brain microstructure across individuals and species -teasing: Develops innovative methods to map the brain structural connectome, cortex cytoarchitectony and myeloarchitectony at the individual scale, from animals to humans using ultra-high field and extreme field MRI. -leader: Ivy Uszynski -site: https://ginkgo-team.fr -icon: ginkgo.png -added: 2020 -permalink: teams/gaia-ginkgo.html ---- - - - - - -
-Our Ginkgo team has been developing a software toolbox for 15 years dedicated to ​the analysis of diffusion and quantitative MRI and to the construction of white matter atlases (*). During the past five years, it has -been exploited in the frame of collaborative projects (INRAE, NeuroPSI, iBrain, Collège de France, ENS Paris-Saclay, MD Anderson, Beauval ZooParc) to establish novel connectivity atlases of various species from humans to animals and has made it possible to study the singularity of the connectivity of the human brain compared to the chimpanzee brain. - -In close collaboration with the INSERM iBRAIN Unit, we have also contributed to the Human Brain Project with the Chenonceau project consisting in scanning for 12 000 hours a post-mortem brain on preclinical MRIs at the mesoscale. It allowed the collection of a Big Dataset of anatomical, diffusion and relaxometric MRI, opening the way to the exploration of fine brain structures, of fine anatomical connectivity, and of the cortex cytoarchitectonics and myeloarchitectonics at unprecedented resolutions. - -In the framework of the AIDAS institute, we developed a novel HPC tools for the global inference of the structural connectome capable of scaling and reconstructing connectomes of mesoscopic to microscopic -resolutions from diffusion MRI and PLI. To further improve the ability of diffusion MRI to probe brain cytoarchitecture, the Ginkgo team has developed an innovative simulation framework, Medusa, which aims -to transform MRI into a virtual biopsy tool. It relies on large scale numerical simulations of realistic brain tissue samples and of their corresponding diffusion MRI signatures, and on AI techniques to train decoding tools -able to map brain cytoarchitectonics in vivo at the individual scale. - -We will continue investigating brain microstructure, in the frame of 3 projects aiming at deciphering the cellular disorders at the origin of white matter hyperintensities in small vessel diseases (SUMMIT), characterizing the cytoarchitecture of brain functions (iCORTEX), and collecting a deep phenotyping biobank -of multimodal and multiscale in and ex vivo brain data using outstanding imagers (BrainDeepPhenotyping, PEPR Santé Numérique).​ diff --git a/_collections/_labs/gaia_platform.md b/_collections/_labs/gaia_platform.md deleted file mode 100644 index 89b7e22..0000000 --- a/_collections/_labs/gaia_platform.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -layout: page_team -title: Platform -cat: gaia -subcat: cell -teasing: Our goal is to meet the specific needs of NeuroSpin researchers for software development and analysis of heterogeneous brain data (neuroimaging, omics, clinical and behavioural data) used in the context of research conducted in clinical neuroscience, population imaging or cognitive neuroscience research. -leader: Antoine Grigis -icon: platform.jpg -added: 2020 -permalink: cells/gaia-platform.html ---- - - - - - -
-The mission of the cell is to meet the various needs of research teams in support of software development and brain data analysis, including: - -→The development of ad hoc software tools to meet the specific needs of research teams based in or using the NeuroSpin platform.
-→The development of brain data analysis pipelines based on standard tools used by the scientific community.
-→The development of webservices that allow remote control of the developed pipelines and the access to the data produced.
-→The deployment of these tools on the high performance computing resources of NeuroSpin (CPU and GPU clusters) and of the CEA Très Grand Centre de Calcul (via the EBRAINS/FENIX infrastructure).
-→The availability of a catalogue listing all the tools produced by the cell. More specifically, within the framework of various research projects conducted by the BAOBAB unit, the cell analyses population imaging data from small, medium and large monocentric, multicentric, national, European or international cohorts acquired on healthy subjects (IMAGEN, HCP, UK BioBank, …) or patients (R-link, EUAIMS, HBN, …) in order to develop population stratification approaches and thus be able to identify the predisposition of each individual to develop brain pathologies. This work is carried out in close collaboration with the UMS CATI. - - diff --git a/_collections/_labs/gaia_signature.md b/_collections/_labs/gaia_signature.md deleted file mode 100644 index 91ffc34..0000000 --- a/_collections/_labs/gaia_signature.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -layout: page_team -title: SIGNATURE -cat: gaia -subcat: team -headline: Neuroimaging signatures of brain disorders -teasing: Develops cutting-edge machine learning and statistical models to uncover neural signatures that can stratify psychiatric disorders in the frame of large-scale national and European initiatives. -leader: Edouard Duchesnay -icon: signature.png -added: 2020 -permalink: teams/gaia-signature.html ---- - - - - - - - -
-Artificial Intelligence (AI) combined with neuroimaging opens up possibilities for personalized medicine. With this long-term objective, we developed four lines of research: - -**MODELS TO PRODUCE INT​​​ERPRETABLE BRAIN SIGNATURES OF DISORDERS** - -We investigated new predictive linear models that integrate prior biological knowledge to force the solution to adhere to biological priors, producing more plausible interpretable signatures. These models have been used to uncover an anatomical pattern of schizophrenia and a functional pattern for hallucinations. We embraced the applied mathematic challenge of creating scalable optimization solvers [for high-dimensional neuroimaging data while being flexible enough to integrate various priors. - -**MODELS TO ​​BRIDGE THE GAP BETWEEN BIG AND SMALL DATA** - -Thanks to the award of a Chair in AI (2020-2025), we proposed new weakly-supervised deep neural networks that are pre-trained on large datasets of controls, using auxiliary information such as “age” to improve the embedded representation of the general variability. Models are then transferred to smaller samples of patients to reveal the specific signal associated with psychiatric disorders. - -**MODELS FOR PA​​​TIENTS’ STRATIFICATION ​​INTO HOMOGENEOUS SUBGROUPS** - -With shared etiologies for individualized therapeutic strategy. - -**UNLOCKING TH​​​E DATA ACCESS** - -Learning models require collecting more and better data (wide and deep phenotyping). First, we tackled the “big data challenge” by aggregating open datasets (UKB, ABCD, HBN) into an interoperable database. Second, we actively contributed and will continue to play a major role to the emergence of deeply phenotyped datasets by leading the data management and analysis of several large European and national projects (PEPR PROPSY, RHUs FAME and PsyCARE, European project R-LiNK). ​ diff --git a/_collections/_labs/metric.md b/_collections/_labs/metric.md new file mode 100644 index 0000000..6df4821 --- /dev/null +++ b/_collections/_labs/metric.md @@ -0,0 +1,12 @@ +--- +layout: +title: METRIC +cat: metric +subcat: lab +headline: Ultra-High and Extreme Fields MRI Lab +teasing: Laboratory, directed by Alexandre Vignaud, develops ultra-high and extreme fields MRI methods and hardware to map the human and non-human primate brains at unprecedented resolutions. +site: https://joliot.cea.fr/drf/joliot/en/Pages/research_entities/NeuroSpin/BAOBAB/METRIC.aspx +icon: +added: 2020 +permalink: labs/metric.html +--- diff --git a/_collections/_news/2019_jobs.md b/_collections/_news/2019_jobs.md deleted file mode 100644 index ab1555f..0000000 --- a/_collections/_news/2019_jobs.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -title: We are hiring a research in IA! -page: opportunities/ -date: 2024-09-01 ---- diff --git a/_collections/_news/2024_big2small.md b/_collections/_news/2024_big2small.md deleted file mode 100644 index b9d16e5..0000000 --- a/_collections/_news/2024_big2small.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -title: New paper showing that combining transfer learning and deep ensemble achieves SOTA results on disease classification tasks. -ext_url: https://doi.org/10.1016/j.neuroimage.2024.120665 -date: 2024-07-01 ---- diff --git a/_collections/_opportunities/cdi_ia_2024.md b/_collections/_opportunities/cdi_ia_2024.md deleted file mode 100644 index 48cf113..0000000 --- a/_collections/_opportunities/cdi_ia_2024.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -title: IA researcher in neuroimaging applied to precision psychiatry -cat: gaia -subcat: signature -type: permanent -profile: PhD required -contact: edouard.duchesnay@cea.fr -ext_url: https://www.emploi.cea.fr/Pages/Offre/detailoffre.aspx?idOffre=31315&idOrigine=513&LCID=1036&offerReference=2024-31315 -date: 2024-01-01 ---- diff --git a/_collections/_people/gaia_J-li.md b/_collections/_people/gaia_J-li.md deleted file mode 100644 index 792b94f..0000000 --- a/_collections/_people/gaia_J-li.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Jinpeng Li -desc: Research Engineer 2013-2014 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_a-depierrefeu.md b/_collections/_people/gaia_a-depierrefeu.md deleted file mode 100644 index cc049ce..0000000 --- a/_collections/_people/gaia_a-depierrefeu.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Amicie de Pierrefeu -desc: PhD 2019 (prepared under co-superv. E Duchesnay, P Ciuciu) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2019 ---- - diff --git a/_collections/_people/gaia_a-gaudin.md b/_collections/_people/gaia_a-gaudin.md deleted file mode 100644 index 49b51c3..0000000 --- a/_collections/_people/gaia_a-gaudin.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Aymerci Gaudin -desc: Research Engineer -position: engineer -cat: gaia -subcat: platform -avatar: -joined: 2024 ---- - diff --git a/_collections/_people/gaia_a-gloaguen.md b/_collections/_people/gaia_a-gloaguen.md deleted file mode 100644 index 70c5c83..0000000 --- a/_collections/_people/gaia_a-gloaguen.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Arnaud Gloaguen -desc: PhD 2020 (prepared under co-superv. A Tennenhaus, V Frouin) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2020 ---- - diff --git a/_collections/_people/gaia_a-grigis.md b/_collections/_people/gaia_a-grigis.md deleted file mode 100644 index 6907895..0000000 --- a/_collections/_people/gaia_a-grigis.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Antoine Grigis -desc: Research Engineer, PhD, HdR -position: engineer -cat: gaia -subcat: platform -site: https://agrigis.github.io -avatar: a-grigis.jpg -joined: 2014 ---- - diff --git a/_collections/_people/gaia_a-iftimovici.md b/_collections/_people/gaia_a-iftimovici.md deleted file mode 100644 index 5a655be..0000000 --- a/_collections/_people/gaia_a-iftimovici.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Anton Iftimovici -desc: PhD 2021 (prepared under co-superv. E Duchesnay, MO Krebs) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2021 ---- - diff --git a/_collections/_people/gaia_a-mihailov.md b/_collections/_people/gaia_a-mihailov.md deleted file mode 100644 index f5c86ae..0000000 --- a/_collections/_people/gaia_a-mihailov.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Angeline Mihailov -desc: PhD 2018 (prepared under co-superv. V Frouin, J Houenou, C Philippe) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2018 ---- - diff --git a/_collections/_people/gaia_a-rebei.md b/_collections/_people/gaia_a-rebei.md deleted file mode 100644 index 0e4e483..0000000 --- a/_collections/_people/gaia_a-rebei.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Amine Rebei -desc: PostDoc 2020-2022 (under superv. V Frouin) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2022 ---- - diff --git a/_collections/_people/gaia_b-dolle.md b/_collections/_people/gaia_b-dolle.md deleted file mode 100644 index 3c4ecc9..0000000 --- a/_collections/_people/gaia_b-dolle.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Bérangère Dollé -desc: Engineer 2022-2024 (under co-superv. E Duchesnay, A Grigis) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2022 ---- - diff --git a/_collections/_people/gaia_b-dufumier.md b/_collections/_people/gaia_b-dufumier.md deleted file mode 100644 index e59fd0e..0000000 --- a/_collections/_people/gaia_b-dufumier.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Benoit Dufumier -desc: PhD 2022 (prepared under co-superv. E Duchesnay, A Tenenhaus, P Gori and A Grigis) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2022 ---- - diff --git a/_collections/_people/gaia_c-damon.md b/_collections/_people/gaia_c-damon.md deleted file mode 100644 index b26f61d..0000000 --- a/_collections/_people/gaia_c-damon.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Cecilia Damon -desc: PhD 2011 (prepared under co-superv. E Duchesnay, J Poline, B Thirion) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2011 ---- - diff --git a/_collections/_people/gaia_c-fischer.md b/_collections/_people/gaia_c-fischer.md deleted file mode 100644 index c362acb..0000000 --- a/_collections/_people/gaia_c-fischer.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Clara Fischer -desc: Research Engineer -position: engineer -cat: gaia -subcat: cati -avatar: -joined: 2016 ---- - diff --git a/_collections/_people/gaia_c-philippe.md b/_collections/_people/gaia_c-philippe.md deleted file mode 100644 index 448ed32..0000000 --- a/_collections/_people/gaia_c-philippe.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Cathy Philippe -desc: Research Scientist -position: pi -cat: gaia -subcat: brainomics -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_c-pinaud.md b/_collections/_people/gaia_c-pinaud.md deleted file mode 100644 index d5fbcd3..0000000 --- a/_collections/_people/gaia_c-pinaud.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Clémence Pinaud -desc: Engineer 2014 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2014 ---- - diff --git a/_collections/_people/gaia_d-papadopoulos.md b/_collections/_people/gaia_d-papadopoulos.md deleted file mode 100644 index 128b6a2..0000000 --- a/_collections/_people/gaia_d-papadopoulos.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Dimitri Papadopoulos -desc: Research Engineer, PhD -position: engineer -cat: gaia -subcat: platform -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_d-riviere.md b/_collections/_people/gaia_d-riviere.md deleted file mode 100644 index d1cfc96..0000000 --- a/_collections/_people/gaia_d-riviere.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Denis Rivière -desc: Research Scientist -position: pi -cat: gaia -subcat: architecture -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_e-duchesnay.md b/_collections/_people/gaia_e-duchesnay.md deleted file mode 100644 index c761d87..0000000 --- a/_collections/_people/gaia_e-duchesnay.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Edouard Duchesnay -desc: Head of Laboratory, Research Director -position: pi -cat: gaia -subcat: signature -avatar: e-duchesnay.png -site: https://duchesnay.github.io -joined: 2006 ---- - diff --git a/_collections/_people/gaia_e-lefloch.md b/_collections/_people/gaia_e-lefloch.md deleted file mode 100644 index b0d6b1e..0000000 --- a/_collections/_people/gaia_e-lefloch.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Edith Lefloch -desc: PhD 2012 (prepared under co-superv. E Duchesnay, V Frouin) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2012 ---- - diff --git a/_collections/_people/gaia_f-hadj-selem.md b/_collections/_people/gaia_f-hadj-selem.md deleted file mode 100644 index 990fb79..0000000 --- a/_collections/_people/gaia_f-hadj-selem.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Fouad Hadj Selem -desc: PostDoc 2013-2015 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_i-uszynski.md b/_collections/_people/gaia_i-uszynski.md deleted file mode 100644 index 4c5d5d5..0000000 --- a/_collections/_people/gaia_i-uszynski.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Ivy Uszynski -desc: Research Engineer, PhD -position: engineer -cat: gaia -subcat: ginkgo -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_j-victor.md b/_collections/_people/gaia_j-victor.md deleted file mode 100644 index dd0a474..0000000 --- a/_collections/_people/gaia_j-victor.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Julie Victor -desc: Engineer 2019-2022 (under co-superv. E Duchesnay, A Grigis) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2019 ---- - diff --git a/_collections/_people/gaia_jf-mangin.md b/_collections/_people/gaia_jf-mangin.md deleted file mode 100644 index ec38c98..0000000 --- a/_collections/_people/gaia_jf-mangin.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Jean-François Mangin -desc: Head of BAOBAB research unit, Research Director -position: pi -cat: gaia -subcat: architecture -site: https://sites.google.com/view/jfmangin/ -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_l-dorval.md b/_collections/_people/gaia_l-dorval.md deleted file mode 100644 index 3cfa85f..0000000 --- a/_collections/_people/gaia_l-dorval.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Loic Dorval -desc: Engineer 2021-2024 (under co-superv. E Duchesnay, A Grigis) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2021 ---- - diff --git a/_collections/_people/gaia_l-megret.md b/_collections/_people/gaia_l-megret.md deleted file mode 100644 index 0a92294..0000000 --- a/_collections/_people/gaia_l-megret.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Lucile Mégret -desc: PostDoc 2020-2022 (under superv. V Frouin) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2022 ---- - diff --git a/_collections/_people/gaia_m-dubois.md b/_collections/_people/gaia_m-dubois.md deleted file mode 100644 index 82b4113..0000000 --- a/_collections/_people/gaia_m-dubois.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Mathieu Dubois -desc: PostDoc 2013-2014 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_p-auriau.md b/_collections/_people/gaia_p-auriau.md deleted file mode 100644 index 9320cd3..0000000 --- a/_collections/_people/gaia_p-auriau.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Pierre Auriau -desc: PhD 2025 (prepared under co-superv. E Duchesnay, JF Mangin, P Gorin, A Grigis) -position: gradstudent -cat: gaia -subcat: signature -avatar: -joined: 2021 ---- - diff --git a/_collections/_people/gaia_p-favre.md b/_collections/_people/gaia_p-favre.md deleted file mode 100644 index eb84c48..0000000 --- a/_collections/_people/gaia_p-favre.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Pauline Favre -desc: PostDoc 2016 (under co-superv. E Duchesnay, J. Houenou, and JF Mangin) -position: alumni -cat: gaia -subcat: signature -site: http://pauline.favre-univ.fr/ -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_p-gori.md b/_collections/_people/gaia_p-gori.md deleted file mode 100644 index 7714190..0000000 --- a/_collections/_people/gaia_p-gori.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Pietro Gori -desc: PostDoc 2016 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_r-louiset.md b/_collections/_people/gaia_r-louiset.md deleted file mode 100644 index 2b99942..0000000 --- a/_collections/_people/gaia_r-louiset.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Robin Louiset -desc: PhD 2024 (prepared under co-superv. E Duchesnay, P Gori, A Grigis) -position: alumni -cat: gaia -subcat: signature -avatar: -joined: 2024 ---- - diff --git a/_collections/_people/gaia_r-vock.md b/_collections/_people/gaia_r-vock.md deleted file mode 100644 index a693487..0000000 --- a/_collections/_people/gaia_r-vock.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Raphael Vock -desc: PhD 2027 (prepared under co-superv. E Duchesnay, A Grigis) -position: gradstudent -cat: gaia -subcat: signature -avatar: -joined: 2024 ---- - diff --git a/_collections/_people/gaia_s-kakar.md b/_collections/_people/gaia_s-kakar.md deleted file mode 100644 index ea715a0..0000000 --- a/_collections/_people/gaia_s-kakar.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Slim Karkar -desc: PostDoc 2018-2020 (under superv. V Frouin) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2020 ---- - diff --git a/_collections/_people/gaia_s-petiton.md b/_collections/_people/gaia_s-petiton.md deleted file mode 100644 index e404bd2..0000000 --- a/_collections/_people/gaia_s-petiton.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Sara Petiton -desc: PhD 2025 (prepared under co-superv. E Duchesnay, A Grigis) -position: gradstudent -cat: gaia -subcat: signature -avatar: -joined: 2022 ---- - diff --git a/_collections/_people/gaia_t-dupont.md b/_collections/_people/gaia_t-dupont.md deleted file mode 100644 index 85e615d..0000000 --- a/_collections/_people/gaia_t-dupont.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Thibault Dupont -desc: PhD 2026 (prepared under superv. E Duchesnay) -position: gradstudent -cat: gaia -subcat: signature -avatar: -site: https://www.researchgate.net/profile/Thibault-Dupont -joined: 2022 ---- - diff --git a/_collections/_people/gaia_t-lofstedt.md b/_collections/_people/gaia_t-lofstedt.md deleted file mode 100644 index 262ccd4..0000000 --- a/_collections/_people/gaia_t-lofstedt.md +++ /dev/null @@ -1,12 +0,0 @@ ---- -layout: -name: Tommy Lofstedt -desc: PostDoc 2013-2015 (under superv. E Duchesnay) -position: alumni -cat: gaia -subcat: signature -site: https://www.umu.se/en/staff/tommy-lofstedt/ -avatar: -joined: 2013 ---- - diff --git a/_collections/_people/gaia_v-frouin.md b/_collections/_people/gaia_v-frouin.md deleted file mode 100644 index 45774e9..0000000 --- a/_collections/_people/gaia_v-frouin.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Vincent Frouin -desc: Research Director -position: pi -cat: gaia -subcat: brainomics -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_y-cointepas.md b/_collections/_people/gaia_y-cointepas.md deleted file mode 100644 index e217aed..0000000 --- a/_collections/_people/gaia_y-cointepas.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Yann Cointepas -desc: Research Engineer -position: engineer -cat: gaia -subcat: cati -avatar: -joined: 2006 ---- - diff --git a/_collections/_people/gaia_y-mekki.md b/_collections/_people/gaia_y-mekki.md deleted file mode 100644 index c9a70f4..0000000 --- a/_collections/_people/gaia_y-mekki.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: -name: Yasmina Mekki -desc: PhD 2022 (prepared under co-superv. V Frouin, C Philippe, V Guillemot) -position: alumni -cat: gaia -subcat: brainomics -avatar: -joined: 2022 ---- - diff --git a/_collections/_research/gaia_architecture_isomap.md b/_collections/_research/gaia_architecture_isomap.md deleted file mode 100644 index dc785b3..0000000 --- a/_collections/_research/gaia_architecture_isomap.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: Comparative​​​ morphometry of the shape of the central sulcus using Isomap -cat: gaia -subcat: architecture -teasing: We examined here the morphological variability of the central sulcus in hominids, with a focus on the motor hand region, significant issue of human evolution. -icon: architecture_isomap.png -site: https://hal.science/hal-03824219 -added: 2022 ---- diff --git a/_collections/_research/gaia_brainomics_languageh2gwas.md b/_collections/_research/gaia_brainomics_languageh2gwas.md deleted file mode 100644 index a9487fe..0000000 --- a/_collections/_research/gaia_brainomics_languageh2gwas.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: The genetic architecture of language functional connectivity -cat: gaia -subcat: brainomics -teasing: Using data from the UK Biobank, the world's largest general population imaging-genetics cohort, a collaboration led by a team at BAOBAB (NeuroSpin) has identified genes involved in the genetic architecture of functional language connectivity. These genes could be a priority for studying natural language. -icon: brainomics_languageh2gwas.png -site: https://hal.sorbonne-universite.fr/hal-03566120v1 -added: 2022 ---- diff --git a/_collections/_research/gaia_ginkgo_micro.md b/_collections/_research/gaia_ginkgo_micro.md deleted file mode 100644 index 803e615..0000000 --- a/_collections/_research/gaia_ginkgo_micro.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: Mapping the brain microstructure across individuals and species -cat: gaia -subcat: ginkgo -teasing: White matter atlases of the human [a], chimpanzee [b] and Japanese quail brains [c]; Medusa simulations of realistic cortex [d] and white matter [e] brain tissues; color-encoded direction map of the Chenonceau brain scanned using 11.7 Tesla diffusion MRI at the mesoscale [f] and ​inference of the fine structural connectivity of the Chenonceau brain cortical ribbon using HPC spin- glass tractography [g]. -icon: ginkgo_micro.jpg -site: https://doi.org/10.21203/rs.3.rs-3772776/v1 -added: 2023 ---- diff --git a/_collections/_research/gaia_platform_bhb.md b/_collections/_research/gaia_platform_bhb.md deleted file mode 100644 index 78cfa4d..0000000 --- a/_collections/_research/gaia_platform_bhb.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: A Large-Scale Multi-Site Brain MRI Data-set for Age Prediction and Debiasing -cat: gaia -subcat: platform -teasing: BHB aggregates 10 publicly available datasets. Currently, it is focused only on Healthy Controls (HC) since the main challenge consists in modeling the (normal) brain development by building a robust brain age predictor. BHB contains N=5330 3D T1 brain MRI scans from HC acquired on 71 different acquisition sites coming from European-American, European, and Asian individuals. BHB provides the participants phenotype as well as site and scanner information associated with each image. Some widespread confounds are also proposed, such as the Total Intracranial Volume (TIV), the CerebroSpinal Fluid Volume (CSFV), the Gray Matter Volume (GMV), and the White Matter Volume (WMV). -icon: platform_bhb.jpg -site: https://hal.science/hal-04482833 -added: 2022 ---- diff --git a/_collections/_research/gaia_platform_surfify.md b/_collections/_research/gaia_platform_surfify.md deleted file mode 100644 index 8e37ce3..0000000 --- a/_collections/_research/gaia_platform_surfify.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: Cortical brain surface and deep learning -cat: gaia -subcat: platform -teasing: Surfify is an open source Python module that simplifies the development of neural network architectures that relies on cortical surfaces. It provides common architectures, icosahedral mesh operators, and cortical augmentations. -icon: platform_surfify.png -site: https://hal.science/hal-04471607 -added: 2024 ---- diff --git a/_collections/_research/gaia_signature_big2small.md b/_collections/_research/gaia_signature_big2small.md deleted file mode 100644 index 6e8710b..0000000 --- a/_collections/_research/gaia_signature_big2small.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -layout: -title: Tranfer learning strategy to bridge the gap between big and small data -cat: gaia -subcat: signature -teasing: Exploring the potential of representation and transfer learning for anatomical neuroimaging - application to psychiatry. -icon: signature_big2small.png -site: https://hal.science/hal-04436585 -added: 2024 ---- diff --git a/_config.yml b/_config.yml index d768bdf..5949610 100644 --- a/_config.yml +++ b/_config.yml @@ -1,12 +1,12 @@ # Site settings -title: GAIA -subtitle: Brain Imaging and Data Science Lab -baseurl: #gaia -url: # https://baobablab.github.io/ +title: BAOBAB +subtitle: Unit +baseurl: #baobab +url: # https://neurospin.github.io/ # Contacts -email: edouard.duchesnay@cea.fr +email: jean-francois.mangin@cea.fr author: street_address: city: @@ -38,31 +38,6 @@ markdown: kramdown collections_dir: _collections collections: - opportunities: - output : true - permalink : /:collection/:path - - collaborators: - output : true - permalink : /colleborators/:title/index.html - - people: - output : true - permalink : /people/:title/index.html - - news: - output : true - permalink : /news/:title/index.html - - biblio: - output : true - permalink : /biblio/:title/index.html - - research: - output : true - permalink : /research/:title/index.html - labs: output : true permalink : /labs/:title/index.html - diff --git a/_layouts/page.html b/_layouts/page.html index 23ef088..a52bbb9 100644 --- a/_layouts/page.html +++ b/_layouts/page.html @@ -36,8 +36,6 @@

{{ page.title }}

- {% include sidebar.html %} - {% include footer.html %} diff --git a/_layouts/page_lab.html b/_layouts/page_lab.html index 1efe6cc..fc5f60c 100644 --- a/_layouts/page_lab.html +++ b/_layouts/page_lab.html @@ -4,10 +4,7 @@ html5up.net | @ajlkn Free for personal and commercial use under the CCA 3.0 license (html5up.net/license) --> -{% assign lab = "gaia" %} -{% assign teams_sorted = site.labs | where: "cat", lab | where: "subcat", "team" | sort: "title" %} -{% assign cells_sorted = site.labs | where: "cat", lab | where: "subcat", "cell" | sort: "title" %} -{% assign research_sorted = site.research | sort: 'added' | reverse %} +{% assign labs_sorted = site.labs | sort: "title" %} @@ -36,10 +33,10 @@

{{ page.title }}

{{ content }} - +
-

Teams

+

Labs

- {% for team in teams_sorted %} + {% for team in labs_sorted %}
-

{{ team.title }}: {{team.headline}}

-

- Leader: - -

-

{{ team.teasing }}

    {% if team.site %} @@ -74,70 +60,9 @@

    {{ team.title }}: {{team.headline}}

- - -
-
-

Cells

-
- -
- {% for cell in cells_sorted %} -
- -

{{ cell.title }}

-

- Leader: - -

- -

{{ cell.teasing }}

-
    - {% if cell.site %} -
  • More
    • - {% else %} -
  • More
    • - {% endif %} -
-
- {% endfor %} -
-
- - - - - - {% include sidebar.html %} - {% include footer.html %} diff --git a/biblio_other.md b/biblio_other.md deleted file mode 100644 index dccb8a9..0000000 --- a/biblio_other.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: -layout: page_select -permalink: bibliography.html ---- - - -

Publications of the {{site.title}}

- -{% assign today = site.time | date: '%Y' %} -{% assign biblio_sorted = site.biblio | sort: 'subcat' | reverse %} - -{% for idx in (0..4) %} - -{% assign year = today | minus: idx %} - -
-

{{year}}

-
- -{% assign section = "" %} -
- {% for entry in biblio_sorted %} - {% if entry.year == year %} - {% if section != entry.subcat %} - {% assign section = entry.subcat %} -
- {{section|upcase}}: -
- {% endif %} -
  • -
    - • - {% if entry.doi %} - {% capture title %}{{entry.title}}{% endcapture %} - {% else %} - {% assign title = {{entry.title}} %} - {% endif %} - {% if entry.journal %} - {{entry.author}}: {{title}}, {{entry.journal}} ({{entry.year}}) - {% elsif entry.booktitle %} - {{entry.author}}: {{title}}, {{entry.booktitle}} ({{entry.year}}) - {% else %} - {{entry.author}}: {{title}} ({{entry.year}}) - {% endif %} -
    -
    • - {% endif %} - {% endfor %} -
    -
    - -{% endfor %} - diff --git a/biblio_selected.md b/biblio_selected.md deleted file mode 100644 index 938767c..0000000 --- a/biblio_selected.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: -layout: page_select -permalink: bibliography/bestof.html ---- - -

    Selected publications of the {{site.title}}

    - -{% assign today = site.time | date: '%Y' %} -{% assign biblio_sorted = site.biblio | sort: 'year' | reverse %} -{% assign year = today | minus: 5 %} - -
    - {% for entry in biblio_sorted %} - {% if entry.year > year and entry.bestof %} -
  • -
    - • - {% if entry.doi %} - {% capture title %}{{entry.title}}{% endcapture %} - {% else %} - {% assign title = {{entry.title}} %} - {% endif %} - {% if entry.journal %} - {{entry.author}}: {{title}}, {{entry.journal}} ({{entry.year}}) - {% elsif entry.booktitle %} - {{entry.author}}: {{title}}, {{entry.booktitle}} ({{entry.year}}) - {% else %} - {{entry.author}}: {{title}} ({{entry.year}}) - {% endif %} -
    -
    • - {% endif %} - {% endfor %} -
    -
    - - diff --git a/bibutils/bib2md b/bibutils/bib2md deleted file mode 100644 index 91f2b59..0000000 --- a/bibutils/bib2md +++ /dev/null @@ -1,89 +0,0 @@ -########################################################################## -# NSAp - Copyright (C) CEA, 2019 -# Distributed under the terms of the CeCILL-B license, as published by -# the CEA-CNRS-INRIA. Refer to the LICENSE file or to -# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html -# for details. -########################################################################## - - -# Imports -from pprint import pprint -import os -import argparse -import subprocess -import yaml - -# Define command line -doc = """ -Convert BIBTEX to MD. -Must install first pybtex. -python3 bib2md -i data/architecture_v-20240621.bib -o ../_collections/_biblio/architecture -c gaia -s architecture -python3 bib2md -i data/signature_v-20240621.bib -o ../_collections/_biblio/signature -c gaia -s signature -python3 bib2md -i data/brainomics_v-20240621.bib -o ../_collections/_biblio/brainomics -c gaia -s brainomics -python3 bib2md -i data/platform_v-20240621.bib -o ../_collections/_biblio/platform -c gaia -s platform -python3 bib2md -i data/ginkgo_v-20240621.bib -o ../_collections/_biblio/ginkgo -c gaia -s ginkgo -""" -parser = argparse.ArgumentParser(description=doc) -parser.add_argument( - "-i", "--infile", - help="the input .bib file.") -parser.add_argument( - "-o", "--outdir", - help="the destination folder.") -parser.add_argument( - "-c", "--cat", - help="the category.") -parser.add_argument( - "-s", "--subcat", - help="the category.") -args = parser.parse_args() - - -# Create output directory -if not os.path.isdir(args.outdir): - os.mkdir(args.outdir) - - -# Convert bib to yaml with pybtex-convert -bibfile = os.path.join(args.outdir, "bib.yaml") -cmd = ["pybtex-convert", args.infile, bibfile] -subprocess.call(cmd) - - -# Load biblio -with open(bibfile, "rt") as of: - biblio = yaml.safe_load(of)["entries"] - - -# Create single entries -for key, item in biblio.items(): - print("--", key) - # pprint(item) - key = key.replace(os.sep, "_") - if not "first" in item["author"][0]: - continue - item["author"] = "{0} {1} et al.".format( - item["author"][0]["first"], - item["author"][0]["last"]) - md_file = os.path.join(args.outdir, f"{args.subcat}_{key}.md") - content = ["---", f"cat: {args.cat}", f"subcat: {args.subcat}", - "bestof: false"] - for _key in ["author", "title", "journal", "year", "type", "url", "doi", - "booktitle", "team"]: - value = item.get(_key, None) - if value is None: - continue - for char in ("\n", "{", "}", "\\'", '"'): - value = value.replace(char, "") - for char in (":", ): - value = value.replace(char, " -") - content.append(u"{0}: {1}".format(_key, value)) - content += ["---"] - print(content) - with open(md_file, "wt") as of: - of.write("\n".join(content)) - - -# Cleaning -os.remove(bibfile) diff --git a/bibutils/data/architecture_v-20240621.bib b/bibutils/data/architecture_v-20240621.bib deleted file mode 100644 index 32110ab..0000000 --- a/bibutils/data/architecture_v-20240621.bib +++ /dev/null @@ -1,5682 +0,0 @@ - -@misc{sun_constructing_2009, - address = {London, UK}, - title = {Constructing a {Dictionary} of {Human} {Brain} {Folding} {Patterns}}, - copyright = {All rights reserved}, - author = {Sun, Z. Y. and Perrot, M. and Tucholka, A. and Riviere, D. and Mangin, J. F.}, - year = {2009}, -} - -@article{mangin_-vivo_2010, - title = {In-vivo measurement of cortical morphology: means and meanings}, - volume = {23}, - issn = {1350-7540}, - shorttitle = {In-vivo measurement of cortical morphology}, - url = {https://journals.lww.com/co-neurology/Abstract/2010/08000/In_vivo_measurement_of_cortical_morphology__means.4.aspx}, - doi = {10.1097/WCO.0b013e32833a0afc}, - abstract = {Purpose of review  - Study of the variability of the cortical mantle thickness is now a key issue in neuroimaging. Here we describe a more recent trend aiming at the study of the variability of the cortical folding morphology. - Recent findings  - Computerized three-dimensional versions of gyrification index and other morphometric features dedicated to the folding patterns are modified in psychiatric syndromes and neurologic disorders. These observations provide new insights into the mechanisms involved in abnormal development or abnormal aging. - Summary  - Quantification of the folding morphology will contribute to the global endeavor aiming at building biomarkers from neuroimaging data, with a specific focus on developmental diseases.}, - language = {en-US}, - number = {4}, - urldate = {2021-02-09}, - journal = {Current Opinion in Neurology}, - author = {Mangin, Jean-François and Jouvent, Eric and Cachia, Arnaud}, - month = aug, - year = {2010}, - keywords = {gyrification index, morphometry, Cortical folding, plasticity}, - pages = {359--367}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: Neurospin}, - annote = {Times Cited: 58}, - annote = {Unati}, - file = {Mangin et al. - 2010 - In-vivo measurement of cortical morphology means .pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/J44T8WFM/Mangin et al. - 2010 - In-vivo measurement of cortical morphology means .pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/C79XPYX5/In_vivo_measurement_of_cortical_morphology__means.4.html:text/html}, -} - -@article{cachia_shape_2014, - title = {The shape of the {ACC} contributes to cognitive control efficiency in preschoolers}, - volume = {26}, - issn = {1530-8898}, - doi = {10.1162/jocn_a_00459}, - abstract = {Cognitive success at school and later in life is supported by executive functions including cognitive control (CC). The pFC plays a major role in CC, particularly the dorsal part of ACC or midcingulate cortex. Genes, environment (including school curricula), and neuroplasticity affect CC. However, no study to date has investigated whether ACC sulcal pattern, a stable brain feature primarily determined in utero, influences CC efficiency in the early stages of cognitive and neural development. Using anatomical MRI and three-dimensional reconstruction of cortical folds, we investigated the effect that ACC sulcal pattern may have on the Stroop score, a classical behavioral index of CC efficiency, in 5-year-old preschoolers. We found higher CC efficiency, that is, lower Stroop interference scores for both RTs and error rates, in children with asymmetrical ACC sulcal pattern (i.e., different pattern in each hemisphere) compared with children with symmetrical pattern (i.e., same pattern in both hemispheres). Critically, ACC sulcal pattern had no effect on performance in the forward and backward digit span tasks suggesting that ACC sulcal pattern contributes to the executive ability to resolve conflicts but not to the ability to maintain and manipulate information in working memory. This finding provides the first evidence that preschoolers' CC efficiency is likely associated with ACC sulcal pattern, thereby suggesting that the brain shape could result in early constraints on human executive ability.}, - language = {eng}, - number = {1}, - journal = {Journal of Cognitive Neuroscience}, - author = {Cachia, Arnaud and Borst, Grégoire and Vidal, Julie and Fischer, Clara and Pineau, Arlette and Mangin, Jean-François and Houdé, Olivier}, - month = jan, - year = {2014}, - pmid = {23915057}, - keywords = {Humans, Brain Mapping, Female, Male, Reaction Time, Psychomotor Performance, Photic Stimulation, Cognition, Gyrus Cinguli, Child, Preschool, Memory, Short-Term}, - pages = {96--106}, -} - -@article{roca_sulcus-based_2015, - title = {Sulcus-based {MR} analysis of focal cortical dysplasia located in the central region}, - volume = {10}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0122252}, - abstract = {OBJECTIVE: Focal cortical dysplasias (FCDs) are mainly located in the frontal region, with a particular tropism for the central sulcus. Up to 30\% of lesions are undetected (magnetic resonance [MR]-negative FCD patients) or belatedly diagnosed by visual analysis of MR images. We propose an automated sulcus-based method to analyze abnormal sulcal patterns associated with central FCD, taking into account the normal interindividual sulcal variability. -METHODS: We retrospectively studied 29 right-handed patients with FCD in the central region (including 12 MR negative histologically-confirmed cases) and 29 right-handed controls. The analysis of sulcal abnormalities from T1-weighted MR imaging (MRI) was performed using a graph-based representation of the cortical folds and an automated sulci recognition system, providing a new quantitative criterion to describe sulcal patterns, termed sulcus energy. -RESULTS: Group analysis showed that the central sulcus in the hemisphere ipsilateral to the FCD exhibited an abnormal sulcal pattern compared with controls (p = 0.032). FCDs were associated with abnormal patterns of the central sulci compared with controls (p = 0.006), a result that remained significant when MR-negative and MR-positive patients were considered separately, while the effects of sex, age and MR-field were not significant. At the individual level, sulcus energy alone failed to detect the FCD lesion. We found, however, a significant association between maximum z-scores and the site of FCD (p = 0.0046) which remained significant in MR-negative (p = 0.024) but not in MR-positive patients (p = 0.058). The maximum z-score pointed to an FCD sulcus in four MR-negative and five MR-positive patients. -CONCLUSIONS: We identified abnormal sulcal patterns in patients with FCD of the central region compared with healthy controls. The abnormal sulcal patterns ipsilateral to the FCD and the link between sulcus energy and the FCD location strengthen the interest of sulcal abnormalities in FCD patients.}, - language = {eng}, - number = {3}, - journal = {PloS One}, - author = {Roca, Pauline and Mellerio, Charles and Chassoux, Francine and Rivière, Denis and Cachia, Arnaud and Charron, Sylvain and Lion, Stéphanie and Mangin, Jean-François and Devaux, Bertrand and Meder, Jean-François and Oppenheim, Catherine}, - year = {2015}, - pmid = {25822985}, - pmcid = {PMC4378936}, - keywords = {Humans, Adult, Adolescent, Female, Male, Young Adult, Cerebral Cortex, Case-Control Studies, Retrospective Studies, Frontal Lobe, Malformations of Cortical Development}, - pages = {e0122252}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 25822985}, -} - -@article{pardo_study_2013, - title = {Study of the variability of short association bundles on a {HARDI} database}, - volume = {2013}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2013.6609441}, - abstract = {The construction of an atlas of the human brain connectome, in particular, the cartography of fiber bundles of superficial white matter (SWM) is a complex and unachieved task. Its description is essential for the understanding of human brain function and the study of several pathologies. In this work we applied an automatic white matter bundle segmentation method proposed in the literature for the analysis of the variability of a big amount of superficial white matter bundles. The method was applied to 30 subjects of a high quality HARDI database, adding several processing steps in order to improve the results. Then we calculated some indices for studying the variability of 40 SWM fiber bundles from each hemisphere, and we constructed a model of these bundles in the MNI standard space.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Pardo, Edison and Guevara, Pamela and Duclap, Delphine and Houenou, Josselin and Lebois, Alice and Schmitt, Benoît and Le Bihan, Denis and Mangin, Jean-François and Poupon, Cyril}, - year = {2013}, - pmid = {24109628}, - keywords = {Humans, Automatic Data Processing, Diffusion Magnetic Resonance Imaging, Databases, Factual, Connectome, Radiography}, - pages = {77--80}, -} - -@article{mangin_spatial_2016, - title = {Spatial normalization of brain images and beyond}, - volume = {33}, - issn = {1361-8423}, - doi = {10.1016/j.media.2016.06.008}, - abstract = {The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images.}, - language = {eng}, - journal = {Medical Image Analysis}, - author = {Mangin, J.-F. and Lebenberg, J. and Lefranc, S. and Labra, N. and Auzias, G. and Labit, M. and Guevara, M. and Mohlberg, H. and Roca, P. and Guevara, P. and Dubois, J. and Leroy, F. and Dehaene-Lambertz, G. and Cachia, A. and Dickscheid, T. and Coulon, O. and Poupon, C. and Rivière, D. and Amunts, K. and Sun, Z. Y.}, - month = oct, - year = {2016}, - pmid = {27344104}, - keywords = {Algorithms, Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Connectome, Diffeomorphism, Spatial normalization, Cortical folding pattern}, - pages = {127--133}, -} - -@article{germanaud_simplified_2014, - title = {Simplified gyral pattern in severe developmental microcephalies? {New} insights from allometric modeling for spatial and spectral analysis of gyrification}, - volume = {102 Pt 2}, - issn = {1095-9572}, - shorttitle = {Simplified gyral pattern in severe developmental microcephalies?}, - doi = {10.1016/j.neuroimage.2014.07.057}, - abstract = {The strong positive-allometric relationship between brain size, cortical extension and gyrification complexity, recently highlighted in the general population, could be modified by brain developmental disorders. Indeed, in case of brain growth insufficiency, the pathophysiological relevance of the "simplified gyral pattern" phenotype is strongly disputed since almost no genotype-phenotype correlations have been found in primary microcephalies. Using surface scaling analysis and newly-developed spectral analysis of gyrification (Spangy), we tested whether the gyral simplification in groups of severe microcephalies related to ASPM, PQBP1 or fetal-alcohol-syndrome could be fully explained by brain size reduction according to the allometric scaling law established in typically-developing control groups, or whether an additional disease effect was to be suspected. We found the surface area reductions to be fully explained by scaling effect, leading to predictable folding intensities measured by gyrification indices. As for folding pattern assessed by spectral analysis, scaling effect also accounted for the majority of the variations, but an additional negative or positive disease effect was found in the case of ASPM and PQBP1-linked microcephalies, respectively. Our results point out the necessity of taking allometric scaling into account when studying the gyrification variability in pathological conditions. They also show that the quantitative analysis of gyrification complexity through spectral analysis can enable distinguishing between even (predictable, non-specific) and uneven (unpredictable, maybe disease-specific) gyral simplifications.}, - language = {eng}, - journal = {NeuroImage}, - author = {Germanaud, D. and Lefèvre, J. and Fischer, C. and Bintner, M. and Curie, A. and des Portes, V. and Eliez, S. and Elmaleh-Bergès, M. and Lamblin, D. and Passemard, S. and Operto, G. and Schaer, M. and Verloes, A. and Toro, R. and Mangin, J. F. and Hertz-Pannier, L.}, - month = nov, - year = {2014}, - pmid = {25107856}, - keywords = {Humans, Image Interpretation, Computer-Assisted, Brain Mapping, Adult, Adolescent, Child, Female, Male, Young Adult, Middle Aged, allometry, Carrier Proteins, Complexity, Fetal Alcohol Spectrum Disorders, Microcephaly, Mutation, Nerve Tissue Proteins, Nuclear Proteins, Spatial Analysis, Spectral}, - pages = {317--331}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {Times Cited: 2}, - annote = {UnatiPMID: 25107856}, -} - -@article{katz_similar_2016, - title = {Similar white matter but opposite grey matter changes in schizophrenia and high-functioning autism}, - volume = {134}, - issn = {1600-0447}, - doi = {10.1111/acps.12579}, - abstract = {OBJECTIVE: High-functioning autism (HFA) and schizophrenia (SZ) are two of the main neurodevelopmental disorders, sharing several clinical dimensions and risk factors. Their exact relationship is poorly understood, and few studies have directly compared both disorders. Our aim was thus to directly compare neuroanatomy of HFA and SZ using a multimodal MRI design. -METHODS: We scanned 79 male adult subjects with 3T MRI (23 with HFA, 24 with SZ and 32 healthy controls, with similar non-verbal IQ). We compared them using both diffusion-based whole-brain tractography and T1 voxel-based morphometry. -RESULTS: HFA and SZ groups exhibited similar white matter alterations in the left fronto-occipital inferior fasciculus with a decrease in generalized fractional anisotropy compared with controls. In grey matter, the HFA group demonstrated bilateral prefrontal and anterior cingulate increases in contrast with prefrontal and left temporal reductions in SZ. -CONCLUSION: HFA and SZ may share common white matter deficits in long-range connections involved in social functions, but opposite grey matter abnormalities in frontal regions that subserve complex cognitive functions. Our results are consistent with the fronto-occipital underconnectivity theory of HFA and the altered connectivity hypothesis of SZ and suggest the existence of both associated and diametrical liabilities to these two conditions.}, - language = {eng}, - number = {1}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Katz, J. and d'Albis, M.-A. and Boisgontier, J. and Poupon, C. and Mangin, J.-F. and Guevara, P. and Duclap, D. and Hamdani, N. and Petit, J. and Monnet, D. and Le Corvoisier, P. and Leboyer, M. and Delorme, R. and Houenou, J.}, - month = jul, - year = {2016}, - pmid = {27105136}, - keywords = {Humans, MRI, Brain Mapping, Adult, Male, Autistic Disorder, Young Adult, Anisotropy, Gray Matter, Cross-Sectional Studies, Multimodal Imaging, autism, connectivity}, - pages = {31--39}, -} - -@article{sun_shape_2017, - title = {Shape analysis of the cingulum, uncinate and arcuate fasciculi in patients with bipolar disorder}, - volume = {42}, - issn = {1488-2434}, - abstract = {BACKGROUND: Abnormal maturation of brain connectivity is supposed to underlie the dysfunctional emotion regulation in patients with bipolar disorder (BD). To test this hypothesis, white matter integrity is usually investigated using measures of water diffusivity provided by MRI. Here we consider a more intuitive aspect of the morphometry of the white matter tracts: the shape of the fibre bundles, which is associated with neurodevelopment. We analyzed the shape of 3 tracts involved in BD: the cingulum (CG), uncinate fasciculus (UF) and arcuate fasciculus (AF). -METHODS: We analyzed diffusion MRI data in patients with BD and healthy controls. The fibre bundles were reconstructed using Q-ball-based tractography and automated segmentation. Using Isomap, a manifold learning method, the differences in the shape of the reconstructed bundles were visualized and quantified. -RESULTS: We included 112 patients and 82 controls in our analysis. We found the left AF of patients to be further extended toward the temporal pole, forming a tighter hook than in controls. We found no significant difference in terms of shape for the left UF, the left CG or the 3 right fasciculi. However, in patients compared with controls, the ventrolateral branch of the left UF in the orbitofrontal region had a tendency to be larger, and the left CG of patients had a tendency to be smaller in the frontal lobe and larger in the parietal lobe. -LIMITATIONS: This was a cross-sectional study. -CONCLUSION: Our results suggest neurodevelopmental abnormalities in the left AF in patients with BD. The statistical tendencies observed for the left UF and left CG deserve further study.}, - language = {eng}, - number = {1}, - journal = {Journal of psychiatry \& neuroscience: JPN}, - author = {Sun, Zhong Yi and Houenou, Josselin and Duclap, Delphine and Sarrazin, Samuel and Linke, Julia and Daban, Claire and Hamdani, Nora and d'Albis, Marc-Antoine and Le Corvoisier, Philippe and Guevara, Pamela and Delavest, Marine and Bellivier, Frank and Bellivier, Frank and Almeida, Jorge and Versace, Amelia and Poupon, Cyril and Leboyer, Marion and Phillips, Mary and Wessa, Michèle and Mangin, Jean-François}, - year = {2017}, - pmid = {28234596}, - pmcid = {PMC5373709}, - keywords = {Brain, Humans, Image Processing, Computer-Assisted, Adult, Adolescent, Female, Male, Young Adult, Bipolar Disorder, Middle Aged, Diffusion Magnetic Resonance Imaging, Neural Pathways, Aged, Machine Learning, Cross-Sectional Studies, ABNORMALITIES, CORPUS-CALLOSUM, I DISORDER, INDIVIDUALS, KeyWords Plus:SPATIAL STATISTICS, NERVOUS-SYSTEM, RATING-SCALE}, - pages = {27--36}, - annote = {The following values have no corresponding Zotero field:number: 1}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unirs}, - annote = {UnirsPMID: 28234596 PMCID: PMC5373709}, -} - -@article{guevara_reproducibility_2017, - title = {Reproducibility of superficial white matter tracts using diffusion-weighted imaging tractography}, - volume = {147}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2016.11.066}, - abstract = {Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of pathogenesis triggered by abnormal connectivity. In this work we automatically created a multi-subject atlas of SWM diffusion-based bundles of the whole brain. For each subject, the complete cortico-cortical tractogram is first split into sub-tractograms connecting pairs of gyri. Then intra-subject shape-based fiber clustering performs compression of each sub-tractogram into a set of bundles. Proceeding further with shape-based clustering provides a match of the bundles across subjects. Bundles found in most of the subjects are instantiated in the atlas. To increase robustness, this procedure was performed with two independent groups of subjects, in order to discard bundles without match across the two independent atlases. Finally, the resulting intersection atlas was projected on a third independent group of subjects in order to filter out bundles without reproducible and reliable projection. The final multi-subject diffusion-based U-fiber atlas is composed of 100 bundles in total, 50 per hemisphere, from which 35 are common to both hemispheres.}, - language = {eng}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Román, Claudio and Houenou, Josselin and Duclap, Delphine and Poupon, Cyril and Mangin, Jean François and Guevara, Pamela}, - month = feb, - year = {2017}, - pmid = {28034765}, - keywords = {Brain, Humans, Reproducibility of Results, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Diffusion Tensor Imaging, White Matter, Segmentation, Atlases as Topic, Bundle atlas, Fiber clustering, Short association fibers, Tractography segmentation, White matter tracts, ATLAS, Author Keywords:Diffusion MRI, CONNECTIONS, DATASETS, DISSECTION, FIBERS, IMAGES, KeyWords Plus:HUMAN BRAIN, RECONSTRUCTION, Diffusion MRI}, - pages = {703--725}, - annote = {The following values have no corresponding Zotero field:section: label: ACL}, - annote = {Unirs}, -} - -@article{kersbergen_relation_2016, - title = {Relation between clinical risk factors, early cortical changes, and neurodevelopmental outcome in preterm infants}, - volume = {142}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2016.07.010}, - abstract = {Cortical folding mainly takes place in the third trimester of pregnancy and may therefore be influenced by preterm birth. The aim of this study was to evaluate the development of specific cortical structures between early age (around 30weeks postmenstrual age) and term-equivalent age (TEA, around 40weeks postmenstrual age) in 71 extremely preterm infants, and to associate this to clinical characteristics and neurodevelopmental outcome at two years of age. First, analysis showed that the central sulcus (CS), lateral fissure (LF) and insula (INS) were present at early MRI in all infants, whereas the other sulci (post-central sulcus [PCS], superior temporal sulcus [STS], superior [SFS] and inferior [IFS] frontal sulcus) were only seen in part of the infants. Relative growth from early to TEA examination was largest in the SFS. A rightward asymmetry of the surface area was seen in development between both examinations except for the LF, which showed a leftward asymmetry at both time points. Second, lower birth weight z-score, multiple pregnancy and prolonged mechanical ventilation showed negative effects on cortical folding of the CS, LF, INS, STS and PCS, mainly on the first examination, suggesting that sulci developing the earliest were the most affected by clinical factors. Finally, in this cohort, a clear association between cortical folding and neurodevelopmental outcome at two years corrected age was found, particularly for receptive language.}, - language = {eng}, - journal = {NeuroImage}, - author = {Kersbergen, Karina J. and Leroy, François and Išgum, Ivana and Groenendaal, Floris and de Vries, Linda S. and Claessens, Nathalie H. P. and van Haastert, Ingrid C. and Moeskops, Pim and Fischer, Clara and Mangin, Jean-François and Viergever, Max A. and Dubois, Jessica and Benders, Manon J. N. L.}, - month = nov, - year = {2016}, - pmid = {27395393}, - keywords = {Humans, Female, Male, Cerebral Cortex, Infant, Newborn, Infant, Premature, Child, Preschool, Child Development, Clinical data, Cortical folding, Gestational Age, Infant, Extremely Premature, Neurodevelopmental outcome, Preterm infants}, - pages = {301--310}, -} - -@article{benezit_organising_2015, - title = {Organising white matter in a brain without corpus callosum fibres}, - volume = {63}, - issn = {1973-8102}, - doi = {10.1016/j.cortex.2014.08.022}, - abstract = {Isolated corpus callosum dysgenesis (CCD) is a congenital malformation which occurs during early development of the brain. In this study, we aimed to identify and describe its consequences beyond the lack of callosal fibres, on the morphology, microstructure and asymmetries of the main white matter bundles with diffusion imaging and fibre tractography. Seven children aged between 9 and 13 years old and seven age- and gender-matched control children were studied. First, we focused on bundles within the mesial region of the cerebral hemispheres: the corpus callosum, Probst bundles and cingulum which were selected using a conventional region-based approach. We demonstrated that the Probst bundles have a wider connectivity than the previously described rostrocaudal direction, and a microstructure rather distinct from the cingulum but relatively close to callosal remnant fibres. A sigmoid bundle was found in two partial ageneses. Second, the corticospinal tract, thalamic radiations and association bundles were extracted automatically via an atlas of adult white matter bundles to overcome bias resulting from a priori knowledge of the bundles' anatomical morphology and trajectory. Despite the lack of callosal fibres and the colpocephaly observed in CCD, all major white matter bundles were identified with a relatively normal morphology, and preserved microstructure (i.e. fractional anisotropy, mean diffusivity) and asymmetries. Consequently the bundles' organisation seems well conserved in brains with CCD. These results await further investigations with functional imaging before apprehending the cognition variability in children with isolated dysgenesis.}, - language = {eng}, - journal = {Cortex; a Journal Devoted to the Study of the Nervous System and Behavior}, - author = {Bénézit, Audrey and Hertz-Pannier, Lucie and Dehaene-Lambertz, Ghislaine and Monzalvo, Karla and Germanaud, David and Duclap, Delphine and Guevara, Pamela and Mangin, Jean-François and Poupon, Cyril and Moutard, Marie-Laure and Dubois, Jessica}, - month = feb, - year = {2015}, - pmid = {25282054}, - keywords = {Brain, Humans, MRI, Adolescent, Child, Female, Male, Corpus Callosum, Nerve Fibers, Tractography, Atlas, Diffusion magnetic resonance imaging, agenesis, Agenesis of Corpus Callosum, Corpus callosum dysgenesis, Hypoplasia, Probst bundle, White matter bundles}, - pages = {155--171}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Times Cited: 3}, - annote = {Unati - Unirs - UniactPMID: 25282054 }, -} - -@article{leroy_new_2015, - title = {New human-specific brain landmark: the depth asymmetry of superior temporal sulcus}, - volume = {112}, - issn = {1091-6490}, - shorttitle = {New human-specific brain landmark}, - doi = {10.1073/pnas.1412389112}, - abstract = {Identifying potentially unique features of the human cerebral cortex is a first step to understanding how evolution has shaped the brain in our species. By analyzing MR images obtained from 177 humans and 73 chimpanzees, we observed a human-specific asymmetry in the superior temporal sulcus at the heart of the communication regions and which we have named the "superior temporal asymmetrical pit" (STAP). This 45-mm-long segment ventral to Heschl's gyrus is deeper in the right hemisphere than in the left in 95\% of typical human subjects, from infanthood till adulthood, and is present, irrespective of handedness, language lateralization, and sex although it is greater in males than in females. The STAP also is seen in several groups of atypical subjects including persons with situs inversus, autistic spectrum disorder, Turner syndrome, and corpus callosum agenesis. It is explained in part by the larger number of sulcal interruptions in the left than in the right hemisphere. Its early presence in the infants of this study as well as in fetuses and premature infants suggests a strong genetic influence. Because this asymmetry is barely visible in chimpanzees, we recommend the STAP region during midgestation as an important phenotype to investigate asymmetrical variations of gene expression among the primate lineage. This genetic target may provide important insights regarding the evolution of the crucial cognitive abilities sustained by this sulcus in our species, namely communication and social cognition.}, - language = {eng}, - number = {4}, - journal = {Proceedings of the National Academy of Sciences of the United States of America}, - author = {Leroy, François and Cai, Qing and Bogart, Stephanie L. and Dubois, Jessica and Coulon, Olivier and Monzalvo, Karla and Fischer, Clara and Glasel, Hervé and Van der Haegen, Lise and Bénézit, Audrey and Lin, Ching-Po and Kennedy, David N. and Ihara, Aya S. and Hertz-Pannier, Lucie and Moutard, Marie-Laure and Poupon, Cyril and Brysbaert, Marc and Roberts, Neil and Hopkins, William D. and Mangin, Jean-François and Dehaene-Lambertz, Ghislaine}, - month = jan, - year = {2015}, - pmid = {25583500}, - pmcid = {PMC4313811}, - keywords = {anatomy, Humans, Adult, Child, Child Development Disorders, Pervasive, Female, Male, Temporal Lobe, Middle Aged, Infant, Animals, Cognition, Radiography, Agenesis of Corpus Callosum, human-specific, Pan troglodytes, Situs Inversus, STS, Turner Syndrome}, - pages = {1208--1213}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACL}, - annote = {Times Cited: 7}, - annote = {Unicog - Unati - UnirsPMID: 25583500 }, -} - -@article{andoh_modulation_2006, - title = {Modulation of language areas with functional {MR} image-guided magnetic stimulation}, - volume = {29}, - copyright = {All rights reserved}, - abstract = {Repetitive transcranial magnetic stimulation (rTMS) can interfere with linguistic performance when delivered over language areas. At low frequency (1 Hz), rTMS is assumed to decrease cortical excitability; however, the degree of TMS effect on cortical language areas may depend on the localization of the stimulation coil with respect to the inter-individual anatomo-functional variations. Hence, we aimed at investigating individual brain areas involved in semantic and phonological auditory processes. We hypothesized that active rTMS targeted over Wernicke's area might modify the performance during a language-fragment-detection task. Sentences in native or foreign languages were presented to 12 right-handed male healthy volunteers during functional magnetic resonance imaging (fMRI). 3D-functional maps localized the posterior temporal activation (Wernicke) in each subject and MRI anatomical cortical landmarks were used to define Broca's pars opercularis (F3Op). A frameless stereotaxy system was used to guide the TMS coil position over Wernicke's and F3Op areas in each subject. Active and placebo randomized rTMS sessions were applied at 1 Hz, 110{\textbackslash}\% of motor threshold, during the same language-fragment-detection task. Accuracy and response time (RT) were recorded. RT was significantly decreased by active rTMS compared to placebo over Wernicke's area, and was more decreased for native than for foreign languages. No significant RT change was observed for F3Op area. rTMS conditions did not impair participants' accuracy. Thus, low-frequency rTMS over Wernicke's area can speed-up the response to a task tapping on native language perception in healthy volunteers. This individually-guided stimulation study confirms that facilitatory effects are not confined to high-frequency rTMS.}, - journal = {Neuroimage}, - author = {Andoh, J. and Artiges, E. and Pallier, C. and Rivière, D. and Mangin, J.-F. and Cachia, A. and Plaze, M. and Paillère-Martinot, M.-L. and Martinot, J.-L.}, - month = jan, - year = {2006}, - pages = {619--627}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NEUROSPINcustom5: chrplr}, - annote = {The following values have no corresponding Zotero field:secondary-title: Neuroimagepages: 619--627volume: 29number: 2isbn: \%(label: ACLcustom1: http://www.pallier.org/papers/Andoh.tms.Neuroimage.2006custom3: articlecustom5: chrplr}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Andoh-NI06.pdf}, -} - -@article{borst_folding_2014, - title = {Folding of the anterior cingulate cortex partially explains inhibitory control during childhood: a longitudinal study}, - volume = {9}, - issn = {1878-9307}, - shorttitle = {Folding of the anterior cingulate cortex partially explains inhibitory control during childhood}, - doi = {10.1016/j.dcn.2014.02.006}, - abstract = {Difficulties in cognitive control including inhibitory control (IC) are related to the pathophysiology of several psychiatric conditions. In healthy subjects, IC efficiency in childhood is a strong predictor of academic and professional successes later in life. The dorsal anterior cingulate cortex (ACC) is one of the core structures responsible for IC. Although quantitative structural characteristics of the ACC contribute to IC efficiency, the qualitative structural brain characteristics contributing to IC development are less-understood. Using anatomical magnetic resonance imaging, we investigated whether the ACC sulcal pattern at age 5, a stable qualitative characteristic of the brain determined in utero, explains IC at age 9. 18 children performed Stroop tasks at age 5 and age 9. Children with asymmetrical ACC sulcal patterns (n=7) had better IC efficiency at age 5 and age 9 than children with symmetrical ACC sulcal patterns (n=11). The ACC sulcal patterns appear to affect specifically IC efficiency given that the ACC sulcal patterns had no effect on verbal working memory. Our study provides the first evidence that the ACC sulcal pattern - a qualitative structural characteristic of the brain not affected by maturation and learning after birth - partially explains IC efficiency during childhood.}, - language = {eng}, - journal = {Developmental Cognitive Neuroscience}, - author = {Borst, G. and Cachia, A. and Vidal, J. and Simon, G. and Fischer, C. and Pineau, A. and Poirel, N. and Mangin, J.-F. and Houdé, O.}, - month = jul, - year = {2014}, - pmid = {24642370}, - keywords = {Humans, Brain Mapping, Child, Female, Male, Longitudinal Studies, Gyrus Cinguli, Brain imaging, Executive Function, Child, Preschool, Memory, Short-Term, Child Behavior, Cognitive control, Inhibition (Psychology), Inhibitory control, Stroop, Sulcal pattern}, - pages = {126--135}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Times Cited: 4}, - annote = {UnatiPMID: 24642370 }, -} - -@article{marrakchi-kacem_mapping_2013, - title = {Mapping cortico-striatal connectivity onto the cortical surface: a new tractography-based approach to study {Huntington} disease}, - volume = {8}, - issn = {1932-6203}, - shorttitle = {Mapping cortico-striatal connectivity onto the cortical surface}, - doi = {10.1371/journal.pone.0053135}, - abstract = {Huntington disease (HD) is associated with early and severe damage to the basal ganglia and particularly the striatum. We investigated cortico-striatal connectivity modifications occurring in HD patients using a novel approach which focuses on the projection of the connectivity profile of the basal ganglia onto the cortex. This approach consists in computing, for each subcortical structure, surface connectivity measures representing its strength of connections to the cortex and comparing these measures across groups. In this study, we focused on Huntington disease as an application of this new approach. First, surface cortico-striatal connectivity measures of a group of healthy subjects were averaged in order to infer the "normal" connectivity profile of the striatum to the cortex. Second, a statistical analysis was performed from the surface connectivity measures of healthy subjects and HD patients in order to detect the cortical gyri presenting altered cortico-striatal connectivity in HD. Lastly, percentage differences of connectivity between healthy subjects and patients were inferred, for each nucleus of the striatum, from the connectivity measures of the cortical gyri presenting a significant connectivity difference between the two groups. These percentage differences characterize the axonal disruptions between the striatum and the cortex occurring in HD. We found selective region-specific degeneration of cortical connections predominating for associative and primary sensorimotor connections and with relative preservation of limbic connections. Our method can be used to infer novel connectivity-based markers of HD pathological process.}, - language = {eng}, - number = {2}, - journal = {PloS One}, - author = {Marrakchi-Kacem, Linda and Delmaire, Christine and Guevara, Pamela and Poupon, Fabrice and Lecomte, Sophie and Tucholka, Alan and Roca, Pauline and Yelnik, Jérôme and Durr, Alexandra and Mangin, Jean-François and Lehéricy, Stéphane and Poupon, Cyril}, - year = {2013}, - pmid = {23405066}, - pmcid = {PMC3566172}, - keywords = {Humans, Brain Mapping, Female, Male, Middle Aged, Diffusion Tensor Imaging, Limbic System, Corpus Striatum, Huntington Disease, Motor Cortex, Sensory Receptor Cells}, - pages = {e53135}, -} - -@article{cachia_longitudinal_2016, - title = {Longitudinal stability of the folding pattern of the anterior cingulate cortex during development}, - volume = {19}, - issn = {1878-9307}, - doi = {10.1016/j.dcn.2016.02.011}, - abstract = {Prenatal processes are likely critical for the differences in cognitive ability and disease risk that unfold in postnatal life. Prenatally established cortical folding patterns are increasingly studied as an adult proxy for earlier development events - under the as yet untested assumption that an individual's folding pattern is developmentally fixed. Here, we provide the first empirical test of this stability assumption using 263 longitudinally-acquired structural MRI brain scans from 75 typically developing individuals spanning ages 7 to 32 years. We focus on the anterior cingulate cortex (ACC) - an intensely studied cortical region that presents two qualitatively distinct and reliably classifiable sulcal patterns with links to postnatal behavior. We show - without exception-that individual ACC sulcal patterns are fixed from childhood to adulthood, at the same time that quantitative anatomical ACC metrics are undergoing profound developmental change. Our findings buttress use of folding typology as a postnatally-stable marker for linking variations in early brain development to later neurocognitive outcomes in ex utero life.}, - language = {eng}, - journal = {Developmental Cognitive Neuroscience}, - author = {Cachia, A. and Borst, G. and Tissier, C. and Fisher, C. and Plaze, M. and Gay, O. and Rivière, D. and Gogtay, N. and Giedd, J. and Mangin, J.-F. and Houdé, O. and Raznahan, A.}, - year = {2016}, - pmid = {26974743}, - pmcid = {PMC4912935}, - keywords = {Humans, MRI, Adult, Adolescent, Child, Female, Male, Young Adult, Cerebral Cortex, Follow-Up Studies, Longitudinal Studies, Nerve Net, Gyrus Cinguli, Neurodevelopment, Sulcal pattern, ACC, Executive control, Fetal life}, - pages = {122--127}, -} - -@article{sun_linking_2016, - title = {Linking morphological and functional variability in hand movement and silent reading}, - volume = {221}, - issn = {1863-2661}, - doi = {10.1007/s00429-015-1106-8}, - abstract = {It is generally accepted in neuroscience that anatomy and function go hand in hand. Accordingly, a local morphological variability could lead to a corresponding functional variability. In this study, we tested this hypothesis by linking the variability of the cortical folding pattern of 252 right-handed subjects to the localization or the pattern of functional activations induced by hand motion or silent reading. Three regions are selected: the central sulcus, the precentral sulcus and the superior temporal sulcus (STS). "Essential morphological variability traits" are identified using a method building upon multidimensional scaling. The link between variability in anatomy and function is confirmed by the perfect match between the central sulcus morphological "hand knob" and the corresponding motor activation: as the location of the hand knob moves more or less dorsally along the central sulcus, the motor hand activation moves accordingly. Furthermore, the size of the left hand activation in the right hemisphere is correlated with the knob location in the central sulcus. A new link between functional and morphological variability is discovered relative to the location of a premotor activation induced by silent reading. While this reading activation is located next to the wall of the central sulcus when the hand knob has a ventral positioning, it is pushed into a deep gyrus interrupting the precentral sulcus when the knob is more dorsal. Finally, it is shown that the size of the reading activation along the STS is larger when the posterior branches are less developed.}, - language = {eng}, - number = {7}, - journal = {Brain Structure \& Function}, - author = {Sun, Z. Y. and Pinel, P. and Rivière, D. and Moreno, A. and Dehaene, S. and Mangin, J.-F.}, - year = {2016}, - pmid = {26346119}, - keywords = {Humans, Brain Mapping, Temporal Lobe, Cortical folding, Hand, Motor Cortex, STS, Central sulcus, Functional activation, Hand knob, Motor Activity, Variability}, - pages = {3361--3371}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 7label: ACL}, - annote = {UnatiPMID: 26346119}, - annote = {UnatiPMID: 26346119}, -} - -@article{germanaud_larger_2012, - title = {Larger is twistier: spectral analysis of gyrification ({SPANGY}) applied to adult brain size polymorphism}, - volume = {63}, - issn = {1095-9572}, - shorttitle = {Larger is twistier}, - doi = {10.1016/j.neuroimage.2012.07.053}, - abstract = {The description of cortical folding pattern (CFP) is challenging because of geometric complexity and inter-subject variability. On a cortical surface mesh, curvature estimation provides a good scalar proxy of CFP. The oscillations of this function can be studied using a Fourier-like analysis to produce a power spectrum representative of the spatial frequency composition of CFP. First, we introduce an original method for the SPectral ANalysis of GYrication (Spangy), which performs a spectral decomposition of the mean curvature of the grey/white interface mesh based on the Laplace-Beltrami operator eigenfunctions. Spangy produces an ordered 7 bands power spectrum of curvature (B0-B6) and provides an anatomically relevant segmentation of CFP based on local spectral composition. A spatial frequency being associated with each eigenfunction, the bandwidth design assumes frequency doubling between consecutive spectral bands. Next, we observed that the last 3 spectral bands (B4, 5 and 6) accounted for 93\% of the analyzed spectral power and were associated with fold-related variations of curvature, whereas the lower frequency bands were related to global brain shape. The spectral segmentation of CFP revealed 1st, 2nd and 3rd order elements associated with B4, B5 and B6 respectively. These elements could be related to developmentally-defined primary, secondary and tertiary folds. Finally, we used allometric scaling of frequency bands power and segmentation to analyze the relationship between the spectral composition of CFP and brain size in a large adult dataset. Total folding power followed a positive allometric scaling which did not divide up proportionally between the bands: B4 contribution was constant, B5 increased like total folding power and B6 much faster. Besides, apparition of new elements of pattern with increasing size only concerned the 3rd order. Hence, we demonstrate that large brains are twistier than smaller ones because of an increased number of high spatial frequency folds, ramifications and kinks that accommodate the allometric increase of cortical surface.}, - language = {eng}, - number = {3}, - journal = {NeuroImage}, - author = {Germanaud, David and Lefèvre, Julien and Toro, Roberto and Fischer, Clara and Dubois, Jessica and Hertz-Pannier, Lucie and Mangin, Jean-Francois}, - month = nov, - year = {2012}, - pmid = {22877579}, - keywords = {Algorithms, Humans, Image Interpretation, Computer-Assisted, Software, Brain Mapping, Adult, Adolescent, Female, Male, Young Adult}, - pages = {1257--1272}, -} - -@article{fish_influences_2017, - title = {Influences of {Brain} {Size}, {Sex}, and {Sex} {Chromosome} {Complement} on the {Architecture} of {Human} {Cortical} {Folding}}, - volume = {27}, - issn = {1460-2199}, - doi = {10.1093/cercor/bhw323}, - abstract = {Gyrification is a fundamental property of the human cortex that is increasingly studied by basic and clinical neuroscience. However, it remains unclear if and how the global architecture of cortical folding varies with 3 interwoven sources of anatomical variation: brain size, sex, and sex chromosome dosage (SCD). Here, for 375 individuals spanning 7 karyotype groups (XX, XY, XXX, XYY, XXY, XXYY, XXXXY), we use structural neuroimaging to measure a global sulcation index (SI, total sulcal/cortical hull area) and both determinants of sulcal area: total sulcal length and mean sulcal depth. We detail large and patterned effects of sex and SCD across all folding metrics, but show that these effects are in fact largely consistent with the normative scaling of cortical folding in health: larger human brains have disproportionately high SI due to a relative expansion of sulcal area versus hull area, which arises because disproportionate sulcal lengthening overcomes a lack of proportionate sulcal deepening. Accounting for these normative allometries reveals 1) brain size-independent sulcal lengthening in males versus females, and 2) insensitivity of overall folding architecture to SCD. Our methodology and findings provide a novel context for future studies of human cortical folding in health and disease.}, - language = {eng}, - number = {12}, - journal = {Cerebral Cortex (New York, N.Y.: 1991)}, - author = {Fish, Ari M. and Cachia, Arnaud and Fischer, Clara and Mankiw, Catherine and Reardon, P. K. and Clasen, Liv S. and Blumenthal, Jonathan D. and Greenstein, Deanna and Giedd, Jay N. and Mangin, Jean-François and Raznahan, Armin}, - month = dec, - year = {2017}, - pmid = {27799275}, - keywords = {Brain, Humans, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Adult, Adolescent, Child, Female, Male, Young Adult, Longitudinal Studies, Organ Size, Sex Characteristics, Child, Preschool, allometry, sex chromosome aneuploidy, sex differences, sulci, gyrification, Karyotype, Sex Chromosome Aberrations}, - pages = {5557--5567}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3DS59CW8/Fish et al. - 2017 - Influences of Brain Size, Sex, and Sex Chromosome .pdf:application/pdf}, -} - -@article{cury_incomplete_2015, - title = {Incomplete {Hippocampal} {Inversion}: {A} {Comprehensive} {MRI} {Study} of {Over} 2000 {Subjects}}, - volume = {9}, - copyright = {All rights reserved}, - issn = {1662-5129}, - doi = {10.3389/fnana.2015.00160}, - abstract = {The incomplete-hippocampal-inversion (IHI), also known as malrotation, is an atypical anatomical pattern of the hippocampus, which has been reported in healthy subjects in different studies. However, extensive characterization of IHI in a large sample has not yet been performed. Furthermore, it is unclear whether IHI are restricted to the medial-temporal lobe or are associated with more extensive anatomical changes. Here, we studied the characteristics of IHI in a community based sample of 2008 subjects of the IMAGEN database and their association with extra-hippocampal anatomical variations. The presence of IHI was assessed on Ti-weighted anatomical magnetic resonance imaging (MRI) using visual criteria. We assessed the association of IHI with other anatomical changes throughout the brain using automatic morphometry of cortical sulci. We found that IHI were much more frequent in the left hippocampus (left: 17\%, right: 6\%, chi(2) - test, p {\textless} 10(-28)). Compared to subjects without IHI, subjects with IHI displayed morphological changes in several sulci located mainly in the limbic lobe. Our results demonstrate that IHI are a common left-sided phenomenon in normal subjects and that they are associated with morphological changes outside the medial temporal lobe.}, - journal = {FRONTIERS IN NEUROANATOMY}, - author = {Cury, Claire and Toro, Roberto and Cohen, Fanny and Fischer, Clara and Mhaya, Amel and Samper-Gonzalez, Jorge and Hasboun, Dominique and Mangin, Jean-Francois and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Buechel, Christian and Cattrell, Anna and Conrod, Patricia and Flor, Herta and Gallinat, Juergen and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Lemaitre, Herve and Martinot, Jean-Luc and Nees, Frauke and Martinot, Marie-Laure Paillere and Orfanos, Dimitri P. and Paus, Tomas and Poustka, Luise and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Frouin, Vincent and Schumann, Gunter and Glaunes, Joan A. and Colliot, Olivier}, - month = dec, - year = {2015}, - keywords = {MRI, cortical sulci, anatomical variability, IMAGEN database, Large database, malrotation, Human hippocampus}, - pages = {160}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UnatiPMID: 26733822}, -} - -@article{labra_gpu-based_2013, - title = {{GPU}-based acceleration of an automatic white matter segmentation algorithm using {CUDA}}, - volume = {2013}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2013.6609444}, - abstract = {This paper presents a parallel implementation of an algorithm for automatic segmentation of white matter fibers from tractography data. We execute the algorithm in parallel using a high-end video card with a Graphics Processing Unit (GPU) as a computation accelerator, using the CUDA language. By exploiting the parallelism and the properties of the memory hierarchy available on the GPU, we obtain a speedup in execution time of 33.6 with respect to an optimized sequential version of the algorithm written in C, and of 240 with respect to the original Python/C++ implementation. The execution time is reduced from more than two hours to only 35 seconds for a subject dataset of 800,000 fibers, thus enabling applications that use interactive segmentation and visualization of small to medium-sized tractography datasets.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Labra, Nicole and Figueroa, Miguel and Guevara, Pamela and Duclap, Delphine and Hoeunou, Josselin and Poupon, Cyril and Mangin, Jean-Francois}, - year = {2013}, - pmid = {24109631}, - keywords = {Algorithms, Humans, Software, Brain Mapping, Image Processing, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Databases, Factual, Radiography}, - pages = {89--92}, -} - -@article{labra_fast_2017, - title = {Fast {Automatic} {Segmentation} of {White} {Matter} {Streamlines} {Based} on a {Multi}-{Subject} {Bundle} {Atlas}}, - volume = {15}, - issn = {1559-0089}, - doi = {10.1007/s12021-016-9316-7}, - abstract = {This paper presents an algorithm for fast segmentation of white matter bundles from massive dMRI tractography datasets using a multisubject atlas. We use a distance metric to compare streamlines in a subject dataset to labeled centroids in the atlas, and label them using a per-bundle configurable threshold. In order to reduce segmentation time, the algorithm first preprocesses the data using a simplified distance metric to rapidly discard candidate streamlines in multiple stages, while guaranteeing that no false negatives are produced. The smaller set of remaining streamlines is then segmented using the original metric, thus eliminating any false positives from the preprocessing stage. As a result, a single-thread implementation of the algorithm can segment a dataset of almost 9 million streamlines in less than 6 minutes. Moreover, parallel versions of our algorithm for multicore processors and graphics processing units further reduce the segmentation time to less than 22 seconds and to 5 seconds, respectively. This performance enables the use of the algorithm in truly interactive applications for visualization, analysis, and segmentation of large white matter tractography datasets.}, - language = {eng}, - number = {1}, - journal = {Neuroinformatics}, - author = {Labra, Nicole and Guevara, Pamela and Duclap, Delphine and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Figueroa, Miguel}, - year = {2017}, - pmid = {27722821}, - keywords = {Algorithms, Brain, Humans, Pattern Recognition, Automated, Software, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Diffusion Magnetic Resonance Imaging, Neural Pathways, Connectome, Tractography segmentation, White matter tracts, Diffusion-weighted MRI, GPU programming, HARDI data, Streamline distance}, - pages = {71--86}, -} - -@article{sarrazin_corpus_2015, - title = {Corpus callosum area in patients with bipolar disorder with and without psychotic features: an international multicentre study}, - volume = {40}, - copyright = {All rights reserved}, - issn = {1180-4882}, - doi = {10.1503/jpn.140262}, - abstract = {Background Previous studies have reported MRI abnormalities of the corpus callosum (CC) in patients with bipolar disorder (BD), although only a few studies have directly compared callosal areas in psychotic versus nonpsychotic patients with this disorder. We sought to compare regional callosal areas in a large international multicentre sample of patients with BD and healthy controls. Methods We analyzed anatomic T-1 MRI data of patients with BD-I and healthy controls recruited from 4 sites (France, Germany, Ireland and the United States). We obtained the mid-sagittal areas of 7 CC subregions using an automatic CC delineation. Differences in regional callosal areas between patients and controls were compared using linear mixed models (adjusting for age, sex, handedness, brain volume, history of alcohol abuse/dependence, lithium or antipsychotic medication status, symptomatic status and site) and multiple comparisons correction. We also compared regional areas of the CC between patients with BD with and without a history of psychotic features. Results We included 172 patients and 146 controls in our study. Patients with BD had smaller adjusted mid-sagittal CC areas than controls along the posterior body, the isthmus and the splenium of the CC. Patients with a positive history of psychotic features had greater adjusted area of the rostral CC region than those without a history of psychotic features. Limitations We found small to medium effect sizes, and there was no calibration technique among the sites. Conclusion Our results suggest that BD with psychosis is associated with a different pattern of interhemispheric connectivity than BD without psychosis and could be considered a relevant neuroimaging subtype of BD.}, - number = {5}, - journal = {JOURNAL OF PSYCHIATRY \& NEUROSCIENCE}, - author = {Sarrazin, Samuel and d'Albis, Marc-Antoine and McDonald, Colm and Linke, Julia and Wessa, Michele and Phillips, Mary and Delavest, Marine and Emsell, Louise and Versace, Amelia and Almeida, Jorge and Mangin, Jean-Francois and Poupon, Cyril and Le Dudal, Katia and Daban, Claire and Hamdani, Nora and Leboyer, Marion and Houenou, Josselin}, - month = sep, - year = {2015}, - keywords = {Humans, Image Processing, Computer-Assisted, Adult, Female, Male, Bipolar Disorder, Corpus Callosum, United States, Middle Aged, Linear Models, Antipsychotic Agents, Lithium, Diagnostic and Statistical Manual of Mental Disorders, France, Germany, Ireland}, - pages = {352--359}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 26151452}, -} - -@article{tucholka_probabilistic_2008, - title = {Probabilistic anatomo-functional parcellation of the cortex: how many regions?}, - volume = {11}, - copyright = {All rights reserved}, - abstract = {Understanding brain structure and function entails the inclusion of anatomical and functional information in a common space, in order to study how these different informations relate to each other in a population of subjects. In this paper, we revisit the parcellation model and explicitly combine anatomical features, i.e. a segmentation of the cortex into gyri, with a functional information under the form of several cortical maps, which are used to further subdivide the gyri into functionally consistent regions. A probabilistic model is introduced, and the parcellation model is estimated using a Variational Bayes approach. The number of regions in the model is validated based on cross-validation. It is found that about 250 patches of cortex can be delineated both in the left and right hemisphere based on this procedure.}, - journal = {Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv}, - author = {Tucholka, Alan and Thirion, Bertrand and Perrot, Matthieu and Pinel, Philippe and Mangin, Jean-François and Poline, Jean-Baptiste}, - year = {2008}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Data Interpretation, Statistical, Bayes Theorem}, - pages = {399--406}, - annote = {The following values have no corresponding Zotero field:number: Pt 2label: ACTIcustom1: NeuroSpin}, - annote = {Unati - articlejb}, -} - -@article{thirion_structural_2007, - title = {Structural analysis of {fMRI} data revisited: improving the sensitivity and reliability of {fMRI} group studies}, - volume = {26}, - copyright = {All rights reserved}, - issn = {0278-0062 (Print)}, - doi = {10.1109/TMI.2007.903226}, - abstract = {Group studies of functional magnetic resonance imaging datasets are usually based on the computation of the mean signal across subjects at each voxel (random effects analyses), assuming that all subjects have been set in the same anatomical space (normalization). Although this approach allows for a correct specificity (rate of false detections), it is not very efficient for three reasons: i) its underlying hypotheses, perfect coregistration of the individual datasets and normality of the measured signal at the group level are frequently violated; ii) the group size is small in general, so that asymptotic approximations on the parameters distributions do not hold; iii) the large size of the images requires some conservative strategies to control the false detection rate, at the risk of increasing the number of false negatives. Given that it is still very challenging to build generative or parametric models of intersubject variability, we rely on a rule based, bottom-up approach: we present a set of procedures that detect structures of interest from each subject's data, then search for correspondences across subjects and outline the most reproducible activation regions in the group studied. This framework enables a strict control on the number of false detections. It is shown here that this analysis demonstrates increased validity and improves both the sensitivity and reliability of group analyses compared with standard methods. Moreover, it directly provides information on the spatial position correspondence or variability of the activated regions across subjects, which is difficult to obtain in standard voxel-based analyses.}, - language = {eng}, - journal = {IEEE Trans Med Imaging}, - author = {Thirion, B. and Pinel, P. and Tucholka, A. and Roche, A. and Ciuciu, P. and Mangin, J. F. and Poline, J. B.}, - month = sep, - year = {2007}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Brain Mapping, Subtraction Technique, Brain Mapping/*methods, Magnetic Resonance Imaging/*methods, Image Interpretation, Computer-Assisted/*methods, Brain/*anatomy \& histology/*physiology, *Subtraction Technique, Evoked Potentials, Evoked Potentials/physiology, Image Enhancement/*methods, Information Storage and Retrieval/methods, Pattern Recognition, Automated/methods}, - pages = {1256--69}, - annote = {The following values have no corresponding Zotero field:auth-address: INRIA Futurs Research Institute, Parc Club Orsay Universit ZAC des Vignes, 91893 Orsay Cedex, France. bertrand.thirion@inria.frnumber: 9edition: 2007/09/28accession-num: 17896597label: ACLcustom1: NEUROSPIN}, - annote = {The following values have no corresponding Zotero field:number: 9label: ACLcustom1: NeuroSpin}, - annote = {Unati}, - annote = {Unati - articlejb}, -} - -@phdthesis{mangin_hdr_2005, - address = {Orsay}, - type = {Habilitation à diriger des recherches}, - title = {{HDR} = {Une} vision structurelle de l'analyse des images cérébrales}, - copyright = {All rights reserved}, - school = {Université Paris Sud}, - author = {Mangin, J. F.}, - year = {2005}, - keywords = {sulci}, - annote = {The following values have no corresponding Zotero field:label: HDRcustom1: NeuroSpincustom2: In}, - annote = {Unati - http://brainvisa.info/pdf/mangin-HDR05.pdfphdthesis}, -} - -@article{dehaene_cerebral_2001, - title = {Cerebral mechanisms of word masking and unconscious repetition priming}, - volume = {4}, - copyright = {All rights reserved}, - abstract = {We used functional magnetic resonance imaging (fMRI) and event-related potentials (ERPs) to visualize the cerebral processing of unseen masked words. Within the areas associated with conscious reading, masked words activated left extrastriate, fusiform and precentral areas. Furthermore, masked words reduced the amount of activation evoked by a subsequent conscious presentation of the same word. In the left fusiform gyrus, this repetition suppression phenomenon was independent of whether the prime and target shared the same case, indicating that case-independent information about letter strings was extracted unconsciously. In comparison to an unmasked situation, however, the activation evoked by masked words was drastically reduced and was undetectable in prefrontal and parietal areas, correlating with participants' inability to report the masked words.}, - journal = {Nat Neurosci}, - author = {Dehaene, S. and Naccache, L. and Cohen, L. and Bihan, D. L. and Mangin, J. F. and Poline, J. B. and Riviere, D.}, - year = {2001}, - keywords = {Adult, Female, Male, Photic Stimulation, *Brain Mapping, Parietal Lobe/physiology, Visual Perception/*physiology, Occipital Lobe/physiology, Evoked Potentials, Support, Non-U.S. Gov't, *Perceptual Masking, Frontal Lobe/physiology}, - pages = {752--8.}, - annote = {The following values have no corresponding Zotero field:number: 7label: ACL}, -} - -@article{ghadery_r2*mapping_2015, - title = {R2*mapping for brain iron: associations with cognition in normal aging}, - volume = {36}, - copyright = {All rights reserved}, - issn = {0197-4580}, - doi = {10.1016/j.neurobiolaging.2014.09.013}, - number = {2}, - journal = {NEUROBIOLOGY OF AGING}, - author = {Ghadery, Christine and Pirpamer, Lukas and Hofer, Edith and Langkammer, Christian and Petrovic, Katja and Loitfelder, Marisa and Schwingenschuh, Petra and Seiler, Stephan and Duering, Marco and Jouvent, Eric and Schmidt, Helena and Fazekas, Franz and Mangin, Jean-Francois and Chabriat, Hugues and Dichgans, Martin and Ropele, Stefan and Schmidt, Reinhold}, - month = feb, - year = {2015}, - keywords = {MRI, Cognition, All cognitive disorders/dementia, Cognitive aging, R2* brain iron mapping}, - pages = {925--932}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {Times Cited: 3}, - annote = {UnatiPMID: 25443291}, -} - -@article{de_guio_white_2015, - title = {White {Matter} {Edema} at the {Early} {Stage} of {Cerebral} {Autosomal}-{Dominant} {Arteriopathy} {With} {Subcortical} {Infarcts} and {Leukoencephalopathy}}, - volume = {46}, - copyright = {All rights reserved}, - issn = {0039-2499}, - doi = {10.1161/STROKEAHA.114.007018}, - number = {1}, - journal = {STROKE}, - author = {De Guio, Francois and Mangin, Jean-Francois and Duering, Marco and Ropele, Stefan and Chabriat, Hugues and Jouvent, Eric}, - month = jan, - year = {2015}, - keywords = {CADASIL, cerebral small vessel diseases, edema, white matter diseases}, - pages = {258--261}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Times Cited: 1}, - annote = {UnatiPMID: 25370582}, -} - -@article{redolfi_head--head_2015, - title = {Head-to-{Head} {Comparison} of {Two} {Popular} {Cortical} {Thickness} {Extraction} {Algorithms}: {A} {Cross}-{Sectional} and {Longitudinal} {Study}}, - volume = {10}, - copyright = {All rights reserved}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0117692}, - number = {3}, - journal = {PLOS ONE}, - author = {Redolfi, Alberto and Manset, David and Barkhof, Frederik and Wahlund, Lars-Olof and Glatard, Tristan and Mangin, Jean-Francois and Frisoni, Giovanni B.}, - month = mar, - year = {2015}, - pages = {e0117692}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACL}, - annote = {Times Cited: 2}, - annote = {UnatiPMID: 25781983}, -} - -@inproceedings{guevara_creation_2016, - title = {Creation of a whole brain short association bundle atlas using a hybrid approach.}, - copyright = {All rights reserved}, - doi = {10.1109/EMBC.2016.7590899}, - author = {Guevara, M. and Roman, C. and Houenou, J. and Duclap, D. and Poupon, C. and Mangin, J. F. and Guevara, P.}, - month = aug, - year = {2016}, - keywords = {Brain, Humans, Reproducibility of Results, Brain Mapping, White Matter, Cluster Analysis}, - pages = {1115--1119}, - annote = {The following values have no corresponding Zotero field:pub-location: Strasbourg, France}, - annote = {UnirsPMID: 28268521.}, -} - -@inproceedings{pepe_spectral_2015, - title = {Spectral clustering based parcellation of fetal brain {MRI}}, - copyright = {All rights reserved}, - author = {Pepe, A. and Auzias, G. and De Guio, F. and Rousseau, F. and Mangin, J.-F. and Girard, N. and Coulon, O. and Lefèvre, J.}, - year = {2015}, - annote = {The following values have no corresponding Zotero field:pub-location: Brooklin, USAlabel: ACTI}, - annote = {Unati}, -} - -@inproceedings{coulon_quasi-isometric_2015, - title = {Quasi-isometric length parameterization of cortical sulci: application to handedness and the central sulcus morphology}, - copyright = {All rights reserved}, - author = {Coulon, O. and Lefèvre, J. and Klöppel, S. and Siebner, H. and Mangin, J.-F.}, - year = {2015}, - annote = {The following values have no corresponding Zotero field:pub-location: Brooklin, USAlabel: ACTI}, - annote = {Unati}, -} - -@inproceedings{roman_automatic_2015, - title = {Automatic clustering of short association white matter fibers from {HARDI} tractography datasets."}, - copyright = {All rights reserved}, - author = {Roman, C. and Guevara, P. and Guevara, M. and Duclap, D. and Lebois, A. and Poupon, C. and Mangin, J. F.}, - year = {2015}, - pages = {440--444}, - annote = {The following values have no corresponding Zotero field:pub-location: Brooklin, USAlabel: ACTI}, - annote = {Unati}, -} - -@incollection{mangin_sulcus_2015, - edition = {Academic Press : Elsevier}, - title = {Sulcus identification and {Labeling}}, - volume = {1}, - copyright = {All rights reserved}, - booktitle = {Brain {Mapping}: {An} {Encyclopedic} {Reference}}, - author = {Mangin, J. F. and Perrot, M. and Operto, G. and Cachia, A. and Fischer, C. and Lefèvre, J. and Rivière, D.}, - editor = {Arthur W. Toga}, - year = {2015}, - pages = {365--371}, - annote = {The following values have no corresponding Zotero field:label: OS}, - annote = {Unati}, -} - -@incollection{mangin_sulci_2015, - title = {Sulci as {Landmarks}}, - volume = {2}, - copyright = {All rights reserved}, - booktitle = {Brain {Mapping}: {An} {Encyclopedic} {Reference}}, - publisher = {Academic Press: Elsevir}, - author = {Mangin, J. F. and Auzias, G. and Coulon, O. and Sun, Z.-Y. and Rivière, D. and Régis, J.}, - editor = {Arthur W. Toga}, - year = {2015}, - pages = {45--52}, - annote = {The following values have no corresponding Zotero field:label: OS}, - annote = {Unati}, -} - -@inproceedings{auzias_model-driven_2015, - title = {Model-driven parametrization of fetal cortical surfaces}, - copyright = {All rights reserved}, - author = {Auzias, G. and De Guio, F. and Pepe, A. and Rousseau, F. and Mangin, J.-F. and Girard, N. and Lefèvre, J. and Coulon, O.}, - year = {2015}, - annote = {The following values have no corresponding Zotero field:pub-location: Brooklin, USAlabel: ACTI}, - annote = {Unati}, -} - -@misc{riviere_anatomist:_2011, - address = {Paris, France}, - title = {Anatomist: a python framework for interactive {3D} visualization of neuroimaging data}, - copyright = {All rights reserved}, - author = {Rivière, D.}, - year = {2011}, - annote = {The following values have no corresponding Zotero field:label: ACTNcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_vie_2011, - address = {Paris, France}, - title = {La vie des formes}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2011}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@article{fillard_quantitative_2011, - title = {Quantitative evaluation of 10 tractography algorithms on a realistic diffusion {MR} phantom}, - volume = {56}, - copyright = {All rights reserved}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2011.01.032}, - number = {1}, - journal = {NEUROIMAGE}, - author = {Fillard, Pierre and Descoteaux, Maxime and Goh, Alvina and Gouttard, Sylvain and Jeurissen, Ben and Malcolm, James and Ramirez-Manzanares, Alonso and Reisert, Marco and Sakaie, Ken and Tensaouti, Fatima and Yo, Ting and Mangin, Jean-Francois and Poupon, Cyril}, - month = may, - year = {2011}, - pages = {220--234}, - annote = {The following values have no corresponding Zotero field:auth-address: PARIETAL - INRIA Saclay - Ile de France - INRIA - Laboratoire de Neuroimagerie Assistée par Ordinateur - Unati - CEA : DSV/I2BM/NEUROSPIN - MOIVRE Centre - Sherbrooke University - Department of Mathematics [Singapore] - National University of Singapore (NUS) - Scientific Computing and Imaging Institute - SCI Institute - University of Utah - Vision Lab - University of Antwerp - Psychiatry Neuroimaging Laboratory - PNL - Brigham and Women's Hospital - Harvard Medical School - Centro de Investigación en Matemáticas - CIMAT - University of Guanajuato - Department of Radiology, Medical Physics - University Hospital Freiburg - Universitäts Klinikum Freiburg - Imaging Institute [Cleveland] - The Cleveland Clinic - Imagerie cérébrale et handicaps neurologiques - INSERM : U825 - Université Paul Sabatier - Toulouse III - Max-Planck-Institute for Human Cognitive and Brain Sciences - Max-Planck-Institut - Laboratoire d'Imagerie et de Spectroscopie - Unirs - CEA : DSV/I2BM/NEUROSPINnumber: 1label: ACLcustom1: Neurospin}, - annote = {Times Cited: 118}, - annote = {UnatiPMID: 21256221}, -} - -@article{sarrazin_mri_2011, - title = {{MRI} exploration of pineal volume in bipolar disorder}, - volume = {135}, - copyright = {All rights reserved}, - issn = {0165-0327}, - doi = {10.1016/j.jad.2011.06.001}, - number = {1-3}, - journal = {JOURNAL OF AFFECTIVE DISORDERS}, - author = {Sarrazin, Samuel and Etain, Bruno and Vederine, Francois-Eric and d'Albis, Marc-Antoine and Hamdani, Nora and Daban, Claire and Delavest, Marine and Lepine, Jean-Pierre and Leboyer, Marion and Mangin, Jean-Francois and Poupon, Cyril and Houenou, Josselin}, - month = dec, - year = {2011}, - pages = {377--379}, - annote = {PubMed ID: 21700342 }, - annote = {The following values have no corresponding Zotero field:number: 1-3edition: 2011 Jun 22label: ACLcustom1: Neurospin}, - annote = {Times Cited: 7}, -} - -@misc{riviere_focal_2011, - address = {Québec, Canada}, - title = {Focal epileptogenic malformations of cortical development are associated with diffuse sulcal anomalies}, - copyright = {All rights reserved}, - author = {Rivière, D.}, - year = {2011}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@article{jouvent_apathy_2011, - title = {Apathy is related to cortex morphology in {CADASIL} {A} sulcal-based morphometry study}, - volume = {76}, - copyright = {All rights reserved}, - issn = {0028-3878}, - number = {17}, - journal = {NEUROLOGY}, - author = {Jouvent, E. and Reyes, S. and Mangin, J.-F. and Roca, P. and Perrot, M. and Thyreau, B. and Herve, D. and Dichgans, M. and Chabriat, H.}, - month = apr, - year = {2011}, - pages = {1472--1477}, - annote = {The following values have no corresponding Zotero field:number: 17.label: ACLcustom1: Neurospin}, - annote = {Times Cited: 12}, - annote = {UnatiPMID: 21518996}, -} - -@misc{mangin_notitle_2010, - address = {Korea Advanced Institute of Science and Technology}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2010}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_structural_2010, - address = {The University of Texas Health Science, USA}, - title = {Structural approaches to study variability of brain architecture}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2010}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{roca_tractography-based_2009, - address = {London, UK}, - title = {Tractography-{Based} {Parcellation} of the {Cortex} using a {Spatially}-{Informed} {Dimension} {Reduction} of the {Connectivity} {Matrix}}, - copyright = {All rights reserved}, - author = {Roca, P. and Riviere, D. and Guevara, P. and Poupon, C. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:publisher: Springer-Verlaglabel: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Roca-MICCAI09.pdfLNCS 5762inproceedings}, -} - -@misc{riviere_brainvisa:_2009, - title = {{BrainVISA}: an extensible software environment for sharing multimodal neuroimaging data and processing tools}, - copyright = {All rights reserved}, - author = {Riviere, D. and Geffroy, D. and Denghien, I. and Souedet, N. and Cointepas, Y.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - }, -} - -@article{plaze_brain_2009, - title = {A brain morphometry study of schizophrenia patients with inner or outer space hallucinations}, - copyright = {All rights reserved}, - journal = {Schizophrenia Bulletin}, - author = {Plaze, M. and Paillère, M. L. and Penttilä, J. and Januel, D. and de Beaurepaire, Renaud and Bellivier, F. and Andoh, J. and Galinowski, A. and Gallarda, T. and Artiges, E. and Olié, J. P. and Mangin, J. F. and Martinot, J. L. and Cachia, A.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Plaze-SchizoBull09.pdfarticle}, -} - -@misc{perrot_joint_2009, - address = {Williamsburg, \{VA\}, USA}, - title = {Joint {Bayesian} {Cortical} {Sulci} {Recognition} and {Spatial} {Normalization}}, - copyright = {All rights reserved}, - author = {Perrot, M. and Rivière, D. and Tucholka, A. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:tertiary-title: LNCS-5636pages: 176--187publisher: Springer Verlaglabel: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Perrot-IPMI09.pdfinproceedings}, -} - -@misc{mangin_variability_2010, - address = {Sick Kids Hospital, Toronto, Canada}, - title = {Variability of cortical anatomy: a challenge for computer vision}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2010}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@article{im_spatial_2010, - title = {Spatial {Distribution} of {Deep} {Sulcal} {Landmarks} and {Hemispherical} {Asymmetry} on the {Cortical} {Surface}}, - volume = {20}, - copyright = {All rights reserved}, - issn = {1047-3211}, - doi = {10.1093/cercor/bhp127}, - number = {3}, - journal = {CEREBRAL CORTEX}, - author = {Im, Kiho and Jo, Hang Joon and Mangin, Jean-Francois and Evans, Alan C. and Kim, Sun I. and Lee, Jong-Min}, - month = mar, - year = {2010}, - pages = {602--611}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Times Cited: 29}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Im-CC2009.pdfarticle}, -} - -@misc{mangin_structural_2007, - address = {Dead Sea, Israel}, - title = {The structural paradigm when analyzing diffusion data}, - copyright = {All rights reserved}, - author = {Mangin, J. F. and El Kouby, V. and Guevara, P. and Perrin, M. and Cathier, P. and Cointepas, Y. and Poupon, C.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - }, -} - -@misc{mangin_variability_2007, - address = {Chicago, USA}, - title = {Variability of the cortical folding patterns}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_structural_2007-1, - address = {Israël}, - title = {The structural paradigm}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_machine_2007, - address = {Singapour}, - title = {Machine learning for {Early} {Diagnosis} of {Brain} {Diseases}}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{kochunov_genetic_2007, - title = {Genetic analysis of cerebral volume and cortical sulci in baboons}, - copyright = {All rights reserved}, - author = {Kochunov, P. and Rogers, J. and Glahn, D. and Lancaster, J. and Coulon, O. and Mangin, J. F. and Rivière, D. and Blangero, J. and Fox, P.}, - year = {2007}, - keywords = {brainvisa, cortical\_surface}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - }, -} - -@misc{kochunov_relationship_2007, - title = {Relationship between regional {FDG} uptake and other markers of cerebral health in normal aging}, - copyright = {All rights reserved}, - author = {Kochunov, P. and Lancaster, J. and Narayana, S. and Operto, G. and Coulon, O. and Mangin, J. F. and Fox, P.}, - year = {2007}, - keywords = {brainvisa, cortical\_surface}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - }, -} - -@article{dauguet_three-dimensional_2007, - title = {Three-dimensional reconstruction of stained histological slices and {3D} non-linear registration with in-vivo {MRI} for whole baboon brain}, - volume = {164}, - copyright = {All rights reserved}, - journal = {J Neurosci Methods}, - author = {Dauguet, J. and Delzescaux, T. and Condé, F. and Mangin, J. F. and Ayache, N. and Hantraye, P. and Frouin, V.}, - year = {2007}, - keywords = {Registration,brainvisa}, - pages = {191--204}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Dauguet-JNM07.pdf}, -} - -@article{cohen_individual_2006, - title = {Individual cognitive training of reading disability improves word identification and sentence comprehension in adults with mild mental retardation}, - volume = {27}, - copyright = {All rights reserved}, - issn = {0891-4222 (Print)}, - doi = {S0891-4222(05)00069-7 [pii] 10.1016/j.ridd.2004.07.008}, - abstract = {Reading therapy has been shown to be effective in treating reading disabilities (RD) in dyslexic children, but little is known of its use in subjects with mild mental retardation (MR). Twenty adult volunteers, with both RD and mild MR, underwent 60 consecutive weeks in a cognitive remediation program, and were compared with 32 untreated control subjects. The experimental group showed a significant improvement in word identification, as measured by oral production (p=0.0004) or silent reading (p=0.023), and sentence comprehension (p=0.0002). Adults with MR appear to benefit from new approaches in the field of RD.}, - language = {eng}, - journal = {Res Dev Disabil}, - author = {Cohen, D. and Plaza, M. and Perez-Diaz, F. and Lanthier, O. and Chauvin, D. and Hambourg, N. and Wilson, A. J. and Basquin, M. and Mazet, P. and Riviere, J. P.}, - month = oct, - year = {2006}, - keywords = {Humans, Adult, Female, Male, Middle Aged, Case-Control Studies, *Reading, Cognition/*physiology, *Word Association Tests, Comprehension/*physiology, Learning Disorders/*complications/*rehabilitation, Mental Retardation/*complications/rehabilitation}, - pages = {501--16}, - annote = {Cohen, DavidPlaza, MoniquePerez-Diaz, FernandoLanthier, OdileChauvin, DominiqueHambourg, NicoleWilson, Anna JBasquin, MichelMazet, PhilippeRiviere, Jean PhilippeClinical TrialResearch Support, Non-U.S. Gov'tUnited StatesResearch in developmental disabilitiesRes Dev Disabil. 2006 Sep-Oct;27(5):501-16. Epub 2005 Sep 28.}, - annote = {The following values have no corresponding Zotero field:auth-address: Departement de Psychiatrie de l'Enfant et de l'Adolescent, Centre Referent Langage, Groupe-Hospitalier Pitie-Salpetriere, AP-HP, 47-83, Boulevard de l'Hopital, 75651 Paris Cedex 13, France. david.cohen@psl.ap-hop-paris.frnumber: 5edition: 2005/10/04accession-num: 16198084label: ACLcustom1: NEUROSPIN}, -} - -@misc{clouchoux_cortical_2006, - title = {Cortical localization via hemisphere surface parameterization}, - copyright = {All rights reserved}, - author = {Clouchoux, C. and Coulon, O. and Operto, G. and Rivière, D. and Dauchot, K. and Sirigu, A. and Anton, J. L.}, - year = {2006}, - keywords = {brainvisa, cortical\_surface}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - }, -} - -@misc{clouchoux_new_2006, - address = {Copenhaegen, Danemark}, - title = {A new cortical surface parcellation model and its automatic implementation}, - copyright = {All rights reserved}, - author = {Clouchoux, C. and Coulon, O. and Anton, J. L. and Mangin, J. F. and Régis, J.}, - month = oct, - year = {2006}, - keywords = {brainvisa, cortical\_surface}, - annote = {The following values have no corresponding Zotero field:tertiary-title: \{LNCS\} 4191pages: 193--200publisher: Springer Verlaglabel: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati }, -} - -@misc{poupon_database_2006, - address = {Florence, Italie}, - title = {A database dedicated to anatomo-functional study of human brain connectivity}, - copyright = {All rights reserved}, - author = {Poupon, C. and Poupon, F. and Allirol, L. and Mangin, J. F.}, - year = {2006}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - inproceedings}, -} - -@misc{perrin_q-ball_2006, - address = {Florence, Italie}, - title = {Q-ball imaging simulation with a numerical diffusion fiber crossing phantom}, - copyright = {All rights reserved}, - author = {Perrin, M. and Poupon, C. and Rivière, D. and Constantinesco, A. and Le Bihan, D. and Mangin, J. F.}, - year = {2006}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - inproceedings}, -} - -@misc{martinot_cortical_2006, - address = {Nice, France}, - title = {Cortical gyrification and (developmental) pathopsychology}, - copyright = {All rights reserved}, - author = {Martinot, J. L. and Kircher, T. and McGuire and P Paillère-Martinot, M. L. and Galinowski, A. and De Beaurepaire, R. and Januel, D. and Ringuenet, D. and Plaze, M. and Andoh, J. and Artiges, E. and Bellivier, F. and Duchesnay, E. and Cachia, A. and Mangin, J. F.}, - year = {2006}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTNcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@article{coyle_cortical_2006, - title = {Cortical sulci and bipolar disorder}, - volume = {17}, - copyright = {All rights reserved}, - journal = {NeuroReport}, - author = {Coyle, T. R. and Kochunov, P. and Patel, R. D. and Nery, F. G. and Lancaster, J. L. and Mangin, J. F. and Rivière, D. and Pillow, D. R. and Davis, G. J. and Nicoletti, M. A. and Serap Monkul, E. and Fox, P. T. and Soares, J. C.}, - year = {2006}, - keywords = {Sulci,brainvisa}, - pages = {1739--42}, - annote = {The following values have no corresponding Zotero field:number: 16label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati}, -} - -@misc{cathier_registration_2006, - address = {New York, USA}, - title = {Registration of cortical connectivity matrices}, - copyright = {All rights reserved}, - author = {Cathier, P. and Mangin, J. F.}, - year = {2006}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Cathier-MMBIA06.pdf}, -} - -@misc{ringuenet_cingulate_2005, - address = {Toronto, Canada}, - title = {Cingulate cortex and resistant depression : {3D} sulci measurment and voxel-based morphometry abnormalities}, - copyright = {All rights reserved}, - author = {Ringuenet, D. and Paillère-Martinot, M. L. and Bartrés-Faz, D. and Galinowski, A. and Bellivier, F. and Gallarda, T. and Lefaucheur, J. P. and Rivière, D. and Leprovost, J. B. and Cachia, A. and Mangin, J. F. and Martinot, J. L. and E, Artiges}, - year = {2005}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@article{ragis_sulcal_2005, - title = {"{Sulcal} root" generic model: a hypothesis to overcome the variability of the human cortex folding patterns}, - volume = {45}, - copyright = {All rights reserved}, - journal = {Neurol Med Chir (Tokyo)}, - author = {Régis, J. and Mangin, J. F. and Ochiai, T. and Frouin, V. and Rivière, D. and Cachia, A. and Tamura, M. and Samson, Y.}, - year = {2005}, - pages = {1--17}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - http://brainvisa.info/pdf/regis-NMChir05.pdfarticle}, -} - -@misc{perrin_fiber_2005, - address = {Glenwood Spring, USA}, - title = {Fiber tracking in q-ball fields using regularized particle trajectories}, - copyright = {All rights reserved}, - abstract = {Most of the approaches dedicated to fiber tracking from diffusion-weighted MR data rely on a tensor model. However, the tensor model can only resolve a single fiber orientation within each imaging voxel. New emerging approaches have been proposed to obtain a better representation of the diffusion process occurring in fiber crossing. In this paper, we adapt a tracking algorithm to the q-ball representation, which results from a spherical Radon transform of high angular resolution data. This algorithm is based on a Monte-Carlo strategy, using regularized particle trajectories to sample the white matter geometry. The method is validated using a phantom of bundle crossing made up of haemodialysis fibers. The method is also applied to the detection of the auditory tract in three human subjects.}, - author = {Perrin, M. and Poupon, C. and Cointepas, Y. and Rieul, B. and Golestani, N. and Pallier, C. and Rivière, D. and Constantinesco, A. and Bihan, D. Le and Mangin, J. F.}, - year = {2005}, - keywords = {Algorithms, Artificial Intelligence, Humans, Reproducibility of Results, Sensitivity and Specificity, Diffusion Magnetic Resonance Imaging, methods, Brain, cytology, Image Enhancement, methods, Image Interpretation, Computer-Assisted, methods, Imaging, Three-Dimensional, methods, Nerve Fibers, Myelinated, ultrastructure, Pattern Recognition, Automated, methods}, - annote = {The following values have no corresponding Zotero field:pages: 52--63volume: 19label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - articleMH212867}, -} - -@misc{perrin_regularized_2005, - title = {Regularized probabilistic tracking with {Q}-ball fields}, - copyright = {All rights reserved}, - author = {Perrin, M. and Cointepas, Y. and Poupon, C. and Rieul, B. and Golestani, N. and Pallier, C. and Rivière, D. and Constantinesco, A. and Le Bihan, D. and Mangin, J. F.}, - year = {2005}, - keywords = {Diffusion,brainvisa}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - http://brainvisa.info/pdf/perrin-ISMRM05.pdfinproceedings}, -} - -@misc{patel_comparison_2005, - address = {Toronto, Canada}, - title = {Comparison of age-related sulcal opening trends between bipolar {II} patients and normal individuals}, - copyright = {All rights reserved}, - author = {Patel, R. and Kochunov, P. and Lancaster, J. L. and Mangin, J. F. and Rivière, D. and Cointepas, Y. and Nicoletti, M. and Monkul, S. and Najt, P. and Kaur, S. and Glahn, D. and Bowder, C. and Fox, P. and Soares, J.}, - year = {2005}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@misc{martinot_brain_2005, - address = {Vienna, Austria}, - title = {Brain folding in schizophrenia}, - copyright = {All rights reserved}, - author = {Martinot, J. L. and Kircher, T. and Paillère-Martinot, M. L. and Plaze, M. and Januel, D. and Bellivier, F. and Andoh, J. and De Beaurepaire, R. and Chanraud, S. and Artiges, E. and Duchesnay, E. and Mangin, J. F. and Kellermann, T. and Leube, D. and Bartrés-Faz, D. and Cachia, A.}, - year = {2005}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {The following values have no corresponding Zotero field:pages: 57label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, - annote = {Unati - inproceedings}, -} - -@misc{poupon_validation_2005, - title = {Validation of {Q}-ball imaging with a diffusion fiber crossing phantom on a clinical scanner}, - copyright = {All rights reserved}, - author = {Poupon, C. and Perrin, M. and Rieul, B. and Mangin, J. F. and Le Bihan, D.}, - year = {2005}, - keywords = {Diffusion,brainvisa}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - http://brainvisa.info/pdf/cpoupon-ISMRM05.pdfinproceedings}, -} - -@article{perrin_validation_2005, - title = {Validation of q-ball imaging with a diffusion fibre-crossing phantom on a clinical scanner}, - volume = {360}, - copyright = {All rights reserved}, - abstract = {Magnetic resonance (MR) diffusion imaging provides a valuable tool used for inferring structural anisotropy of brain white matter connectivity from diffusion tensor imaging. Recently, several high angular resolution diffusion models were introduced in order to overcome the inadequacy of the tensor model for describing fibre crossing within a single voxel. Among them, q-ball imaging (QBI), inherited from the q-space method, relies on a spherical Radon transform providing a direct relationship between the diffusion-weighted MR signal and the orientation distribution function (ODF). Experimental validation of these methods in a model system is necessary to determine the accuracy of the methods and to optimize them. A diffusion phantom made up of two textile rayon fibre (comparable in diameter to axons) bundles, crossing at 90 degrees , was designed and dedicated to ex vivo q-ball validation on a clinical scanner. Normalized ODFs were calculated inside regions of interest corresponding to monomodal and bimodal configurations of underlying structures. Three-dimensional renderings of ODFs revealed monomodal shapes for voxels containing single-fibre population and bimodal patterns for voxels located within the crossing area. Principal orientations were estimated from ODFs and were compared with a priori structural fibre directions, validating efficiency of QBI for depicting fibre crossing. In the homogeneous regions, QBI detected the fibre angle with an accuracy of 19 degrees and in the fibre-crossing region with an accuracy of 30 degrees .}, - journal = {Philos Trans R Soc Lond B Biol Sci}, - author = {Perrin, Muriel and Poupon, Cyril and Rieul, Bernard and Leroux, Patrick and Constantinesco, André and Mangin, Jean-François and Lebihan, Denis}, - month = may, - year = {2005}, - keywords = {Humans, Models, Neurological, Anisotropy, Magnetic Resonance Imaging, methods, Brain, anatomy /\&/ histology/physiology, Image Processing, Computer-Assisted, methods, Brain Mapping, instrumentation/methods, Nerve Fibers, physiology}, - pages = {881--891}, - annote = {The following values have no corresponding Zotero field:number: 1457label: ACLcustom1: NeuroSpin}, - annote = {Unirs - articleMH212867}, -} - -@inproceedings{martinot_brain_2005-1, - address = {Vienna, Austria}, - title = {Brain folding in schizophrenia}, - copyright = {All rights reserved}, - booktitle = {Proc. 8th {World} congress of biological psychiatry. {The} world journal of biological psychiatry vol 6 (1)}, - author = {Martinot, J.-L. and Kircher, T and Paillère-Martinot, M-L and Plaze, M and Januel, D and Bellivier, F and Andoh, J and De Beaurepaire, R and Chanraud, S and Artiges, E and Duchesnay, E and Mangin, J.-F. and Kellermann, T and Leube, D and Bartrés-Faz, D and Cachia, A}, - year = {2005}, - pages = {57}, -} - -@article{herve_shape_2005, - title = {Shape and volume of lacunar infarcts: a {3D} {MRI} study in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy}, - volume = {36}, - copyright = {All rights reserved}, - journal = {Stroke}, - author = {Herve, D. and Mangin, J. F. and Molko, N. and Bousser, M. G. and Chabriat, H.}, - year = {2005}, - pages = {2384--2388}, - annote = {The following values have no corresponding Zotero field:number: 11label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati}, -} - -@misc{el_kouby_main_2005, - address = {Toronto, Canada}, - title = {Main fiber tracks detection through classification of {MR} diffusion imaging data}, - copyright = {All rights reserved}, - author = {El Kouby, V. and Cointepas, Y. and Poupon, C. and Poline, J. B. and Mangin, J. F.}, - year = {2005}, - keywords = {Diffusion,brainvisa}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati}, -} - -@misc{clouchoux_anatomically_2005, - title = {Anatomically constrained surface parameterization for cortical localization}, - copyright = {All rights reserved}, - author = {Clouchoux, C. and Coulon, O. and Rivière, D. and Cachia, A. and Mangin, J. F. and Régis, J.}, - year = {2005}, - keywords = {Sulci,LongConfPaper,brainvisa, cortical\_surface}, - annote = {The following values have no corresponding Zotero field:pages: 344-351label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - http://brainvisa.info/pdf/clouchoux-MICCAI05.pdfinproceedings}, -} - -@article{molko_brain_2004, - title = {Brain {Anatomy} in {Turner} {Syndrome}: {Evidence} for {Impaired} {Social} and {Spatial}-{Numerical} {Networks}}, - copyright = {All rights reserved}, - abstract = {Analysis of brain structure in Turner syndrome (TS) provides the opportunity to identify the consequences of the loss of one X chromosome on brain anatomy and to characterize the neural bases underlying the specific cognitive profile of TS subjects which includes deficits in spatial-numerical processing and social cognition. Fourteen subjects with TS and fourteen controls were investigated using voxel-based analysis of high resolution anatomical and diffusion tensor images and using sulcal morphometry. The analysis of anatomical images provided evidence for macroscopical changes in cortical regions involved in social cognition such as the left superior temporal sulcus and orbito-frontal cortex and in a region involved in spatial and numerical cognition such as the right intraparietal sulcus. Diffusion tensor images showed a displacement of the grey-white matter interface of the left and right superior temporal sulcus and revealed bilateral microstuctural anomalies in the temporal white matter. The analysis of fiber orientation suggests specific alterations of fiber tracts connecting posterior to anterior temporal regions. Last, sulcal morphometry confirmed the anomalies of the left and right superior temporal sulci and of the right intraparietal sulcus. Our results thus provide converging evidence of regionally specific structural changes in TS that are highly consistent with the hallmark symptoms associated with TS.}, - journal = {Cereb Cortex}, - author = {Molko, N. and Cachia, A. and Riviere, D. and Mangin, J. F. and Bruandet, M. and LeBihan, D. and Cohen, L. and Dehaene, S.}, - month = mar, - year = {2004}, - annote = {1047-3211Journal article}, - annote = {The following values have no corresponding Zotero field:auth-address: INSERM U 562, Service Hospitalier Frederic Joliot, CEA/DSV, IFR 49, Orsay, France.accession-num: 15054057label: ACL}, -} - -@misc{kochunov_development_2005, - address = {Toronto, Canada}, - title = {Development of high-resolution {MRI} imaging and image processing for live and post-mortem primates ({Papio} hamadryas)}, - copyright = {All rights reserved}, - author = {Kochunov, P. and Rivière, D. and Lancaster, J. L. and Mangin, J. F. and Cointepas, Y. and D, evelopmental P. sychology and Glahn, D. and Fox, P. and Rogers, J.}, - year = {2005}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@article{kochunov_age-related_2005, - title = {Age-related morphology trends of cortical sulci}, - volume = {26}, - copyright = {All rights reserved}, - journal = {Hum Brain Mapp.}, - author = {Kochunov, P. and Mangin, J. F. and Coyle, T. R. and Lancaster, J. L. and Thompson, P. M. and Rivière, D. and Cointepas, Y. and Régis, J. and Schlosser, A. and Royall, D. R. and Zilles, K. and Mazziotta, J. and Toga, A. W. and Fox, P. T.}, - year = {2005}, - keywords = {Sulci,brainvisa}, - pages = {210--220}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - http://brainvisa.info/pdf/kochunov-HBM05.pdfarticle}, -} - -@article{delmaire_disorganized_2005, - title = {Disorganized somatotopy in the putamen of patients with focal hand dystonia}, - volume = {64}, - copyright = {All rights reserved}, - journal = {Neurology}, - author = {Delmaire, C. and Krainik, A. and Tezenas du Montcel, S. and Gerardin, E. and Meunier, S. and Mangin, J. F. and Sangla, S. and Garnero, L. and Vidailhet, M. and Lehéricy, S.}, - year = {2005}, - keywords = {AP-HP GH Pitié Salpêtrière Service de Neuroradiologie}, - pages = {1391--1396}, - annote = {The following values have no corresponding Zotero field:number: 8label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati}, -} - -@article{simon_automatized_2004, - title = {Automatized clustering and functional geometry of human parietofrontal networks for language, space, and number}, - volume = {23}, - copyright = {All rights reserved}, - abstract = {Human functional MRI studies frequently reveal the joint activation of parietal and of lateral and mesial frontal areas during various cognitive tasks. To analyze the geometrical organization of those networks, we used an automatized clustering algorithm that parcels out sets of areas based on their similar profile of task-related activations or deactivations. This algorithm allowed us to reanalyze published fMRI data (Simon, O., Mangin, J.F., Cohen, L., Le Bihan, D., Dehaene, S., 2002. Topographical layout of hand, eye, calculation, and language-related areas in the human parietal lobe. Neuron 33, 475-487) and to reproduce the previously observed geometrical organization of activations for saccades, attention, grasping, pointing, calculation, and language processing in the parietal lobe. Further, we show that this organization extends to lateral and mesial prefrontal regions. Relative to the parietal lobe, the prefrontal functional geometry is characterized by a partially symmetrical anteroposterior ordering of activations, a decreased representation of effector-specific tasks, and a greater emphasis on higher cognitive functions of attention, higher-order spatial representation, calculation, and language. Anatomically, our results in humans are closely homologous to the known connectivity of parietal and frontal regions in the macaque monkey.}, - journal = {Neuroimage}, - author = {Simon, O. and Kherif, F. and Flandin, G. and Poline, J. B. and Riviere, D. and Mangin, J. F. and Le Bihan, D. and Dehaene, S.}, - month = nov, - year = {2004}, - keywords = {Image Processing, Computer-Assisted, Animals, Cluster Analysis, Visual Perception/*physiology, Attention/physiology, Parietal Lobe/*physiology, *Language, Frontal Lobe/*physiology, Nerve Net/*physiology, Laterality/physiology, Parietal Lobe, physiology, Functional Laterality, physiology, Saccades/physiology, Space Perception/*physiology, Attention, physiology, Frontal Lobe, physiology, Hand Strength, physiology, Hand Strength/physiology, Macaca, Nerve Net, physiology, Saccades, physiology, Space Perception, physiology, Visual Perception, physiology}, - pages = {1192--202}, - annote = {1053-8119Journal Article}, - annote = {The following values have no corresponding Zotero field:auth-address: Service hospitalier Frederic Joliot, CEA/DSV, Orsay, France.number: 3accession-num: 15528119label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - articlejp137830}, -} - -@article{molko_estimation_2004, - title = {Estimation of the hemodynamic response in event-related functional {MRI} : {Bayesian} networks as a framework for efficient bayesian modeling and inference}, - volume = {23}, - copyright = {All rights reserved}, - journal = {IEEE transactions of Medical Imaging}, - author = {Molko, N. and Cachia, A. and Rivière, D. and Bruandet, M. and Cohen, L. and Dehaene, S.}, - year = {2004}, - pages = {959--967}, - annote = {The following values have no corresponding Zotero field:number: 8section: 959label: ACL}, -} - -@misc{molko_monitoring_2002, - title = {Monitoring disease progression in {CADASIL} with diffusion magnetic resonance imaging a study with whole brain histogram analysis}, - copyright = {All rights reserved}, - author = {Molko, Nicolas and Pappata, Sabina and Mangin, Jean-François and Poupon, F. and LeBihan, Denis and Bousser, M. G. and Chabriat, H.}, - year = {2002}, - annote = {The following values have no corresponding Zotero field:secondary-title: Strokepages: 2902--2908volume: 33isbn: \%(label: ACLcustom1: http://www.Unicog.org/publications/molko\_stroke2002.pdfcustom3: article}, -} - -@article{molko_diffusion_2001, - title = {Diffusion tensor imaging study of subcortical gray matter in cadasil}, - volume = {32}, - copyright = {All rights reserved}, - issn = {1524-4628 (Electronic)}, - abstract = {BACKGROUND AND PURPOSE: In cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), water diffusion changes suggestive of microstructural tissue alterations have been recently reported in abnormal- and normal-appearing white matter as seen on T2-weighted images. In the subcortical gray matter, typical lacunar infarcts are repeatedly observed. Whether microstructural tissue changes are also present outside these lesions within the putamen or thalamus remains unknown. METHODS: We used diffusion tensor imaging, an MRI method highly sensitive to cerebral microstructure, in 20 CADASIL patients and 12 controls. Both the trace of the diffusion tensor [Tr(D)] and an anisotropic diffusion index (volume ratio) of diffusion were measured within the putamen and thalamus outside typical lacunar infarcts as detected on both T1- and T2-weighted images. RESULTS: A significant increase in Tr(D) and a decrease in anisotropy were observed in the putamen and thalamus in patients. The right/left indices of Tr(D) in the thalamus, but not in the putamen, were strongly correlated with the corresponding indices calculated in the white matter of the centrum semiovale. In addition, the diffusion increase in the thalamus was positively correlated with Tr(D) and with the load of small deep infarcts within the white matter and negatively correlated with the Mini-Mental State Examination score. CONCLUSIONS: Our results suggest that microstructural tissue alterations are present in the putamen and thalamus, outside the typical lacunar infarcts in CADASIL. In the thalamus, these microstructural changes appear constant and are even observed in asymptomatic subjects. Some of these thalamic changes appear to result from degeneration of thalamocortical pathways secondary to ischemic white matter damage. The importance of this degenerative phenomenon in the pathophysiology of CADASIL requires further investigation.}, - language = {eng}, - journal = {Stroke}, - author = {Molko, N. and Pappata, S. and Mangin, J. F. and Poupon, C. and Vahedi, K. and Jobert, A. and LeBihan, D. and Bousser, M. G. and Chabriat, H.}, - month = sep, - year = {2001}, - keywords = {Humans, Neuropsychological Tests, Middle Aged, Anisotropy, Diffusion, Analysis of Variance, Magnetic Resonance Imaging/*methods, Nerve Fibers, Myelinated/pathology, *Receptors, Cell Surface, Cerebral Infarction/complications/diagnosis, Dementia, Multi-Infarct/complications/*diagnosis/genetics, Proto-Oncogene Proteins/genetics, Putamen/*pathology, Thalamus/*pathology}, - pages = {2049--54}, - annote = {Molko, NPappata, SMangin, J FPoupon, CVahedi, KJobert, ALeBihan, DBousser, M GChabriat, HClinical TrialControlled Clinical TrialResearch Support, Non-U.S. Gov'tUnited StatesStroke; a journal of cerebral circulationStroke. 2001 Sep;32(9):2049-54.}, - annote = {The following values have no corresponding Zotero field:auth-address: Unite Neuroimagerie Anatomo-Fonctionelle, INSERM U334, Paris, France.number: 9edition: 2001/09/08accession-num: 11546896label: ACL}, -} - -@article{klein_retinotopic_2004, - title = {Retinotopic organization of visual mental images as revealed by functional magnetic resonance imaging}, - volume = {22}, - copyright = {All rights reserved}, - abstract = {In this study, we used event-related functional magnetic resonance imaging to investigate whether visual mental images retinotopically activate early visual cortex. Six participants were instructed to visualize or view horizontally or vertically oriented flashing bow-tie shaped stimuli. When compared to baseline, imagery globally activated Area V1. When the activation evoked by the stimuli at the different orientations was directly compared, distinct spatial activation patterns were obtained for each orientation in most participants. Not only was the topography of the activation patterns from imagery similar to the topography obtained with a corresponding visual perception task, but it closely matched the individual cortical representation of either the horizontal or the vertical visual field meridians. These findings strongly support that visual imagery and perception share low-level anatomical substrate and functional processes. Binding of spatial features is suggested as one possible mechanism.}, - journal = {Brain Res Cogn Brain Res}, - author = {Klein, Isabelle and Dubois, Jessica and Mangin, Jean-François and Kherif, Ferath and Flandin, Guillaume and Poline, Jean-Baptiste and Denis, Michel and Kosslyn, Stephen M. and Bihan, Denis Le}, - month = dec, - year = {2004}, - keywords = {Humans, Brain Mapping, Adult, Female, Male, Cluster Analysis, Orientation, Acoustic Stimulation, methods, Magnetic Resonance Imaging, methods, Photic Stimulation, methods, Imagination, physiology, Oxygen, blood, Visual Cortex, blood supply/physiology, Visual Perception, physiology, Evoked Potentials, physiology, Mental Processes, physiology, Visual Pathways, blood supply/physiology}, - pages = {26--31}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: NeuroSpin}, - annote = {Unati - articlejp137830}, -} - -@article{molko_functional_2003, - title = {Functional and structural alterations of the intraparietal sulcus in a developmental dyscalculia of genetic origin}, - volume = {40}, - copyright = {All rights reserved}, - abstract = {Cognitive theories of numerical representation suggest that understanding of numerical quantities is driven by a magnitude representation associated with the intraparietal sulcus and possibly under genetic control. The aim of this study was to investigate, using fMRI and structural imaging, the interaction between the abnormal development of numerical representation in an X-linked condition, Turner syndrome (TS), and the development of the intraparietal sulcus. fMRI during exact and approximate calculation in TS showed an abnormal modulation of intraparietal activations as a function of number size. Morphological analysis revealed an abnormal length, depth, and sulcal geometry of the right intraparietal sulcus, suggesting an important disorganization of this region in TS. Thus, a genetic form of developmental dyscalculia can be related to both functional and structural anomalies of the right intraparietal sulcus, suggesting a crucial role of this region in the development of arithmetic abilities.}, - journal = {Neuron}, - author = {Molko, N. and Cachia, A. and Riviere, D. and Mangin, J. F. and Bruandet, M. and Le Bihan, D. and Cohen, L. and Dehaene, S.}, - month = nov, - year = {2003}, - pages = {847--58}, - annote = {229870660896-6273Journal Article}, - annote = {The following values have no corresponding Zotero field:auth-address: INSERM U 562, Cognitive Neuroimaging, Service Hospitalier Frederic Joliot, CEA/DSV, IFR 49, Orsay, Francenumber: 4accession-num: 14622587label: ACL}, -} - -@article{krainik_postoperative_2003, - title = {Postoperative speech disorder after medial frontal surgery: {Role} of the supplementary motor area}, - volume = {60}, - copyright = {All rights reserved}, - abstract = {BACKGROUND: Patients undergoing surgical resection of medial frontal lesions may present transient postoperative speech disorders that remain largely unpredictable. OBJECTIVE: To relate the occurrence of this speech deficit to the specific surgical lesion of the supplementary motor area (SMA) involved during language tasks using fMRI. METHODS: Twelve patients were studied using a verbal fluency task before resection of a low-grade glioma of the medial frontal lobe and compared with six healthy subjects. Pre- and postoperative MR variables including the hemispheric dominance for language, the extent of SMA removal, and the volume of resection were compared to the clinical outcome. RESULTS: Following surgery, 6 of 12 patients presented speech disorders. The deficit was similar across patients, consisting of a global reduction in spontaneous speech, ranging from a complete mutism to a less severe speech reduction, which recovered within a few weeks or months. The occurrence of the deficit was related to the resection of the activation in the SMA of the dominant hemisphere for language (p {\textless} 0.01). Increased activation in the SMA of the healthy hemisphere on the preoperative fMRI was observed in patients with postoperative speech deficit. CONCLUSIONS: fMRI is able to identify the area at risk in the SMA, of which resection is related to the occurrence of characteristic transient postoperative speech disorders. Increased SMA activation in the healthy hemisphere suggested that a plastic change of SMA function occurred in these patients.}, - journal = {Neurology}, - author = {Krainik, A. and Lehericy, S. and Duffau, H. and Capelle, L. and Chainay, H. and Cornu, P. and Cohen, L. and Boch, A. L. and Mangin, J. F. and Le Bihan, D. and Marsault, C.}, - month = feb, - year = {2003}, - pages = {587--94}, - annote = {1526-632xJournal Article}, - annote = {The following values have no corresponding Zotero field:auth-address: Departments of Neuroradiology (Drs. Krainik, Lehericy, Chainay, and Marsault), Neurosurgery (Drs. Duffau, Capelle, Cornu, and Boch), and Neurology (Dr. Cohen), Hopital de la Salpetriere, Paris.number: 4accession-num: 12601097label: ACL}, -} - -@article{molko_visualizing_2002, - title = {Visualizing the neural bases of a disconnection syndrome with diffusion tensor imaging}, - volume = {14}, - copyright = {All rights reserved}, - journal = {Journal of Cognitive Neuroscience}, - author = {Molko, N. and Cohen, L. and Mangin, J. F. and Chochon, F. and Lehéricy, S. and Le Bihan, D. and Dehaene, S.}, - year = {2002}, - pages = {629--636}, - annote = {The following values have no corresponding Zotero field:label: ACL}, -} - -@article{pinel_modulation_2001, - title = {Modulation of parietal activation by semantic distance in a number comparison task}, - volume = {14}, - copyright = {All rights reserved}, - abstract = {The time to compare two numbers shows additive effects of number notation and of semantic distance, suggesting that the comparison task can be decomposed into distinct stages of identification and semantic processing. Using event-related fMRI and high-density ERPs, we isolated cerebral areas where activation was influenced by input notation (verbal or Arabic notation). The bilateral extrastriate cortices and a left precentral region were more activated during verbal than during Arabic stimulation, while the right fusiform gyrus and a set of bilateral inferoparietal and frontal regions were more activated during Arabic than during verbal stimulation. We also identified areas that were influenced solely by the semantic content of the stimuli (numerical distance between numbers to be compared) independent of the input notation. Activation tightly correlated with numerical distance was observed mainly in a group of parietal areas distributed bilaterally along the intraparietal sulci and in the precuneus, as well as in the left middle temporal gyrus and posterior cingulate. Our results support the assumption of a central semantic representation of numerical quantity that relies on a common parietal network shared among notations.}, - journal = {Neuroimage}, - author = {Pinel, P. and Dehaene, S. and Riviere, D. and LeBihan, D.}, - year = {2001}, - keywords = {Brain Mapping, Reference Values, Adult, Female, Male, *Magnetic Resonance Imaging, Dominance, Cerebral/physiology, Nerve Net/physiology, Temporal Lobe/physiology, Evoked Potentials/physiology, Parietal Lobe/*physiology, Support, Non-U.S. Gov't, Attention/*physiology, *Semantics, Gyrus Cinguli/physiology, Problem Solving/*physiology}, - pages = {1013--26.}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, -} - -@article{andrade_detection_2001, - title = {Detection of {fMRI} activation using cortical surface mapping}, - volume = {12}, - copyright = {All rights reserved}, - abstract = {A methodology for fMRI data analysis confined to the cortex, Cortical Surface Mapping (CSM), is presented. CSM retains the flexibility of the General Linear Model based estimation, but the procedures involved are adapted to operate on the cortical surface, while avoiding to resort to explicit flattening. The methodology is tested by means of simulations and application to a real fMRI protocol. The results are compared with those obtained with a standard, volume-oriented approach (SPM), and it is shown that CSM leads to local differences in sensitivity, with generally higher sensitivity for CSM in two of the three subjects studied. The discussion provided is focused on the benefits of the introduction of anatomical information in fMRI data analysis, and the relevance of CSM as a step toward this goal.}, - journal = {Hum Brain Mapp}, - author = {Andrade, A. and Kherif, F. and Mangin, J. F. and Worsley, K. J. and Paradis, A. L. and Simon, O. and Dehaene, S. and Le Bihan, D. and Poline, J. B.}, - year = {2001}, - pages = {79--93.}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, -} - -@article{chabriat_clinical_1999, - title = {Clinical severity in {CADASIL} related to ultrastructural damage in white matter: in vivo study with diffusion tensor {MRI}}, - volume = {30}, - copyright = {All rights reserved}, - issn = {0039-2499 (Print)}, - abstract = {BACKGROUND AND PURPOSE: CADASIL is a newly recognized cause of subcortical ischemic strokes that progressively leads to dementia associated with pseudobulbar palsy and severe motor disability. This deleterious progression and the severity of clinical presentation are widely variable among affected subjects. The exact role played by MRI white-matter abnormalities, a hallmark of the disease, in the severity of the clinical phenotype remains poorly understood. METHODS: To address this issue, we used diffusion tensor imaging (DTI), a new MRI technique highly sensitive to white-matter microstructural changes, in 16 symptomatic patients and 10 age-matched controls. Mean diffusivity and anisotropy of diffusion were measured within hyperintensities identified on T2-weighted images (T2WI) and outside these lesions on 4 slices at the level of centrum semiovale. RESULTS: We found a 60\% increase of water mean diffusivity and a parallel loss of diffusion anisotropy in hyperintensities identified on T2WI. The same pattern of diffusion changes, but of lesser intensity, was found in the normal-appearing white matter on T2WI. Mean diffusivity in regions with increased signal on T2WI was higher in patients with severe clinical disability compared with those with no or mild deficit (1.33+/-0.11 versus 1.13+/-0.11 10(-3) mm(2)/s, P{\textless}0.01). Furthermore, diffusion measured within T2 hyperintensities correlated with both the Mini-Mental State Examination and Rankin scale scores. In patients with a severe clinical status, the increase of water diffusion in these regions exceeded 70\% in comparison with values obtained in the normal white matter in control subjects. CONCLUSIONS: These results indicate that DTI is able to detect important ultrastructural changes in regions with increased signal on T2WI and within the normal-appearing white matter in CADASIL. The diffusion changes might be related to both neuronal loss and demyelination. The degree of the underlying ultrastructural alterations is related to the severity of the clinical status with a possible threshold level of white-matter damage above which severe neurological impairment may occur in this disease. DTI appears to be a promising technique for monitoring disease progression in CADASIL.}, - language = {eng}, - journal = {Stroke}, - author = {Chabriat, H. and Pappata, S. and Poupon, C. and Clark, C. A. and Vahedi, K. and Poupon, F. and Mangin, J. F. and Pachot-Clouard, M. and Jobert, A. and Le Bihan, D. and Bousser, M. G.}, - month = dec, - year = {1999}, - keywords = {Humans, Brain Mapping, Adult, Middle Aged, Diffusion, Aged, Case-Control Studies, Analysis of Variance, Magnetic Resonance Imaging/*methods, Brain/*pathology, Dementia, Multi-Infarct/*pathology, Extracellular Space}, - pages = {2637--43}, - annote = {Chabriat, HPappata, SPoupon, CClark, C AVahedi, KPoupon, FMangin, J FPachot-Clouard, MJobert, ALe Bihan, DBousser, M GResearch Support, Non-U.S. Gov'tUnited statesStroke; a journal of cerebral circulationStroke. 1999 Dec;30(12):2637-43.}, - annote = {The following values have no corresponding Zotero field:auth-address: Department of Neurology, CHU Lariboisiere, Universite Paris VII, France. chabriat@ccr.jussieu.frnumber: 12edition: 1999/12/03accession-num: 10582990label: ACL}, -} - -@article{yoo_example-based_2015, - title = {An {Example}-{Based} {Multi}-{Atlas} {Approach} to {Automatic} {Labeling} of {White} {Matter} {Tracts}}, - volume = {10}, - copyright = {All rights reserved}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0133337}, - number = {7}, - journal = {PLOS ONE}, - author = {Yoo, Sang Wook and Guevara, Pamela and Jeong, Yong and Yoo, Kwangsun and Shin, Joseph S. and Mangin, Jean-Francois and Seong, Joon-Kyung}, - month = jul, - year = {2015}, - pages = {e0133337}, - annote = {The following values have no corresponding Zotero field:number: 7label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 26225419}, -} - -@article{lefevre_are_2015, - title = {Are {Developmental} {Trajectories} of {Cortical} {Folding} {Comparable} {Between} {Cross}-sectional {Datasets} of {Fetuses} and {Preterm} {Newborns}?}, - copyright = {All rights reserved}, - abstract = {Magnetic resonance imaging has proved to be suitable and efficient for in vivo investigation of the early process of brain gyrification in fetuses and preterm newborns but the question remains as to whether cortical-related measurements derived from both cases are comparable or not. Indeed, the developmental folding trajectories drawn up from both populations have not been compared so far, neither from cross-sectional nor from longitudinal datasets. The present study aimed to compare features of cortical folding between healthy fetuses and early imaged preterm newborns on a cross-sectional basis, over a developmental period critical for the folding process (21-36 weeks of gestational age [GA]). A particular attention was carried out to reduce the methodological biases between the 2 populations. To provide an accurate group comparison, several global parameters characterizing the cortical morphometry were derived. In both groups, those metrics provided good proxies for the dramatic brain growth and cortical folding over this developmental period. Except for the cortical volume and the rate of sulci appearance, they depicted different trajectories in both groups suggesting that the transition from into ex utero has a visible impact on cortical morphology that is at least dependent on the GA at birth in preterm newborns.}, - journal = {Cereb Cortex}, - author = {Lefèvre, J. and Germanaud, D. and Dubois, J. and Rousseau, F. and de Macedo Santos, I. and Angleys, H. and Mangin, J. F. and Hüppi, P. S. and Girard, N. and De Guio, F.}, - month = jun, - year = {2015}, - keywords = {morphometry, cortical surface, curvature, development of cortical sulci, fetal MRI, in utero, premature birth}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unicog - Unati - UniactPMID: 26045567}, -} - -@article{vellas_mapt_2014, - title = {{MAPT} {STUDY}: {A} {MULTIDOMAIN} {APPROACH} {FOR} {PREVENTING} {ALZHEIMER}'{S} {DISEASE}: {DESIGN} {AND} {BASELINE} {DATA}.}, - volume = {1}, - copyright = {All rights reserved}, - abstract = {OBJECTIVE: -The Multidomain Alzheimer Preventive Trial (MAPT study) was designed to assess the efficacy of isolated supplementation with omega-3 fatty acid, an isolated multidomain intervention (consisting of nutritional counseling, physical exercise, cognitive stimulation) or a combination of the two interventions on the change of cognitive functions in frail subjects aged 70 years and older for a period of 3 years. Ancillary neuroimaging studies were additionally implemented to evaluate the impact of interventions on cerebral metabolism (FDG PET scans) and atrophy rate (MRIs), as well as brain amyloïd deposit (AV45 PET scans). -DESIGN PATIENTS: -1680 subjects (mean age: 75.3 years; female: 64.8 \%), enrolled by 13 memory clinics, were randomized into one of the following four groups: omega-3 supplementation alone, multidomain intervention alone, omega-3 plus multidomain intervention, or placebo. Participants underwent cognitive, functional and biological assessments at M6, M12, M24 and M36 visits. The primary endpoint is a change of memory function at 3 years, as assessed by the Free and Cued Selective Reminding test. All participants will be followed for 2 additional years after the 3-years intervention (MAPT PLUS extension study). -INTERVENTIONS: -1/Omega-3 supplementation: two soft capsules daily as a single dose, containing a total of 400 mg docosahexaenoic acid (DHA), i.e., 800 mg docosahexaenoic acid per day, for 3 years. 2/ Multidomain intervention: collective training sessions conducted in small groups (6-8 participants) in twelve 120-minute sessions over the first 2 months (two sessions a week for the first month, and one session a week the second month) then a 60-minute session per month in the following three areas: nutrition, physical activity, and cognition until the end of the 3 years. In addition to the collective sessions, individualized preventive outpatient visits exploring possible risk factors for cognitive decline are performed at baseline, M12 and M24. -BASELINE POPULATION: -For cognition, the mean MMSE at baseline was 28.1 (± 1.6). About 58\% and 42\% of participants had a CDR score equal to 0 and 0.5, respectively. Regarding mobility status, 200 (11.9\%) had a 4-m gait speed lower or equal to 0.8 m/s. According to the Fried criteria, 673 (42.1\%) participants were considered pre frail, and 51 (3.2\%) frail. The red blood cell DHA content was 26.1 ± 8.1 µg/g. Five hundred and three participants underwent baseline MRI. AV45 PET scans were performed in 271 individuals and preliminary results showed that 38.0\% had a cortical SUVR {\textgreater} 1.17, which gave an indication of significant brain amyloïd deposit. DISCUSSION: The MAPT trial is presently the first largest and longest multidomain preventive trial relevant to cognitive decline in older adults with subjective memory complaints. The multidomain intervention designed for the MAPT trial is likely to be easily implemented within the general population.}, - journal = {J Prev Alzheimers Dis.}, - author = {Vellas, B. and Carrie, I. and Gillette-Guyonnet, S. and Touchon, J. and Dantoine, T. and Dartigues, J.-F. and Cuffi, M.-N. and Bordes, S. and Gasnier, Y. and Robert, P. and Bories, L. and Rouaud, O. and Desclaux, F. and Sudres, K. and Bonnefoy, M. and Pesce, A. and Dufouil, C. and Lehericy, S. and Chupin, M. and Mangin, J.-F. and Payoux, P. and Adel, D. and Legrand, P. and Catheline, D. and Kanony, C. and Zaim, M. and Molinier, L. and Costa, N. and Delrieu, J. and Voisin, T. and Faisant, C. and Lala, F. and Nourhashémi, F. and Rolland, Y. and Van Kan, G.-A. and Dupuy, C. and Cantet, C. and Cestac, P. and Belleville, S. and Willis, S. and Cesari, M. and Weiner, M.-W. and Soto, M.-E. and Ousset, P.-J. and Andrieu, S.}, - month = jun, - year = {2014}, - keywords = {Alzheimer’s disease, Multidomain intervention, Omega-3 fatty acids, Prevention trials}, - pages = {13--22}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {UnatiPMID: 26594639}, -} - -@misc{poupon_atlas-based_2009, - address = {San-Francisco, USA}, - title = {Atlas-{Based} {Analysis} of {Human} {Brainstem} {Anatomy} as {Revealed} by {Gradient}-{Echo} {T2}* {Weighted} {MR} {Imaging} at {7T}}, - copyright = {All rights reserved}, - author = {Poupon, F. and Bardinet, E. and Hasboun, D. and Marrakchi, L. and Mangin, J. F. and Kezele, I. and Fernandez-Vidal, S. and Ugurbil, K. and Lehericy, S. and Poupon, C. and de Moortele, P. F. Van and Yelnik, J.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/FPoupon-ISMRM09.pdfinproceedings}, - annote = {Unirs - inproceedings}, -} - -@misc{poupon_millimeter_2009, - address = {Honolulu}, - title = {Millimeter analytical {Q}-ball fiber density function for a better separation of fiber populations at {7T}}, - copyright = {All rights reserved}, - abstract = {The purpose of this work was to demonstrate the feasibility of diffusion-weighted imaging at ultra-high field (7T) with a true millimeter resolution within a reasonable acquisition time. We also demonstrate the possibility of using b-values for performing high angular resolution diffusion imaging (HARDI) such as Q-ball imaging. The results show that high resolution structural organization of the fibers can be revealed with such millimeter data that could not be easily extracted from standard 2mm isotropic data at lower 1.5T or 3.0T fields}, - author = {Poupon, C. and Wiggins, C. and Descoteaux, M. and Feiweier, T. and Mangin, J. and Le Bihan, D.}, - month = apr, - year = {2009}, - keywords = {Honolulu1400}, - annote = {The following values have no corresponding Zotero field:auth-address: CEA NeuroSpin Siemens AGpages: 1400isbn: 1545-4428label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - }, -} - -@misc{marrakchi-kacem_multi-contrast_2009, - address = {Hammamet, Tunisia}, - title = {Multi-contrast {T1} and {DTI} deep nuclei segmentation using a probablistic atlas}, - copyright = {All rights reserved}, - author = {Marrakchi-Kacem, L. and Poupon, C. and Mangin, J. F. and Poupon, F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - inproceedings}, -} - -@misc{mangin_modern_2009, - address = {European Association of Neurosurgical Societes, Marseille, France}, - title = {Modern {Neuroimaging}}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{guevara_inference_2009, - title = {Inference of a fiber bundle atlas using a two-level clustering strategy}, - copyright = {All rights reserved}, - author = {Guevara, P. and Cointepas, Y. and Rivière, D. and Poupon, C. and Thirion, B. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati}, -} - -@misc{marrakchi-kacem_using_2009, - address = {Antalya, Turkey}, - title = {Using {DTI} to constrain the automatic segmentation of the deep nuclei from {T1} contrast by surrounding fiber bundles}, - copyright = {All rights reserved}, - author = {Marrakchi-Kacem, L. and Poupon, C. and Mangin, J. F. and Poupon, F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: Incustom5: MH212867}, - annote = {Unirs - }, - annote = {Unirs - inproceedings}, -} - -@misc{kezele_importance_2009, - address = {Honolulu, Hawaii, USA}, - title = {Importance of {Multiscale} {Analysis} in {HARDI} {Studies}}, - copyright = {All rights reserved}, - author = {Kezele, I. and Poupon, C. and Descoteaux, M. and Poupon, F. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Kezele-ISMRM09.pdfinproceedings}, -} - -@misc{fillard_free_2009, - address = {Honolulu, Hawaii, USA}, - title = {Free {Spin} {Tracking}: {A} {Novel} {Global} {Tractography} {Algorithm}}, - copyright = {All rights reserved}, - author = {Fillard, P. and Poupon, C. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Fillard-ISMRM09.pdfinproceedings}, -} - -@misc{fillard_novel_2009, - title = {A {Novel} {Global} {Tractography} {Framework} based on an {Adaptive} {Spin} {Glass} {Model}}, - copyright = {All rights reserved}, - author = {Fillard, P. and Poupon, C. and Mangin, J. F.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Fillard-MICCAI09.pdfinproceedings}, -} - -@article{boulant_counteracting_2009, - title = {Counteracting radio frequency inhomogeneity in the human brain at 7 {Tesla} using strongly modulating pulses}, - volume = {61}, - copyright = {All rights reserved}, - abstract = {We report flip angle and spoiled gradient echo measurements at 7 Tesla on human brains in three-dimensional imaging, using strongly modulating pulses to counteract the transmitted radiofrequency inhomogeneity problem. Compared with the standard square pulse results, three points of improvement are demonstrated, namely: (i) the removal of the bright center (typical at high fields when using a quadrature head coil), (ii) the substantial gain of signal in the regions of low B(1) intensity, and (iii) an increased 35{\textbackslash}\% signal uniformity over the whole brain at the flip angle where maximum contrast between white and gray matter occurs. We also find by means of simulations that standard BIR-4 adiabatic pulses need several times more energy to reach a similar performance at the same field strength.}, - journal = {Magn Reson Med}, - author = {Boulant, N. and Mangin, J. F. and Amadon, A.}, - month = may, - year = {2009}, - keywords = {Algorithms, Humans, Reproducibility of Results, Sensitivity and Specificity, Anisotropy, Artifacts, Magnetic Resonance Imaging, methods, Image Enhancement, methods, Image Interpretation, Computer-Assisted, methods, Imaging, Three-Dimensional, methods, Brain, anatomy /\&/ histology, Radio Waves}, - pages = {1165--1172}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACLcustom1: NeuroSpin}, - annote = {Unirs - articleMH212867}, -} - -@misc{auzias_disco:_2009, - title = {{DISCO}: a {Coherent} {Diffeomorphic} {Framework} for {Brain} {Registration} under {Exhaustive} {Sulcal} {Constraints}}, - copyright = {All rights reserved}, - author = {Auzias, G. and Glaunès, J. and Colliot, O. and Perrot, M. and Mangin, J. F. and Trouvé, A. and Baillet, S.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati }, -} - -@misc{tucholka_triangulating_2008, - address = {Paris, France}, - title = {Triangulating cortical functional networks with anatomical landmarks}, - copyright = {All rights reserved}, - author = {Tucholka, A. and Thirion, B. and Pinel, P. and Poline, J. B. and Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:pages: 612--615label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/madic/publis/Tucholka08.pdfinproceedings}, -} - -@article{dubois_structural_2009, - title = {Structural asymmetries in the infant language and sensori-motor networks}, - volume = {19}, - copyright = {All rights reserved}, - issn = {1460-2199 (Electronic)}, - doi = {bhn097 [pii] 10.1093/cercor/bhn097}, - abstract = {Both language capacity and strongly lateralized hand preference are among the most intriguing particularities of the human species. They are associated in the adult brain with functional and anatomical hemispheric asymmetries in the speech perception-production network and in the sensori-motor system. Only studies in early life can help us to understand how such asymmetries arise during brain development, and to which point structural left-right differences are the source or the consequence of functional lateralization. In this study, we aimed to provide new in vivo structural markers of hemispheric asymmetries in infants from 1 to 4 months of age, with diffusion tensor imaging. We used 3 complementary analysis methods based on local diffusion indices and spatial localizations of tracts. After a prospective approach over the whole brain, we demonstrated early leftward asymmetries in the arcuate fasciculus and in the cortico-spinal tract. These results suggest that the early macroscopic geometry, microscopic organization, and maturation of these white matter bundles are related to the development of later functional lateralization.}, - language = {eng}, - journal = {Cereb Cortex}, - author = {Dubois, J. and Hertz-Pannier, L. and Cachia, A. and Mangin, J. F. and Le Bihan, D. and Dehaene-Lambertz, G.}, - month = feb, - year = {2009}, - keywords = {Humans, Data Interpretation, Statistical, Image Processing, Computer-Assisted, Female, Male, Diffusion Magnetic Resonance Imaging, Functional Laterality/physiology, *Language, Aging/physiology, *Infant, Arcuate Nucleus/anatomy \& histology/physiology, Nerve Net/*anatomy \& histology/physiology, Pyramidal Tracts/anatomy \& histology/physiology}, - pages = {414--23}, - annote = {Dubois, JHertz-Pannier, LCachia, AMangin, J FLe Bihan, DDehaene-Lambertz, GResearch Support, Non-U.S. Gov'tUnited StatesCerebral cortex (New York, N.Y. : 1991)Cereb Cortex. 2009 Feb;19(2):414-23. Epub 2008 Jun 17.}, - annote = {The following values have no corresponding Zotero field:auth-address: CEA, UNAF, CEA/DSV/I2BM/Service Hospitalier Frederic Joliot, 91403 Orsay, France. jessica.dubois@centraliens.netnumber: 2edition: 2008/06/20accession-num: 18562332label: ACLcustom1: NEUROSPIN}, -} - -@article{descoteaux_diffusion_2009, - title = {Diffusion propagator imaging: using {Laplace}'s equation and multiple shell acquisitions to reconstruct the diffusion propagator}, - volume = {21}, - copyright = {All rights reserved}, - abstract = {Many recent single-shell high angular resolution diffusion imaging reconstruction techniques have been introduced to reconstruct orientation distribution functions (ODF) that only capture angular information contained in the diffusion process of water molecules. By also considering the radial part of the diffusion signal, the reconstruction of the ensemble average diffusion propagator (EAP) of water molecules can provide much richer information about complex tissue microstructure than the ODF. In this paper, we present diffusion propagator imaging (DPI), a novel technique to reconstruct the EAP from multiple shell acquisitions. The DPI solution is analytical and linear because it is based on a Laplace equation modeling of the diffusion signal. DPI is validated with ex vivo phantoms and also illustrated on an in vivo human brain dataset. DPI is shown to reconstruct EAP from only two b-value shells and approximately 100 diffusion measurements.}, - journal = {Inf Process Med Imaging}, - author = {Descoteaux, Maxime and Deriche, Rachid and Bihan, Denis Le and Mangin, Jean-François and Poupon, Cyril}, - year = {2009}, - pages = {1--13}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unirs - articleMH212867}, -} - -@article{bristow_hearing_2009, - title = {Hearing faces : {How} the infant brain matches the face it sees with the speech it hears}, - volume = {21}, - copyright = {All rights reserved}, - journal = {J. Cognitive Neuroscience}, - author = {Bristow, D. and Dehaene-Lambertz, G. and Mattout, J. and Soares, C. and Gliga, T. and Baillet, S. and Mangin, J. F.}, - year = {2009}, - pages = {905--21}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACLcustom1: Neurospin}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACLcustom1: NeuroSpin}, - annote = {Unati }, - annote = {Unati}, -} - -@article{andoh_low-cost_2009, - title = {A low-cost {MRI}-guided method for {TMS} coil positioning}, - volume = {2}, - copyright = {All rights reserved}, - journal = {Brain Stimulation}, - author = {Andoh, J. and Rivière, D. and Mangin, J. F. and Artiges, E. and Cointepas, Y. and Paillère-Martinot, M. L. and Martinot, J. L. and Cachia, A.}, - year = {2009}, - pages = {123--131}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Andoh-BrainStim09.pdf}, -} - -@misc{perrot_identifying_2008, - address = {Paris, France}, - title = {Identifying cortical sulci from localizations, shape and local organization}, - copyright = {All rights reserved}, - author = {Perrot, M. and Rivière, D. and Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:pages: 420--423label: ACTNcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Perrot-ISBI08.pdfinproceedings}, -} - -@article{penttila_global_2008, - title = {Global and {Temporal} {Cortical} {Folding} in {Patients} {With} {Early}-{Onset} {Schizophrenia}}, - volume = {47}, - copyright = {All rights reserved}, - journal = {Journal of the American Academy of Child \& Adolescent Psychiatry}, - author = {Penttilä, J. and Cachia, A. and Paillère-Martinot, M. L. and Mangin, J. F. and Burke, L. and Corrigall, R. and Frangou, S. and Martinot, J. L.}, - year = {2008}, - keywords = {Sulci,Anatomy}, - pages = {1125--1133}, - annote = {The following values have no corresponding Zotero field:number: 10label: ACLcustom1: NeuroSpin}, - annote = {Unati - article}, -} - -@misc{mangin_variability_2008, - address = {Université de Genève, Switzerland}, - title = {Variability of the cortical folding patterns and development}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@article{kochunov_relationship_2008, - title = {Relationship among neuroimaging indices of cerebral health during normal aging}, - volume = {29}, - copyright = {All rights reserved}, - journal = {Human Brain Mapping}, - author = {Kochunov, P. and Thompson, P. M. and Coyle, T. R. and Lancaster, J. L. and Kochunov, V. and Royall, D. R. and Mangin, J. F. and Rivière, D. and Fox, P. T.}, - year = {2008}, - keywords = {Sulci,Diffusion,brainvisa}, - pages = {36--45}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: NeuroSpin}, - annote = {Unatiftp://ftp.cea.fr/pub/dsv/anatomist/papers/Kochunov-HBM08.pdf}, -} - -@misc{kezele_computing_2008, - address = {Toronto, Canada}, - title = {Computing strings of average {HARDI} models using {Procrustes}-{Based} {Fibre} {Alignment}}, - copyright = {All rights reserved}, - author = {Kezele, I. and Poupon, C. and Perrin, M. and Cointepas, Y. and V. El{\textasciitilde}Kouby and Poupon, F. and Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@misc{guevara_connectivity-based_2008, - address = {Paris, France}, - title = {Connectivity-based parcellation of the cortical surface using {Q}-ball imaging}, - copyright = {All rights reserved}, - author = {Guevara, P. and Perrin, M. and Cathier, P. and Cointepas, Y. and Rivière, D. and Poupon, C. and Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:pages: 903--906label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Guevara-ISBI08.pdfinproceedings}, -} - -@misc{poupon_real-time_2008, - address = {Toronto, Canada}, - title = {Real-time {MR} diffusion tensor and {Q}-ball imaging using {Kalman} filtering}, - copyright = {All rights reserved}, - author = {Poupon, F. and Roche, A. and Mangin, J. F. and Poupon, C.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unirs - inproceedings}, -} - -@article{poupon_real-time_2008-1, - title = {Real-time {MR} diffusion tensor and {Q}-ball imaging using {Kalman} filtering}, - volume = {12}, - copyright = {All rights reserved}, - abstract = {Diffusion magnetic resonance imaging (dMRI) has become an established research tool for the investigation of tissue structure and orientation. In this paper, we present a method for real-time processing of diffusion tensor and Q-ball imaging. The basic idea is to use Kalman filtering framework to fit either the linear tensor or Q-ball model. Because the Kalman filter is designed to be an incremental algorithm, it naturally enables updating the model estimate after the acquisition of any new diffusion-weighted volume. Processing diffusion models and maps during ongoing scans provides a new useful tool for clinicians, especially when it is not possible to predict how long a subject may remain still in the magnet. First, we introduce the general linear models corresponding to the two diffusion tensor and analytical Q-ball models of interest. Then, we present the Kalman filtering framework and we focus on the optimization of the diffusion orientation sets in order to speed up the convergence of the online processing. Last, we give some results on a healthy volunteer for the online tensor and the Q-ball model, and we make some comparisons with the conventional offline techniques used in the literature. We could achieve full real-time for diffusion tensor imaging and deferred time for Q-ball imaging, using a single workstation.}, - journal = {Med Image Anal}, - author = {Poupon, Cyril and Roche, Alexis and Dubois, Jessica and Mangin, Jean-François and Poupon, Fabrice}, - month = oct, - year = {2008}, - keywords = {Algorithms, Humans, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Diffusion Magnetic Resonance Imaging, methods, Image Enhancement, methods, Image Interpretation, Computer-Assisted, methods, Brain, anatomy /\&/ histology, Computer Systems}, - pages = {527--534}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACLcustom1: NeuroSpin}, - annote = {Unirs - articleMH212867}, -} - -@article{poupon_new_2008, - title = {New diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging ({HARDI}) models}, - volume = {60}, - copyright = {All rights reserved}, - abstract = {We present new diffusion phantoms dedicated to the study and validation of high-angular-resolution diffusion imaging (HARDI) models. The phantom design permits the application of imaging parameters that are typically employed in studies of the human brain. The phantoms were made of small-diameter acrylic fibers, chosen for their high hydrophobicity and flexibility that ensured good control of the phantom geometry. The polyurethane medium was filled under vacuum with an aqueous solution that was previously degassed, doped with gadolinium-tetraazacyclododecanetetraacetic acid (Gd-DOTA), and treated by ultrasonic waves. Two versions of such phantoms were manufactured and tested. The phantom's applicability was demonstrated on an analytical Q-ball model. Numerical simulations were performed to assess the accuracy of the phantom. The phantom data will be made accessible to the community with the objective of analyzing various HARDI models.}, - journal = {Magn Reson Med}, - author = {Poupon, C. and Rieul, B. and Kezele, I. and Perrin, M. and Poupon, F. and Mangin, J.-F.}, - month = dec, - year = {2008}, - keywords = {Algorithms, Reproducibility of Results, Sensitivity and Specificity, Phantoms, Imaging, Equipment Design, Equipment Failure Analysis, Image Enhancement, methods, Image Interpretation, Computer-Assisted, methods, Diffusion Magnetic Resonance Imaging, instrumentation}, - pages = {1276--1283}, - annote = {The following values have no corresponding Zotero field:number: 6label: ACLcustom1: NeuroSpin}, - annote = {Unirs - articleMH212867}, -} - -@misc{mangin_statistical_2008, - address = {The Royal Statistical Society, London, UK}, - title = {Statistical {Methods} in {Brain} {Research}}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_analysing_2008, - address = {Dept of Biomedical Engineering, Hanyang University}, - title = {Analysing the cortical folding patterns}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{kezele_mean_2008, - address = {New-York, USA}, - title = {Mean {Q}-ball strings obtained by constrained {Procrustes} analysis with point sliding}, - copyright = {All rights reserved}, - author = {Kezele, I. and Poupon, C. and Perrin, M. and Cointepas, Y. and V. El{\textasciitilde}Kouby and Poupon, F. and Mangin, J. F.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@article{cykowski_perisylvian_2008, - title = {Perisylvian {Sulcal} {Morphology} and {Cerebral} {Asymmetry} {Patterns} in {Adults} {Who} {Stutter}}, - volume = {18}, - copyright = {All rights reserved}, - journal = {Cereb Cortex}, - author = {Cykowski, M. D. and Kochunov, P. and Ingham, R. J. and Ingham, J. C. and Mangin, J. F. and Rivière, D. and Lancaster, J. L. and Fox, P. T.}, - year = {2008}, - keywords = {Sulci,brainvisa}, - pages = {571--83}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Cykowski-CC08.pdf}, -} - -@misc{auzias_multi-scale_2008, - address = {Paris, France}, - title = {Multi-scale diffeomorphic cortical registration under manifold sulcal constraints}, - copyright = {All rights reserved}, - author = {Auzias, G. and Glaunès, J. A. and Cachia, A. and Cathier, P. and Bardinet, E. and Colliot, O. and Mangin, J. F. and Trouvé, A. and Baillet, S.}, - year = {2008}, - annote = {The following values have no corresponding Zotero field:pages: 1127--1130label: ACTNcustom1: NeuroSpincustom2: In}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Auzias-ISBI08.pdf}, -} - -@article{dubois_asynchrony_2008, - title = {Asynchrony of the early maturation of white matter bundles in healthy infants: quantitative landmarks revealed non-invasively by diffusion tensor imaging}, - volume = {29}, - copyright = {All rights reserved}, - issn = {\%(}, - journal = {Human Brain Mapping}, - author = {Dubois, J. and Dehaene-Lambertz, G. and Perrin, M. and Mangin, J. F. and Cointepas, Y. and Bihan, D. Le and Hertz-Pannier, L.}, - year = {2008}, - pages = {14--27}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: http://www.Unicog.org/publications/DuboisHertzPannierDehaene-Lambertz\_TrackingBB\_NeuroImg2OO6.pdfcustom5: chrplr}, -} - -@article{andoh_priming_2008, - title = {Priming frequencies of transcranial magnetic stimulation over {Wernicke}'s area modulate word detection}, - volume = {18}, - copyright = {All rights reserved}, - journal = {Cereb Cortex}, - author = {Andoh, J. and Artiges, E. and Pallier, C. and Rivière, D. and Mangin, J. F. and Paillère-Martinot, M. L. and Martinot, J. L.}, - year = {2008}, - keywords = {Humans, Adult, Male, Speech Perception/*physiology, Motor Cortex/*physiology, *Vocabulary, *Task Performance and Analysis, Transcranial Magnetic Stimulation/*methods}, - pages = {210--6}, - annote = {Andoh, JamilaArtiges, EricPallier, ChristopheRiviere, DenisMangin, Jean-FrancoisPaillere-Martinot, Marie-LaureMartinot, Jean-LucResearch Support, Non-U.S. Gov'tUnited StatesCerebral cortex (New York, N.Y. : 1991)Cereb Cortex. 2008 Jan;18(1):210-6. Epub 2007 May 8.}, - annote = {The following values have no corresponding Zotero field:auth-address: Inserm U797 Research Unit Neuroimaging and Psychiatry, IFR 49, Orsay, France.number: 1edition: 2007/05/11label: ACLcustom1: NEUROSPIN}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Andoh-CC08.pdf}, -} - -@misc{poupon_new_2007, - address = {Berlin, Germany}, - title = {New diffusion phantoms dedicated to study and validation of {HARDI} diffusion models.}, - copyright = {All rights reserved}, - author = {Poupon, C. and Rieul, B. and Perrin, M. and Mangin, J.-F. and LeBihan, D.}, - month = may, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: COMcustom1: NeuroSpincustom2: In}, - annote = {Unirs - Oral session}, -} - -@misc{mangin_signal_2007, - address = {Lausanne, Switzerland}, - title = {Signal {Processing} {Institute}}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_morphometry_2007, - address = {Chicago, USA}, - title = {Morphometry of the human cortical cortex}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{mangin_image_2007, - address = {Inst. for Pure \& Applied Math., UCLA, USA}, - title = {Image processing for {Random} {Shapes}}, - copyright = {All rights reserved}, - author = {Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: Neurospincustom2: In}, - annote = {Unati}, -} - -@misc{sun_automatic_2007, - title = {Automatic inference of sulcus patterns using {3D} moment invariants}, - copyright = {All rights reserved}, - author = {Sun, Z. Y. and Riviere, D. and Poupon, F. and Regis, J. and Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:pages: 515--522label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Poupon-MICCAI07.pdfinproceedings}, -} - -@article{rodrigo_human_2007, - title = {Human subinsular asymetry studied by diffusion tensor imaging and fiber tracking}, - volume = {28}, - copyright = {All rights reserved}, - journal = {Am J Neuroradiol}, - author = {Rodrigo, S. and Naggara, C. and Oppenheim, C. and Golestani, N. and Poupon, C. and Cointepas, Y. and Mangin, J. F. and Le Bihan, D. and Meder, J. F.}, - year = {2007}, - pages = {1526--31}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NEUROSPIN}, -} - -@misc{poupon_diffusion_2007, - address = {Dead Sea, Israel}, - title = {Diffusion phantoms dedicated to the study and validation of {HARDI} models}, - copyright = {All rights reserved}, - author = {Poupon, C. and Rieul, B. and Perrin, M. and Poupon, F. and Mangin, J. F.}, - year = {2007}, - annote = {The following values have no corresponding Zotero field:label: INVcustom1: NeuroSpincustom2: In}, - annote = {Unirs - }, -} - -@article{cavedo_road_2014, - title = {The {Road} {Ahead} to {Cure} {Alzheimer}'s {Disease}: {Development} of {Biological} {Markers} and {Neuroimaging} {Methods} for {Prevention} {Trials} {Across} all {Stages} and {Target} {Populations}}, - volume = {1}, - issn = {2274-5807}, - shorttitle = {The {Road} {Ahead} to {Cure} {Alzheimer}'s {Disease}}, - doi = {10.14283/jpad.2014.32}, - abstract = {Alzheimer's disease (AD) is a slowly progressing non-linear dynamic brain disease in which pathophysiological abnormalities, detectable in vivo by biological markers, precede overt clinical symptoms by many years to decades. Use of these biomarkers for the detection of early and preclinical AD has become of central importance following publication of two international expert working group's revised criteria for the diagnosis of AD dementia, mild cognitive impairment (MCI) due to AD, prodromal AD and preclinical AD. As a consequence of matured research evidence six AD biomarkers are sufficiently validated and partly qualified to be incorporated into operationalized clinical diagnostic criteria and use in primary and secondary prevention trials. These biomarkers fall into two molecular categories: biomarkers of amyloid-beta (Aβ) deposition and plaque formation as well as of tau-protein related hyperphosphorylation and neurodegeneration. Three of the six gold-standard ("core feasible) biomarkers are neuroimaging measures and three are cerebrospinal fluid (CSF) analytes. CSF Aβ1-42 (Aβ1-42), also expressed as Aβ1-42 : Aβ1-40 ratio, T-tau, and P-tau Thr181 \& Thr231 proteins have proven diagnostic accuracy and risk enhancement in prodromal MCI and AD dementia. Conversely, having all three biomarkers in the normal range rules out AD. Intermediate conditions require further patient follow-up. Magnetic resonance imaging (MRI) at increasing field strength and resolution allows detecting the evolution of distinct types of structural and functional abnormality pattern throughout early to late AD stages. Anatomical or volumetric MRI is the most widely used technique and provides local and global measures of atrophy. The revised diagnostic criteria for "prodromal AD" and "mild cognitive impairment due to AD" include hippocampal atrophy (as the fourth validated biomarker), which is considered an indicator of regional neuronal injury. Advanced image analysis techniques generate automatic and reproducible measures both in regions of interest, such as the hippocampus and in an exploratory fashion, observer and hypothesis-indedendent, throughout the entire brain. Evolving modalities such as diffusion-tensor imaging (DTI) and advanced tractography as well as resting-state functional MRI provide useful additionally useful measures indicating the degree of fiber tract and neural network disintegration (structural, effective and functional connectivity) that may substantially contribute to early detection and the mapping of progression. These modalities require further standardization and validation. The use of molecular in vivo amyloid imaging agents (the fifth validated biomarker), such as the Pittsburgh Compound-B and markers of neurodegeneration, such as fluoro-2-deoxy-D-glucose (FDG) (as the sixth validated biomarker) support the detection of early AD pathological processes and associated neurodegeneration. How to use, interpret, and disclose biomarker results drives the need for optimized standardization. Multimodal AD biomarkers do not evolve in an identical manner but rather in a sequential but temporally overlapping fashion. Models of the temporal evolution of AD biomarkers can take the form of plots of biomarker severity (degree of abnormality) versus time. AD biomarkers can be combined to increase accuracy or risk. A list of genetic risk factors is increasingly included in secondary prevention trials to stratify and select individuals at genetic risk of AD. Although most of these biomarker candidates are not yet qualified and approved by regulatory authorities for their intended use in drug trials, they are nonetheless applied in ongoing clinical studies for the following functions: (i) inclusion/exclusion criteria, (ii) patient stratification, (iii) evaluation of treatment effect, (iv) drug target engagement, and (v) safety. Moreover, novel promising hypothesis-driven, as well as exploratory biochemical, genetic, electrophysiological, and neuroimaging markers for use in clinical trials are being developed. The current state-of-the-art and future perspectives on both biological and neuroimaging derived biomarker discovery and development as well as the intended application in prevention trials is outlined in the present publication.}, - language = {eng}, - number = {3}, - journal = {The Journal of Prevention of Alzheimer's Disease}, - author = {Cavedo, E. and Lista, S. and Khachaturian, Z. and Aisen, P. and Amouyel, P. and Herholz, K. and Jack, C. R. and Sperling, R. and Cummings, J. and Blennow, K. and O'Bryant, S. and Frisoni, G. B. and Khachaturian, A. and Kivipelto, M. and Klunk, W. and Broich, K. and Andrieu, S. and de Schotten, M. Thiebaut and Mangin, J.-F. and Lammertsma, A. A. and Johnson, K. and Teipel, S. and Drzezga, A. and Bokde, A. and Colliot, O. and Bakardjian, H. and Zetterberg, H. and Dubois, B. and Vellas, B. and Schneider, L. S. and Hampel, H.}, - month = dec, - year = {2014}, - pmid = {26478889}, - pmcid = {PMC4606938}, - keywords = {Biomarkers, Alzheimer’s disease, molecular imaging, prevention trials}, - pages = {181--202}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACL}, - annote = {UnatiPMID: 26478889}, -} - -@article{mangin_object-based_2004, - title = {Object-based morphometry of the cerebral cortex}, - volume = {23}, - copyright = {All rights reserved}, - number = {8}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Mangin, J. F. and Rivière, D. and Cachia, A. and Duchesnay, E. and Cointepas, Y. and Papadopoulos-Orfanos, D. and Collins, D. L. and Evans, A. C. and Régis, J.}, - month = aug, - year = {2004}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Numerical Analysis, Computer-Assisted, Signal Processing, Computer-Assisted, Expert Systems}, - pages = {968--982}, -} - -@article{guevara_automatic_2012, - title = {Automatic fiber bundle segmentation in massive tractography datasets using a multi-subject bundle atlas}, - volume = {61}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2012.02.071}, - abstract = {This paper presents a method for automatic segmentation of white matter fiber bundles from massive dMRI tractography datasets. The method is based on a multi-subject bundle atlas derived from a two-level intra-subject and inter-subject clustering strategy. This atlas is a model of the brain white matter organization, computed for a group of subjects, made up of a set of generic fiber bundles that can be detected in most of the population. Each atlas bundle corresponds to several inter-subject clusters manually labeled to account for subdivisions of the underlying pathways often presenting large variability across subjects. An atlas bundle is represented by the multi-subject list of the centroids of all intra-subject clusters in order to get a good sampling of the shape and localization variability. The atlas, composed of 36 known deep white matter bundles and 47 superficial white matter bundles in each hemisphere, was inferred from a first database of 12 brains. It was successfully used to segment the deep white matter bundles in a second database of 20 brains and most of the superficial white matter bundles in 10 subjects of the same database.}, - language = {eng}, - number = {4}, - journal = {NeuroImage}, - author = {Guevara, P. and Duclap, D. and Poupon, C. and Marrakchi-Kacem, L. and Fillard, P. and Le Bihan, D. and Leboyer, M. and Houenou, J. and Mangin, J.-F.}, - month = jul, - year = {2012}, - pmid = {22414992}, - keywords = {Brain, Humans, Nerve Fibers, Myelinated, Neural Pathways, Atlases as Topic, Nerve Fibers, Anatomy, Artistic}, - pages = {1083--1099}, -} - -@article{dubois_[brain_2012, - title = {[{Brain} development of infant and {MRI} by diffusion tensor imaging]}, - volume = {42}, - issn = {1769-7131}, - doi = {10.1016/j.neucli.2011.08.001}, - abstract = {Studying how the brain develops and becomes functional is important to understand how the man has been able to develop specific cognitive abilities, and to comprehend the complexity of some developmental pathologies. Thanks to magnetic resonance imaging (MRI), it is now possible to image the baby's immature brain and to consider subtle correlations between the brain anatomical development and the early acquisition of cognitive functions. Dedicated methodologies for image acquisition and post-treatment must then be used because the size of cerebral structures and the image contrast are very different in comparison with the adult brain, and because the examination length is a major constraint. Two recent studies have evaluated the developing brain under an original perspective. The first one has focused on cortical folding in preterm newborns, from 6 to 8 months of gestational age, assessed with T2-weighted conventional MRI. The second study has mapped the organization and maturation of white matter fiber bundles in 1- to 4-month-old healthy infants with diffusion tensor imaging (DTI). Both studies have enabled to highlight spatio-temporal differences in the brain regions' maturation, as well as early anatomical asymmetries between cerebral hemispheres. These studies emphasize the potential of MRI to evaluate brain development compared with the infant's psychomotor acquisitions after birth.}, - language = {fre}, - number = {1-2}, - journal = {Neurophysiologie Clinique = Clinical Neurophysiology}, - author = {Dubois, J. and Dehaene-Lambertz, G. and Mangin, J.-F. and Le Bihan, D. and Hüppi, P. S. and Hertz-Pannier, L.}, - month = feb, - year = {2012}, - pmid = {22200336}, - keywords = {Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Cerebral Cortex, Infant, Newborn}, - pages = {1--9}, -} - -@article{operto_structural_2012, - title = {Structural analysis of {fMRI} data: a surface-based framework for multi-subject studies}, - volume = {16}, - issn = {1361-8423}, - shorttitle = {Structural analysis of {fMRI} data}, - doi = {10.1016/j.media.2012.02.007}, - abstract = {We present a method for fMRI data group analysis that makes the link between two distinct frameworks: surface-based techniques, which process data in the domain defined by the surface of the cortex, and structural techniques, which use object-based representations of the data as opposed to voxel-based ones. This work is a natural surface-based extension of the volume-based structural approach presented in a previous paper. A multi-scale surface-based representation of individual activation maps is first computed for each subject. Then the inter-subject matching and the activation detection decision are performed jointly by optimization of a Markovian model. Finally, a significance measure is computed in a non-parametric way for the results, in order to assess their relevance and control the risk of type I error. The method is applied on simulated and real data and the results are compared to those produced by standard analyses. The surface-based structural analysis is shown to be particularly robust to inter-subject spatial variability and to produce relevant results with good specificity and sensitivity. We also demonstrate the advantages of the surface-based approach by comparing with the results of a 3D structural analysis.}, - language = {eng}, - number = {5}, - journal = {Medical Image Analysis}, - author = {Operto, Grégory and Rivière, Denis and Fertil, Bernard and Bulot, Rémy and Mangin, Jean-François and Coulon, Olivier}, - month = jul, - year = {2012}, - pmid = {22465075}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Data Interpretation, Statistical, Sample Size, Evoked Potentials}, - pages = {976--990}, -} - -@article{siless_joint_2012, - title = {Joint {T1} and brain fiber log-demons registration using currents to model geometry}, - volume = {15}, - abstract = {We present an extension of the diffeomorphic Geometric Demons algorithm which combines the iconic registration with geometric constraints. Our algorithm works in the log-domain space, so that one can efficiently compute the deformation field of the geometry. We represent the shape of objects of interest in the space of currents which is sensitive to both location and geometric structure of objects. Currents provides a distance between geometric structures that can be defined without specifying explicit point-to-point correspondences. We demonstrate this framework by registering simultaneously T1 images and 65 fiber bundles consistently extracted in 12 subjects and compare it against non-linear T1, tensor, and multi-modal T1 + Fractional Anisotropy (FA) registration algorithms. Results show the superiority of the Log-domain Geometric Demons over their purely iconic counterparts.}, - language = {eng}, - number = {Pt 2}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {Siless, Viviana and Glaunès, Joan and Guevara, Pamela and Mangin, Jean-François and Poupon, Cyril and Le Bihan, Denis and Thirion, Bertrand and Fillard, Pierre}, - year = {2012}, - pmid = {23286032}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Nerve Fibers, Myelinated}, - pages = {57--65}, -} - -@article{tamura_usefulness_2013, - title = {Usefulness of {Leksell} {GammaPlan} for preoperative planning of brain tumor resection: delineation of the cranial nerves and fusion of the neuroimaging data, including diffusion tensor imaging}, - volume = {116}, - issn = {0065-1419}, - shorttitle = {Usefulness of {Leksell} {GammaPlan} for preoperative planning of brain tumor resection}, - doi = {10.1007/978-3-7091-1376-9_27}, - abstract = {Leksell GammaPlan (LGP) software was initially designed for Gamma Knife radiosurgery, but it can be successfully applied to planning of the open neurosurgical procedures as well. We present our initial experience of delineating the cranial nerves in the vicinity of skull base tumors, combined visualization of the implanted subdural electrodes and cortical anatomy to facilitate brain mapping, and fusion of structural magnetic resonance imaging and diffusion tensor imaging performed with the use of LGP before removal of intracranial neoplasms. Such preoperative information facilitated choosing the optimal approach and general surgical strategy, and corresponded well to the intraoperative findings. Therefore, LGP may be helpful for planning open neurosurgical procedures in cases of both extraaxial and intraaxial intracranial tumors.}, - language = {eng}, - journal = {Acta Neurochirurgica. Supplement}, - author = {Tamura, Manabu and Konishi, Yoshiyuki and Tamura, Noriko and Hayashi, Motohiro and Nakao, Naoyuki and Uematsu, Yuji and Itakura, Toru and Régis, Jean and Mangin, Jean François and Muragaki, Yoshihiro and Iseki, Hiroshi}, - year = {2013}, - pmid = {23417477}, - keywords = {Brain, Humans, Imaging, Three-Dimensional, Software, Brain Mapping, Female, Male, Brain Neoplasms, Electrodes, Implanted, Gadolinium, Cranial Nerves, Preoperative Care, Radiosurgery}, - pages = {179--185}, -} - -@article{lefevre_surface_2013, - title = {Surface smoothing: a way back in early brain morphogenesis}, - volume = {16}, - shorttitle = {Surface smoothing}, - abstract = {In this article we propose to investigate the analogy between early cortical folding process and cortical smoothing by mean curvature flow. First, we introduce a one-parameter model that is able to fit a developmental trajectory as represented in a Volume-Area plot and we propose an efficient optimization strategy for parameter estimation. Second, we validate the model on forty cortical surfaces of preterm newborns by comparing global geometrical indices and trajectories of central sulcus along developmental and simulation time.}, - language = {eng}, - number = {Pt 1}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {Lefèvre, Julien and Intwali, Victor and Hertz-Pannier, Lucie and Hüppi, Petra S. and Mangin, Jean-Francois and Dubois, Jessica and Germanaud, David}, - year = {2013}, - pmid = {24505715}, - pmcid = {PMC3945978}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Female, Male, Infant, Newborn, Infant, Premature, Morphogenesis}, - pages = {590--597}, -} - -@article{sun_effect_2012, - title = {The effect of handedness on the shape of the central sulcus}, - volume = {60}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2011.12.050}, - abstract = {Sinistrals differ from dextrals in the size of certain cortical folds. For instance, handedness has an impact on central sulcus surface area: the sulcus is larger in the dominant left hemisphere of dextrals and vice versa for sinistrals. However, the impact of handedness on the shape of the central sulcus is largely unexplored. In this paper, we propose first an original strategy based on manifold learning to quantify the shape of the central sulcus. Using this approach we show that the "hand knob", a major landmark of the hand motor representation, is sited more dorsally in the left hemisphere in dextrals than in sinistrals. Sinistrals forced to write with their non-preferred right hand display a pattern of central sulcus size asymmetry which is typical of dextrals, yet forced dextrality does not shift the handedness-specific location of the "hand knob". Hence, cortical morphology in adults holds an accumulated record of both innate biases and early developmental experience. Characterizing normal variation of cortical morphology provides a means of systematically correlating behavior with cortical development.}, - language = {eng}, - number = {1}, - journal = {NeuroImage}, - author = {Sun, Zhong Yi and Klöppel, Stefan and Rivière, Denis and Perrot, Matthieu and Frackowiak, Richard and Siebner, Hartwig and Mangin, Jean-François}, - month = mar, - year = {2012}, - pmid = {22227053}, - keywords = {Humans, Imaging, Three-Dimensional, Adult, Female, Male, Young Adult, Middle Aged, Functional Laterality, Motor Cortex}, - pages = {332--339}, -} - -@article{bogart_cortical_2012, - title = {Cortical sulci asymmetries in chimpanzees and macaques: a new look at an old idea}, - volume = {61}, - issn = {1095-9572}, - shorttitle = {Cortical sulci asymmetries in chimpanzees and macaques}, - doi = {10.1016/j.neuroimage.2012.03.082}, - abstract = {Functional and neuroanatomical asymmetries are an important characteristic of the human brain. The evolution of such specializations in the human cortex has provoked great interest in primate brain evolution. Most research on cortical sulci has revolved around linear measurements, which represent only one dimension of sulci organization. Here, we used a software program (BrainVISA) to quantify asymmetries in cortical depth and surface area from magnetic resonance images in a sample of 127 chimpanzees and 49 macaques. Population brain asymmetries were determined from 11 sulci in chimpanzees and seven sulci in macaques. Sulci were taken from the frontal, temporal, parietal, and occipital lobes. Population-level asymmetries were evident in chimpanzees for several sulci, including the fronto-orbital, superior precentral, and sylvian fissure sulci. The macaque population did not reveal significant population-level asymmetries, except for surface area of the superior temporal sulcus. The overall results are discussed within the context of the evolution of higher order cognition and motor functions.}, - language = {eng}, - number = {3}, - journal = {NeuroImage}, - author = {Bogart, Stephanie L. and Mangin, Jean-François and Schapiro, Steven J. and Reamer, Lisa and Bennett, Allyson J. and Pierre, Peter J. and Hopkins, William D.}, - month = jul, - year = {2012}, - pmid = {22504765}, - pmcid = {PMC3358493}, - keywords = {Software, Brain Mapping, Image Processing, Computer-Assisted, Female, Male, Cerebral Cortex, Aging, Functional Laterality, Animals, Sex Characteristics, Species Specificity, Pan troglodytes, Macaca mulatta, Macaca radiata}, - pages = {533--541}, -} - -@article{fouquet_role_2012, - title = {Role of hippocampal {CA1} atrophy in memory encoding deficits in amnestic {Mild} {Cognitive} {Impairment}}, - volume = {59}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2011.11.036}, - abstract = {Identifying the specific substrates of memory deficits in early Alzheimer's disease would help to develop clinically-relevant therapies. The present study assesses the relationships between encoding versus retrieval deficits in patients with amnestic Mild Cognitive Impairment (aMCI) and atrophy specifically within the hippocampus and throughout the white matter. Twenty-two aMCI patients underwent T1-weighted MRI scans and neuropsychological testing. Grey matter and white matter segments obtained from the MRI images were each entered in correlation analyses, assessed only in the hippocampus for grey matter segments, with encoding and retrieval memory performances. For the grey matter segments, the resulting spmT correlation maps were then superimposed onto a 3D surface view of the hippocampus to identify the relative involvement of the different subfields, a method already used and validated elsewhere. Memory encoding deficits specifically correlated with CA1 subfield atrophy, while no relationship was found with white matter atrophy. In contrast, retrieval deficits were weakly related to hippocampal atrophy and did not involve a particular subfield, while they strongly correlated with loss of white matter, specifically in medial parietal and frontal areas. In aMCI patients, encoding impairment appears specifically related to atrophy of the CA1 hippocampal subfield, consistent with the predominance of encoding deficits and CA1 atrophy in aMCI. In contrast, episodic retrieval deficits seem to be underlain by more distributed tissue losses, consistent with a disruption of a hippocampo-parieto-frontal network.}, - language = {eng}, - number = {4}, - journal = {NeuroImage}, - author = {Fouquet, Marine and Desgranges, Béatrice and La Joie, Renaud and Rivière, Denis and Mangin, Jean-François and Landeau, Brigitte and Mézenge, Florence and Pélerin, Alice and de La Sayette, Vincent and Viader, Fausto and Baron, Jean-Claude and Eustache, Francis and Chételat, Gaël}, - month = feb, - year = {2012}, - pmid = {22119654}, - keywords = {Humans, Female, Male, Aged, Atrophy, Hippocampus, Cognitive Dysfunction, Memory Disorders}, - pages = {3309--3315}, -} - -@article{tamura_advanced_2013, - title = {Advanced {Image} {Coregistration} within the {Leksell} {Workstation} for the {Planning} of {Glioma} {Surgery}: {Initial} {Experience}}, - volume = {74}, - issn = {2193-6358}, - shorttitle = {Advanced {Image} {Coregistration} within the {Leksell} {Workstation} for the {Planning} of {Glioma} {Surgery}}, - doi = {10.1055/s-0033-1358380}, - abstract = {Background Leksell GammaPlan (LGP) and SurgiPlan (ELEKTA Instruments AB, Stockholm, Sweden) may be used effectively for the detailed evaluation of regional neuroanatomy before open neurosurgical procedures. We report our initial experience in the cases of cerebral gliomas. Methods LGP v.8.3 was used before the surgical resection of cerebral gliomas for (1) the delineation of subdural grid electrodes and a detailed evaluation of their position relatively to cortical structures, and (2) for the fusion of structural magnetic resonance imaging and diffusion tensor imaging (DTI) for a detailed visualization of the corticospinal tract (CST) and optic radiation. Results Delineation of the subdural grid within LGP in a patient with seizures caused by left parietal glioma permitted a detailed assessment of the location of electrodes relative to the cortical gyri and sulci and significantly facilitated interpretation of brain mapping before tumor resection. In another patient with parieto-occipital glioma, simultaneous three-dimensional visualization of the tumor, CST, and optic radiation with the use of LGP permitted us to perform tumor resection without postoperative neurologic complications. Finally, incorporation of DTI into SurgiPlan resulted in precise planning of stereotactic biopsy for bilateral thalamic glioma. Conclusion The possibility for detailed evaluation of regional neuroanatomy based on various images within LGP and SurgiPlan may facilitate effective and safe surgical management of intracranial gliomas.}, - language = {eng}, - number = {2}, - journal = {Journal of Neurological Surgery Reports}, - author = {Tamura, Manabu and Hayashi, Motohiro and Konishi, Yoshiyuki and Tamura, Noriko and Regis, Jean and Mangin, Jean François and Taira, Takaomi and Okada, Yoshikazu and Muragaki, Yoshihiro and Iseki, Hiroshi}, - month = dec, - year = {2013}, - pmid = {24303347}, - pmcid = {PMC3836959}, - keywords = {brain tumor surgery, gamma knife surgery, image coregistration, Leksell GammaPlan, Leksell SurgiPlan}, - pages = {118--122}, -} - -@article{seiler_lower_2017, - title = {Lower {Magnetization} {Transfer} {Ratio} in the {Forceps} {Minor} {Is} {Associated} with {Poorer} {Gait} {Velocity} in {Older} {Adults}}, - volume = {38}, - issn = {1936-959X}, - doi = {10.3174/ajnr.A5036}, - abstract = {BACKGROUND AND PURPOSE: Gait disturbances in the elderly are disabling and a major public health issue but are poorly understood. In this multimodal MR imaging study, we used 2 voxel-based analysis methods to assess the voxelwise relationship of magnetization transfer ratio and white matter hyperintensity location with gait velocity in older adults. -MATERIALS AND METHODS: We assessed 230 community-dwelling participants of the Austrian Stroke Prevention Family Study. Every participant underwent 3T MR imaging, including magnetization transfer imaging. Voxel-based magnetization transfer ratio-symptom mapping correlated the white matter magnetization transfer ratio of each voxel with gait velocity. To assess a possible relationship between white matter hyperintensity location and gait velocity, we applied voxel-based lesion-symptom mapping. -RESULTS: We found a significant association between the magnetization transfer ratio within the forceps minor and gait velocity (β = 0.134; 95\% CI, 0.011-0.258; P = .033), independent of demographics, general physical performance, vascular risk factors, and brain volume. White matter hyperintensities did not significantly change this association. -CONCLUSIONS: Our study provides new evidence for the importance of magnetization transfer ratio changes in gait disturbances at an older age, particularly in the forceps minor. The histopathologic basis of these findings is yet to be determined.}, - language = {eng}, - number = {3}, - journal = {AJNR. American journal of neuroradiology}, - author = {Seiler, S. and Pirpamer, L. and Gesierich, B. and Hofer, E. and Duering, M. and Pinter, D. and Jouvent, E. and Fazekas, F. and Mangin, J.-F. and Chabriat, H. and Ropele, S. and Schmidt, R.}, - month = mar, - year = {2017}, - pmid = {27979793}, - keywords = {Brain, Humans, Adult, Female, Male, Middle Aged, Aged, Gait, Gait Disorders, Neurologic}, - pages = {500--506}, -} - -@article{hotier_social_2017, - title = {Social cognition in autism is associated with the neurodevelopment of the posterior superior temporal sulcus}, - volume = {136}, - issn = {1600-0447}, - doi = {10.1111/acps.12814}, - abstract = {OBJECTIVE: The posterior superior temporal sulcus (pSTS) plays a critical role in the 'social brain'. Its neurodevelopment and relationship with the social impairment in autism spectrum disorders (ASD) are not well understood. We explored the relationship between social cognition and the neurodevelopment of the pSTS in ASD. -METHOD: We included 44 adults with high-functioning ASD and 36 controls. We assessed their performances on the 'Reading the mind in the eyes' test (for 34 of 44 subjects with ASD and 30 of 36 controls), their fixation time on the eyes with eye tracking (for 35 of 44 subjects with ASD and 30 of 36 controls) and the morphology of the caudal branches of the pSTS (length and depth), markers of the neurodevelopment, with structural MRI. -RESULTS: The right anterior caudal ramus of the pSTS was significantly longer in patients with ASD compared with controls (52.6 mm vs. 38.3 mm; P = 1.4 × 10-3 ; Cohen's d = 0.76). Its length negatively correlated with fixation time on the eyes (P = 0.03) in the ASD group and with the 'Reading the mind in the eyes' test scores in both groups (P = 0.03). -CONCLUSION: Our findings suggest that the neurodevelopment of the pSTS is related to the ASD social impairments.}, - language = {eng}, - number = {5}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Hotier, S. and Leroy, F. and Boisgontier, J. and Laidi, C. and Mangin, J.-F. and Delorme, R. and Bolognani, F. and Czech, C. and Bouquet, C. and Toledano, E. and Bouvard, M. and Petit, J. and Mishchenko, M. and d'Albis, M.-A. and Gras, D. and Gaman, A. and Scheid, I. and Leboyer, M. and Zalla, T. and Houenou, J.}, - year = {2017}, - pmid = {28940401}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Adolescent, Female, Male, Young Adult, Temporal Lobe, Middle Aged, neurodevelopment, neuroimaging, magnetic resonance imaging, Autism Spectrum Disorder, autism, Social Perception}, - pages = {517--525}, -} - -@article{moon_prospective_2018, - title = {Prospective associations between white matter hyperintensities and lower extremity function}, - volume = {90}, - issn = {1526-632X}, - doi = {10.1212/WNL.0000000000005289}, - abstract = {OBJECTIVE: To evaluate the relationship of white matter hyperintensities (WMH) with decline in lower extremity function (LEF) over approximately 3 years in dementia-free older adults with memory complaints. -METHODS: We obtained brain MRI data from 458 community-dwelling adults, aged 70 years or over, at baseline, and from 358 adults over an average follow-up of 963 days. We evaluated LEF using the Short Physical Performance Battery (SPPB). We related baseline WMH volumes and progression to SPPB scores over time, using mixed-effect linear regressions. For the secondary analyses, we categorized baseline WMH volume into quartiles, and dichotomized the WMH progression to compare fast and slow progression. -RESULTS: Baseline WMH volume (β = -0.017, 95\% confidence interval [CI] -0.025 to -0.009), as well as WMH progression (β = -0.002, 95\% CI -0.003 to -0.001), significantly associated with a decline in SPPB performance in adjusted analyses. Compared with the lowest quartile of baseline WMH volume, the highest quartile associated with a decline in SPPB performance (β = -0.301, 95\% CI -0.558 to -0.044). Fast progression also associated with a decline in SPPB performance. We found clinically meaningful differences in the SPPB, with higher scores in participants with slow progression of WMH, at both 24 and 36 months. -CONCLUSIONS: Baseline level and WMH progression associated with longitudinal decline in SPPB performance among older adults. We detected clinically meaningful differences in SPPB performance on comparing fast with slow progression of WMH, suggesting that speed of WMH progression is an important determinant of LEF during aging.}, - language = {eng}, - number = {15}, - journal = {Neurology}, - author = {Moon, So Young and de Souto Barreto, Philipe and Rolland, Yves and Chupin, Marie and Bouyahia, Ali and Fillon, Ludovic and Mangin, Jean François and Andrieu, Sandrine and Cesari, Matteo and Vellas, Bruno and {MAPT/DSA Study Group}}, - month = apr, - year = {2018}, - pmid = {29523640}, - pages = {e1291--e1297}, -} - -@article{katz_similar_2016-1, - title = {Similar white matter but opposite grey matter changes in schizophrenia and high‐functioning autism}, - volume = {134}, - copyright = {All rights reserved}, - issn = {1600-0447}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Katz, J. and d'Albis, M.-A. and Boisgontier, J. and Poupon, C. and Mangin, J.-F. and Guevara, P. and Duclap, D. and Hamdani, N. and Petit, J. and Monnet, D.}, - year = {2016}, - pages = {31--39}, - annote = {The following values have no corresponding Zotero field:number: 1}, -} - -@article{leroy_early_2011, - title = {Early {Maturation} of the {Linguistic} {Dorsal} {Pathway} in {Human} {Infants}}, - volume = {31}, - copyright = {All rights reserved}, - issn = {0270-6474}, - doi = {10.1523/JNEUROSCI.4141-10.2011}, - number = {4}, - journal = {JOURNAL OF NEUROSCIENCE}, - author = {Leroy, Francois and Glasel, Herve and Dubois, Jessica and Hertz-Pannier, Lucie and Thirion, Bertrand and Mangin, Jean-Francois and Dehaene-Lambertz, Ghislaine}, - month = jan, - year = {2011}, - keywords = {MRI, cortical thickness, auditory-cortex, human cerebral-cortex, postnatal-development, speech-perception, Superior temporal sulcus}, - pages = {1500--1506}, - annote = {The following values have no corresponding Zotero field:auth-address: [Leroy, F; Glasel, H; Dubois, J; Dehaene-Lambertz, G] INSERM, U992, F-91191 Gif Sur Yvette, France [Leroy, F; Glasel, H; Dubois, J; Dehaene-Lambertz, G] Univ Paris 11, F-91405 Orsay, France [Leroy, F; Glasel, H; Dubois, J; Hertz-Pannier, L; Thirion, B; Mangin, JF; Dehaene-Lambertz, G] IFR49, F-91191 Gif Sur Yvette, France [Hertz-Pannier, L] INSERM, U663, F-75015 Paris, France [Hertz-Pannier, L] Univ Paris 05, F-75015 Paris, France [Hertz-Pannier, L] CEA, Lab Rech Biomed, NeuroSpin, F-91191 Gif Sur Yvette, France [Thirion, B] INRIA, Parietal Project Team, F-91191 Gif Sur Yvette, France [Mangin, JF] CEA, Lab Neuroimagerie Assistee Ordinateur, NeuroSpin, F-91191 Gif Sur Yvette, Francealt-title: J. Neurosci.number: 4accession-num: WOS:000286655600035label: ACLcustom1: Neurospin}, - annote = {Times Cited: 32}, - annote = {Times Cited: 32}, - annote = {UniactPMID: 21273434ISI Document Delivery No.: 712GZTimes Cited: 0Cited Reference Count: 41EnglishArticle0270-6474}, -} - -@article{glasel_robust_2011, - title = {A robust cerebral asymmetry in the infant brain: {The} rightward superior temporal sulcus}, - volume = {58}, - copyright = {All rights reserved}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2011.06.016}, - number = {3}, - journal = {NEUROIMAGE}, - author = {Glasel, H. and Leroy, F. and Dubois, J. and Hertz-Pannier, L. and Mangin, J. F. and Dehaene-Lambertz, G.}, - month = oct, - year = {2011}, - keywords = {MRI, Infant}, - pages = {716--723}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: neurospin}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: Neurospin}, - annote = {Times Cited: 27}, - annote = {Uniact}, -} - -@article{thirion_high_2007, - title = {High level group analysis of {FMRI} data based on {Dirichlet} process mixture models}, - volume = {20}, - copyright = {All rights reserved}, - abstract = {Inferring the position of functionally active regions from a multi-subject fMRI dataset involves the comparison of the individual data and the inference of a common activity model. While voxel-based analyzes, e.g. Random Effect statistics, are widely used, they do not model each individual activation pattern. Here, we develop a new procedure that extracts structures individually and compares them at the group level. For inference about spatial locations of interest, a Dirichlet Process Mixture Model is used. Finally, inter-subject correspondences are computed with Bayesian Network models. We show the power of the technique on both simulated and real datasets and compare it with standard inference techniques.}, - journal = {Inf Process Med Imaging}, - author = {Thirion, Bertrand and Tucholka, Alan and Keller, Merlin and Pinel, Philippe and Roche, Alexis and Mangin, Jean-François and Poline, Jean-Baptiste}, - year = {2007}, - keywords = {Algorithms, Humans, Image Interpretation, Computer-Assisted, Brain Mapping, Models, Neurological, Computer Simulation, Evoked Potentials}, - pages = {482--494}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpin}, - annote = {Unati - articlejb}, -} - -@article{mangin_coordinate-based_2004, - title = {Coordinate-based versus structural approaches to brain image analysis}, - volume = {30}, - copyright = {All rights reserved}, - abstract = {A basic issue in neurosciences is to look for possible relationships between brain architecture and cognitive models. The lack of architectural information in magnetic resonance images, however, has led the neuroimaging community to develop brain mapping strategies based on various coordinate systems without accurate architectural content. Therefore, the relationships between architectural and functional brain organizations are difficult to study when analyzing neuroimaging experiments. This paper advocates that the design of new brain image analysis methods inspired by the structural strategies often used in computer vision may provide better ways to address these relationships. The key point underlying this new framework is the conversion of the raw images into structural representations before analysis. These representations are made up of data-driven elementary features like activated clusters, cortical folds or fiber bundles. Two classes of methods are introduced. Inference of structural models via matching across a set of individuals is described first. This inference problem is illustrated by the group analysis of functional statistical parametric maps (SPMs). Then, the matching of new individual data with a priori known structural models is described, using the recognition of the cortical sulci as a prototypical example.}, - journal = {Artif Intell Med}, - author = {Mangin, J. F. and Rivière, D. and Coulon, O. and Poupon, C. and Cachia, A. and Cointepas, Y. and Poline, J. B. and Bihan, D. Le and Régis, J. and Papadopoulos-Orfanos, D.}, - month = feb, - year = {2004}, - keywords = {Humans, Brain Mapping, Image Processing, Computer-Assisted, Models, Biological, Markov Chains, Brain, anatomy /\&/ histology/physiology}, - pages = {177--197}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - articlejp137830}, -} - -@article{simon_topographical_2002, - title = {Topographical layout of hand, eye, calculation, and language-related areas in the human parietal lobe}, - volume = {33}, - copyright = {All rights reserved}, - issn = {0896-6273 (Print)}, - doi = {S0896627302005755 [pii]}, - abstract = {To identify subdivisions of the human parietal cortex, we collected fMRI data while ten subjects performed six tasks: grasping, pointing, saccades, attention, calculation, and phoneme detection. Examination of task intersections revealed a systematic anterior-to-posterior organization of activations associated with grasping only, grasping and pointing, all visuomotor tasks, attention and saccades, and saccades only. Calculation yielded two distinct activations: one unique to calculation in the bilateral anterior IPS mesial to the supramarginal gyrus and the other shared with phoneme detection in the left IPS mesial to the angular gyrus. These results suggest human homologs of the monkey areas AIP, MIP, V6A, and LIP and imply a large cortical expansion of the inferior parietal lobule correlated with the development of human language and calculation abilities.}, - language = {eng}, - journal = {Neuron}, - author = {Simon, O. and Mangin, J. F. and Cohen, L. and Le Bihan, D. and Dehaene, S.}, - month = jan, - year = {2002}, - keywords = {Humans, Brain Mapping, Adult, Female, Male, Animals, Models, Anatomic, Haplorhini, Attention/physiology, Cognition/*physiology, *Language, Parietal Lobe/*anatomy \& histology/*physiology, Movement/*physiology, Saccades, Thinking/*physiology}, - pages = {475--87}, - annote = {Simon, OlivierMangin, Jean FrancoisCohen, LaurentLe Bihan, DenisDehaene, StanislasResearch Support, Non-U.S. Gov'tUnited StatesNeuronNeuron. 2002 Jan 31;33(3):475-87.}, - annote = {The following values have no corresponding Zotero field:auth-address: Unite INSERM 334, IFR 49, Service Hospitalier Frederic Joliot, CEA/DSV, Orsay, France.number: 3edition: 2002/02/08accession-num: 11832233label: ACL}, -} - -@article{pappata_vivo_1996, - title = {In vivo imaging of human cerebral acetylcholinesterase}, - volume = {67}, - copyright = {All rights reserved}, - issn = {0022-3042 (Print)}, - abstract = {We report here the first positron emission tomography (PET) images showing the in vivo regional distribution of acetylcholinesterase (AChE) in human brain. The study was carried out in eight healthy human volunteers using as a tracer [11C]-physostigmine ([11C]PHY), an inhibitor of AChE. After intravenous injection of [11C]PHY, radioactivity was rapidly taken up in brain tissue and reached maximal uptake within a few minutes, following a regional pattern mostly related to cerebral perfusion. After the peak, the cerebral radioactivity gradually decreased with a half-life varying from 20 to 35 min, depending on the brain structure. [11C] PHY retention was higher in regions rich in AChE, such as the striatum (half-life, 35 min), than in regions poor in AChE, such as the cerebral cortex (half-life, 20 min). At later times (25-35 min postinjection), the cerebral distribution of [11C]PHY was typical of AChE activity: putamen-caudate {\textgreater} cerebellum {\textgreater} brainstem {\textgreater} thalamus {\textgreater} cerebral cortex, with a striatal to cortex ratio of 2. These results suggest that PET studies with [11C]PHY can provide in vivo brain mapping of human AChE and are promising for the study of changes in AChE levels associated with neurodegenerative diseases.}, - language = {eng}, - journal = {J Neurochem}, - author = {Pappata, S. and Tavitian, B. and Traykov, L. and Jobert, A. and Dalger, A. and Mangin, J. F. and Crouzel, C. and DiGiamberardino, L.}, - month = aug, - year = {1996}, - keywords = {Humans, Adult, Male, Middle Aged, Animals, Aged, Tomography, Emission-Computed, Brain/*enzymology, Acetylcholinesterase/*metabolism, Physostigmine/metabolism}, - pages = {876--9}, - annote = {Pappata, STavitian, BTraykov, LJobert, ADalger, AMangin, J FCrouzel, CDiGiamberardino, LResearch Support, Non-U.S. Gov'tUnited statesJournal of neurochemistryJ Neurochem. 1996 Aug;67(2):876-9.}, - annote = {The following values have no corresponding Zotero field:auth-address: INSERM U334, Orsay, France.number: 2edition: 1996/08/01accession-num: 8764619label: ACL}, -} - -@article{muellner_altered_2015, - title = {Altered {Structure} of {Cortical} {Sulci} in {Gilles} de la {Tourette} {Syndrome}: {Further} {Support} for {Abnormal} {Brain} {Development}}, - volume = {30}, - copyright = {All rights reserved}, - issn = {0885-3185}, - doi = {10.1002/mds.26207}, - number = {5}, - journal = {MOVEMENT DISORDERS}, - author = {Muellner, Julia and Delmaire, Christine and Valabregue, Romain and Schuepbach, Michael and Mangin, Jean-Francois and Vidailhet, Marie and Lehericy, Stephane and Hartmann, Andreas and Worbe, Yulia}, - month = apr, - year = {2015}, - keywords = {sulcal depth, cortical thickness, 3 Tesla MRI, Gilles de la Tourette syndrome, sulcal length, sulcal opening}, - pages = {655--661}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {Times Cited: 2}, - annote = {UnatiPMID: 25820811}, -} - -@article{seiler_magnetization_2014, - title = {Magnetization transfer ratio relates to cognitive impairment in normal elderly}, - volume = {6}, - copyright = {All rights reserved}, - issn = {1663-4365}, - doi = {10.3389/fnagi.2014.00263}, - journal = {FRONTIERS IN AGING NEUROSCIENCE}, - author = {Seiler, Stephan and Pirpamer, Lukas and Hofer, Edith and Duering, Marco and Jouvent, Eric and Fazekas, Franz and Mangin, Jean-Francois and Chabriat, Hugues and Dichgans, Martin and Ropele, Stefan and Schmidt, Reinhold}, - month = sep, - year = {2014}, - keywords = {Cognitive aging, cerebrovascular disease, dementia, magnetization transfer imaging, microstructural tissue damage}, - pages = {263}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Times Cited: 3}, - annote = {UnatiPMID: 25309438}, -} - -@article{senova_optogenetic_2018, - title = {Optogenetic {Tractography} for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates}, - volume = {8}, - issn = {2045-2322}, - doi = {10.1038/s41598-018-21486-8}, - abstract = {Dissecting neural circuitry in non-human primates (NHP) is crucial to identify potential neuromodulation anatomical targets for the treatment of pharmacoresistant neuropsychiatric diseases by electrical neuromodulation. How targets of deep brain stimulation (DBS) and cortical targets of transcranial magnetic stimulation (TMS) compare and might complement one another is an important question. Combining optogenetics and tractography may enable anatomo-functional characterization of large brain cortico-subcortical neural pathways. For the proof-of-concept this approach was used in the NHP brain to characterize the motor cortico-subthalamic pathway (m\_CSP) which might be involved in DBS action mechanism in Parkinson's disease (PD). Rabies-G-pseudotyped and Rabies-G-VSVg-pseudotyped EIAV lentiviral vectors encoding the opsin ChR2 gene were stereotaxically injected into the subthalamic nucleus (STN) and were retrogradely transported to the layer of the motor cortex projecting to STN. A precise anatomical mapping of this pathway was then performed using histology-guided high angular resolution MRI tractography guiding accurately cortical photostimulation of m\_CSP origins. Photoexcitation of m\_CSP axon terminals or m\_CSP cortical origins modified the spikes distribution for photosensitive STN neurons firing rate in non-equivalent ways. Optogenetic tractography might help design preclinical neuromodulation studies in NHP models of neuropsychiatric disease choosing the most appropriate target for the tested hypothesis.}, - language = {eng}, - number = {1}, - journal = {Scientific Reports}, - author = {Senova, S. and Poupon, C. and Dauguet, J. and Stewart, H. J. and Dugué, G. P. and Jan, C. and Hosomi, K. and Ralph, G. S. and Barnes, L. and Drouot, X. and Pouzat, C. and Mangin, J. F. and Pain, F. and Doignon, I. and Aron-Badin, R. and Brouillet, E. and Boyden, E. S. and Mitrophanous, K. A. and Hantraye, P. and Palfi, S.}, - month = feb, - year = {2018}, - pmid = {29463867}, - pmcid = {PMC5820256}, - pages = {3362}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WG2RQFY7/Senova et al. - 2018 - Optogenetic Tractography for anatomo-functional ch.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Y4KZLJ9E/Senova et al. - 2018 - Optogenetic Tractography for anatomo-functional ch.pdf:application/pdf}, -} - -@inproceedings{teillac_colocalization_2016, - series = {Mathematics and {Visualization}}, - title = {Colocalization of {Functional} {Activity} and {Neurite} {Density} {Within} {Cortical} {Areas}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-3-319-54129-7 978-3-319-54130-3}, - url = {https://link.springer.com/chapter/10.1007/978-3-319-54130-3_15}, - doi = {10.1007/978-3-319-54130-3_15}, - abstract = {In this work, we investigated the link between the blood-oxygen-level dependant (BOLD) effect observed using functional magnetic resonance imaging (fMRI) and the neurite density inferred from the Neurite Orientation Dispersion and Density Imaging (NODDI) model in some well-known lateralized cortical areas. We found a strong colocalization between those two parameters in lateralized areas such as the primary motor cortex, the language network, but also the primary visual cortex, which might indicate a strong link between microstructure and functional activity.}, - language = {en}, - urldate = {2017-12-29}, - booktitle = {Computational {Diffusion} {MRI}}, - publisher = {Springer, Cham}, - author = {Teillac, Achille and Lefrance, Sandrine and Duchesnay, Edouard and Poupon, Fabrice and Fuster, Maite Alaitz Ripoll and Bihan, Denis Le and Mangin, Jean-Francois and Poupon, Cyril}, - month = oct, - year = {2016}, - pages = {175--186}, - annote = {The following values have no corresponding Zotero field:pub-location: Athens, Greecelabel: ACTI}, - annote = {UnirsPart of the Mathematics and Visualization book series (MATHVISUAL)}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VEPDYHA5/978-3-319-54130-3_15.html:text/html}, -} - -@inproceedings{sun_defining_2008, - title = {Defining cortical sulcus patterns using partial clustering based on bootstrap and bagging}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-1-4244-2002-5}, - shorttitle = {Biomedical {Imaging}: {From} {Nano} to {Macro}, 2008. {ISBI}}, - url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4541325}, - doi = {10.1109/ISBI.2008.4541325}, - abstract = {The cortical folding patterns are very different from one individual to another. Here we try to find folding patterns automatically using large-scale datasets by non-supervised clustering analysis. The sulci of each brain are detected and identified using the brain VIS A open software. The 3D moment invariants are calculated and used as the shape descriptors of the sulci identified. A partial clustering algorithm using bootstrap sampling and bagging (PCBB) is devised for cortical pattern mining. Partial clusters are found using a modified hierarchical clustering method constrained by an objective function which looks for the most compact and dissimilar clusters. Bagging is used to increase stability. Experiments on simulated and real datasets are used to demonstrate the strength and stability of this algorithm compared to other standard approaches. Some cortical patterns are found using our method. In particular, the patterns found for the left cingulate sulcus are consistent with the patterns described in the atlas of Ono.}, - booktitle = {2008 5th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}: {From} {Nano} to {Macro}}, - publisher = {IEEE}, - author = {Sun, Zhong Yi and Riviere, Denis and Duchesnay, Edouard and Thirion, Bertrand and Poupon, Fabrice and Mangin, Jean-Francois}, - month = may, - year = {2008}, - keywords = {conference, Sampling methods, Clustering, Bagging, Large-scale systems, 3D moment invariant, bootstrap sampling, Clustering algorithms, Clustering methods, cortical pattern mining, cortical sulcus pattern, Data analysis, Frequency, hierarchical clustering, left cingulate sulcus, morphometry, nonsupervised clustering analysis, partial clustering, Pattern analysis, pattern clustering, patterns, Shape, Stability, sulcus, Cortical folding pattern}, - pages = {1629--1632}, -} - -@article{plaze_who_2015, - title = {"{Who} is talking to me?" - {Self}-other attribution of auditory hallucinations and sulcation of the right temporoparietal junction}, - volume = {169}, - issn = {1573-2509}, - shorttitle = {"{Who} is talking to me?}, - doi = {10.1016/j.schres.2015.10.011}, - abstract = {Brain imaging research in schizophrenia has provided a better understanding of the neural basis of auditory hallucinations (AH). Recently, renewed interest in the phenomenology of AH raised questions related to their neural substrates. Hence, the neural basis of AH self/other attribution have yet to be investigated as beliefs regarding the origin of the voices is a cardinal feature of AH phenomenology. As the right temporoparietal junction (TPJ) and the inferior parietal lobule (IPL) play a key role in disentangling the origin of sensory events and in self/other distinction, we tested the hypothesis that the morphology of the IPL/TPJ area may be involved in AH self/other attribution. Magnetic resonance images of 39 right-handed patients with persistent auditory hallucinations and 19 healthy subjects were analyzed with sulcus-based morphometry. AH self-other attribution were found to be associated with the sulcal pattern of the posterior part of the Sylvian fissure, encompassing the IPL/TPJ area. The preference for the attribution of AH to self or to others could be associated with early neurodevelopmental events as the sulcal pattern is determined during fetal life and is stable after birth. Our study also raises basic cognitive questions regarding self-consciousness and suggest that impairments at a pre-reflexive level, leading to hearing his/her thoughts as voices ('I' level or feeling of agency), and a reflexive level leading to attribution belief ('Me' level or judgment of agency) are likely involved in AH.}, - language = {eng}, - number = {1-3}, - journal = {Schizophrenia Research}, - author = {Plaze, Marion and Mangin, Jean-François and Paillère-Martinot, Marie-Laure and Artiges, Eric and Olié, Jean-Pierre and Krebs, Marie-Odile and Gaillard, Raphaël and Martinot, Jean-Luc and Cachia, Arnaud}, - month = dec, - year = {2015}, - pmid = {26463879}, - keywords = {Humans, Adult, Female, Male, Young Adult, Temporal Lobe, Middle Aged, Hallucinations, Psychiatric Status Rating Scales, Parietal Lobe, Neurodevelopment, Speech Perception, Sulcation, Schizophrenic Psychology, Self Concept, Self-other attribution, Self–other attribution}, - pages = {95--100}, - annote = {The following values have no corresponding Zotero field:number: 1-3label: ACL}, - annote = {UnatiPMID: 26463879}, -} - -@article{penttila_cortical_2009, - title = {Cortical folding in patients with bipolar disorder or unipolar depression}, - volume = {34}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1488-2434}, - abstract = {BACKGROUND: Analysis of cortical folding may provide insight into neurodevelopment deviations, which, in turn, can predispose to depression that responds particularly poorly to medications. We hypothesized that patients with treatment-resistant depression would exhibit measurable alterations in cortical folding. -METHODS: We computed hemispheric global sulcal indices (g-SIs) in T(1)-weighted magnetic resonance images obtained from 76 patients and 70 healthy controls. We separately searched for anatomic deviations in patients with bipolar disorder (16 patients with treatment-resistant depression, 25 with euthymia) and unipolar depression (35 patients with treatment-resistant depression). -RESULTS: Compared with healthy controls, both groups of patients with treatment-resistant depression exhibited reduced g-SIs: in the right hemisphere among patients with bipolar disorder and in both hemispheres among those with unipolar depression. Patients with euthymic bipolar disorder did not differ significantly from depressed patients or healthy controls. Among patients with bipolar disorder who were taking lithium, we found positive correlations between current lithium dose and g-SIs in both hemispheres. -LIMITATIONS: We cannot estimate the extent to which the observed g-SI reductions are linked to treatment resistance and to what extent they are state-dependent. Furthermore, we cannot disentangle the impact of medications from that of the affective disorder. Finally, there is interindividual variation and overlap of g-SIs among patients and healthy controls that need to be considered when interpreting our results. -CONCLUSION: Reduced global cortical folding surface appears to be characteristic of patients with treatment-resistant depression, either unipolar or bipolar. In patients with bipolar disorder, treatment with lithium may modify cortical folding surface.}, - language = {eng}, - number = {2}, - journal = {Journal of psychiatry \& neuroscience: JPN}, - author = {Penttilä, Jani and Paillère-Martinot, Marie-Laure and Martinot, Jean-Luc and Ringuenet, Damien and Wessa, Michèle and Houenou, Josselin and Gallarda, Thierry and Bellivier, Frank and Galinowski, André and Bruguière, Pascale and Pinabel, François and Leboyer, Marion and Olié, Jean-Pierre and Duchesnay, Edouard and Artiges, Eric and Mangin, Jean-François and Cachia, Arnaud}, - month = mar, - year = {2009}, - pmid = {19270763}, - pmcid = {PMC2647564}, - keywords = {Humans, Adult, Female, Male, Cerebral Cortex, Depressive Disorder, Middle Aged, Functional Laterality, Psychiatric Status Rating Scales, Antidepressive Agents, Antimanic Agents, Drug Resistance, Electroconvulsive Therapy, Lithium Carbonate}, - pages = {127--135}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Penttila-PsychiatryNeurosci09.pdfarticle}, -} - -@article{penttila_cortical_2009-1, - title = {Cortical folding difference between patients with early-onset and patients with intermediate-onset bipolar disorder}, - volume = {11}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1399-5618}, - doi = {10.1111/j.1399-5618.2009.00683.x}, - abstract = {OBJECTIVES: Cerebral abnormalities have been detected in patients with bipolar disorder (BD). In comparison to BD with a later onset, early-onset BD has been found to have a poorer outcome. However, it is yet unknown whether neuroanatomical abnormalities differ between age-at-onset subgroups of the illness. We searched for cortical folding differences between early-onset (before 25 years) and intermediate-onset (between 25 and 45 years) BD patients. -METHODS: Magnetic resonance images of 22 early-onset BD patients, 14 intermediate-onset BD patients, and 50 healthy participants were analyzed using a fully automated method to extract, label, and measure the sulcal area in the whole cortex. Cortical folding was assessed by computing global sulcal indices (the ratio between total sulcal area and total outer cortex area) for each hemisphere, and local sulcal indices for 12 predefined regions in both hemispheres. -RESULTS: Intermediate-onset BD patients had a significantly reduced local sulcal index in the right dorsolateral prefrontal cortex in comparison to both early-onset BD patients and healthy subjects, and lower global sulcal indices in both hemispheres in comparison to healthy subjects (p {\textless} 0.05, Bonferroni corrected). Brain tissue volumes did not differ between groups. -CONCLUSIONS: This study provided the first evidence of a neuroanatomic difference between intermediate-onset and early-onset BD, which lends further support to the existence of different age-at-onset subgroups of BD.}, - language = {eng}, - number = {4}, - journal = {Bipolar Disorders}, - author = {Penttilä, Jani and Cachia, Arnaud and Martinot, Jean-Luc and Ringuenet, Damien and Wessa, Michèle and Houenou, Josselin and Galinowski, André and Bellivier, Frank and Gallarda, Thierry and Duchesnay, Edouard and Artiges, Eric and Leboyer, Marion and Olié, Jean-Pierre and Mangin, Jean-François and Paillère-Martinot, Marie-Laure}, - month = jun, - year = {2009}, - pmid = {19500089}, - keywords = {Humans, Imaging, Three-Dimensional, Brain Mapping, Adult, Female, Male, Cerebral Cortex, Middle Aged, Functional Laterality, Age Factors, Age of Onset, Suicide, Attempted}, - pages = {361--370}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Penttila-BP2009.pdfarticle}, -} - -@article{hamelin_sulcal_2015, - title = {Sulcal morphology as a new imaging marker for the diagnosis of early onset {Alzheimer}'s disease}, - volume = {36}, - issn = {1558-1497}, - doi = {10.1016/j.neurobiolaging.2015.04.019}, - abstract = {We investigated the utility of sulcal width measures in the diagnosis of Alzheimer's disease (AD). Sixty-six biologically confirmed AD patients (positive amyloid positron emission tomography [PET] and/or AD cerebrospinal fluid profile) were contrasted to 35 controls with negative amyloid PET. Patients were classified into prodromal or dementia stages as well as into late onset (LOAD, n = 31) or early onset (EOAD, n = 35) subgroups according to their age of onset. An automated method was used to calculate sulcal widths and hippocampal volumes (HV). In EOAD, the greatest ability to differentiate patients from age-matched controls, regardless of severity, was displayed by sulcal width of the temporoparietal cortex. In this region, diagnosis accuracy was better than the HV, especially at prodromal stage. In LOAD, HV provided the best discrimination power from age-matched controls. In conclusion, sulcal width measures are better markers than the HV for identifying prodromal AD in patients aged {\textless}65 years. In contrast, in older patients, the risk of over-diagnosis from using only sulcal enlargement is important.}, - language = {eng}, - number = {11}, - journal = {Neurobiology of Aging}, - author = {Hamelin, Lorraine and Bertoux, Maxime and Bottlaender, Michel and Corne, Helene and Lagarde, Julien and Hahn, Valérie and Mangin, Jean-François and Dubois, Bruno and Chupin, Marie and de Souza, Leonardo Cruz and Colliot, Olivier and Sarazin, Marie}, - month = nov, - year = {2015}, - pmid = {26256787}, - keywords = {Humans, MRI, Alzheimer Disease, Female, Male, Cerebral Cortex, Middle Aged, Aged, Aged, 80 and over, Hippocampus, Alzheimer's disease, Diffusion magnetic resonance imaging, Sulcal width}, - pages = {2932--2939}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 26256787}, -} - -@article{dubois_asynchrony_2008-1, - title = {Asynchrony of the early maturation of white matter bundles in healthy infants: quantitative landmarks revealed noninvasively by diffusion tensor imaging}, - volume = {29}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1065-9471}, - shorttitle = {Asynchrony of the early maturation of white matter bundles in healthy infants}, - doi = {10.1002/hbm.20363}, - abstract = {Normal cognitive development in infants follows a well-known temporal sequence, which is assumed to be correlated with the structural maturation of underlying functional networks. Postmortem studies and, more recently, structural MR imaging studies have described qualitatively the heterogeneous spatiotemporal progression of white matter myelination. However, in vivo quantification of the maturation phases of fiber bundles is still lacking. We used noninvasive diffusion tensor MR imaging and tractography in twenty-three 1-4-month-old healthy infants to quantify the early maturation of the main cerebral fascicles. A specific maturation model, based on the respective roles of different maturational processes on the diffusion phenomena, was designed to highlight asynchronous maturation across bundles by evaluating the time-course of mean diffusivity and anisotropy changes over the considered developmental period. Using an original approach, a progression of maturation in four relative stages was determined in each tract by estimating the maturation state and speed, from the diffusion indices over the infants group compared with an adults group on one hand, and in each tract compared with the average over bundles on the other hand. Results were coherent with, and extended previous findings in 8 of 11 bundles, showing the anterior limb of the internal capsule and cingulum as the most immature, followed by the optic radiations, arcuate and inferior longitudinal fascicles, then the spinothalamic tract and fornix, and finally the corticospinal tract as the most mature bundle. Thus, this approach provides new quantitative landmarks for further noninvasive research on brain-behavior relationships during normal and abnormal development.}, - language = {eng}, - number = {1}, - journal = {Human Brain Mapping}, - author = {Dubois, Jessica and Dehaene-Lambertz, Ghislaine and Perrin, Muriel and Mangin, Jean-François and Cointepas, Yann and Duchesnay, Edouard and Le Bihan, Denis and Hertz-Pannier, Lucie}, - month = jan, - year = {2008}, - pmid = {17318834}, - keywords = {Humans, Adult, Female, Male, Cerebral Cortex, Corpus Callosum, Anisotropy, Diffusion Magnetic Resonance Imaging, Aging, Diffusion, Fornix, Brain, Infant, Internal Capsule, Nerve Fibers, Myelinated, Neural Pathways, Pyramidal Tracts, Spinothalamic Tracts, Diffusion magnetic resonance imaging}, - pages = {14--27}, -} - -@article{sarrazin_multicenter_2014, - title = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder: psychotic features and interhemispheric disconnectivity}, - volume = {71}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {2168-6238}, - shorttitle = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder}, - doi = {10.1001/jamapsychiatry.2013.4513}, - abstract = {IMPORTANCE: Tractography studies investigating white matter (WM) abnormalities in patients with bipolar disorder have yielded heterogeneous results owing to small sample sizes. The small size limits their generalizability, a critical issue for neuroimaging studies of biomarkers of bipolar I disorder (BPI). -OBJECTIVES: To study WM abnormalities using whole-brain tractography in a large international multicenter sample of BPI patients and to compare these alterations between patients with or without a history of psychotic features during mood episodes. -DESIGN, SETTING, AND PARTICIPANTS: A cross-sectional, multicenter, international, Q-ball imaging tractography study comparing 118 BPI patients and 86 healthy control individuals. In addition, among the patient group, we compared those with and without a history of psychotic features. University hospitals in France, Germany, and the United States contributed participants. -INTERVENTIONS: Participants underwent assessment using the Diagnostic Interview for Genetic Studies at the French sites or the Structured Clinical Interview for DSM-IV at the German and US sites. Diffusion-weighted magnetic resonance images were acquired using the same acquisition parameters and scanning hardware at each site. We reconstructed 22 known deep WM tracts using Q-ball imaging tractography and an automatized segmentation technique. -MAIN OUTCOMES AND MEASURES: Generalized fractional anisotropy values along each reconstructed WM tract. -RESULTS: Compared with controls, BPI patients had significant reductions in mean generalized fractional anisotropy values along the body and the splenium of the corpus callosum, the left cingulum, and the anterior part of the left arcuate fasciculus when controlling for age, sex, and acquisition site (corrected for multiple testing). Patients with a history of psychotic features had a lower mean generalized fractional anisotropy value than those without along the body of the corpus callosum (corrected for multiple testing). -CONCLUSIONS AND RELEVANCE: In this multicenter sample, BPI patients had reduced WM integrity in interhemispheric, limbic, and arcuate WM tracts. Interhemispheric pathways are more disrupted in patients with than in those without psychotic symptoms. Together these results highlight the existence of an anatomic disconnectivity in BPI and further underscore a role for interhemispheric disconnectivity in the pathophysiological features of psychosis in BPI.}, - language = {eng}, - number = {4}, - journal = {JAMA psychiatry}, - author = {Sarrazin, Samuel and Poupon, Cyril and Linke, Julia and Wessa, Michèle and Phillips, Mary and Delavest, Marine and Versace, Amelia and Almeida, Jorge and Guevara, Pamela and Duclap, Delphine and Duchesnay, Edouard and Mangin, Jean-François and Le Dudal, Katia and Daban, Claire and Hamdani, Nora and D'Albis, Marc-Antoine and Leboyer, Marion and Houenou, Josselin}, - month = apr, - year = {2014}, - pmid = {24522197}, - keywords = {Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Reference Values, Adult, Female, Male, Bipolar Disorder, Cerebral Cortex, Corpus Callosum, Anisotropy, Neural Pathways, Dominance, Cerebral, Psychiatric Status Rating Scales, Diffusion Tensor Imaging, Leukoencephalopathies, Psychotic Disorders}, - pages = {388--396}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QXSGCF5P/Sarrazin et al. - 2014 - A multicenter tractography study of deep white mat.pdf:application/pdf}, -} - -@article{dufouil_cognitive_2017, - title = {Cognitive and imaging markers in non-demented subjects attending a memory clinic: study design and baseline findings of the {MEMENTO} cohort}, - volume = {9}, - issn = {1758-9193}, - shorttitle = {Cognitive and imaging markers in non-demented subjects attending a memory clinic}, - doi = {10.1186/s13195-017-0288-0}, - abstract = {BACKGROUND: The natural history and disease mechanisms of Alzheimer's disease and related disorders (ADRD) are still poorly understood. Very few resources are available to scrutinise patients as early as needed and to use integrative approaches combining standardised, repeated clinical investigations and cutting-edge biomarker measurements. -METHODS: In the nationwide French MEMENTO cohort study, participants were recruited in memory clinics and screened for either isolated subjective cognitive complaints (SCCs) or mild cognitive impairment (MCI; defined as test performance 1.5 SD below age, sex and education-level norms) while not demented (Clinical Dementia Rating [CDR] {\textless}1). Baseline data collection included neurological and physical examinations as well as extensive neuropsychological testing. To be included in the MEMENTO cohort, participants had to agree to undergo both brain magnetic resonance imaging (MRI) and blood sampling. Cerebral 18F-fluorodeoxyglucose positon emission tomography and lumbar puncture were optional. Automated analyses of cerebral MRI included assessments of volumes of whole-brain, hippocampal and white matter lesions. -RESULTS: The 2323 participants, recruited from April 2011 to June 2014, were aged 71 years, on average (SD 8.7), and 62\% were women. CDR was 0 in 40\% of participants, and 30\% carried at least one apolipoprotein E ε4 allele. We observed that more than half (52\%) of participants had amnestic mild cognitive impairment (17\% single-domain aMCI), 32\% had non-amnestic mild cognitive impairment (16.9\% single-domain naMCI) and 16\% had isolated SCCs. Multivariable analyses of neuroimaging markers associations with cognitive categories showed that participants with aMCI had worse levels of imaging biomarkers than the others, whereas participants with naMCI had markers at intermediate levels between SCC and aMCI. The burden of white matter lesions tended to be larger in participants with aMCI. Independently of CDR, all neuroimaging and neuropsychological markers worsened with age, whereas differences were not consistent according to sex. -CONCLUSIONS: MEMENTO is a large cohort with extensive clinical, neuropsychological and neuroimaging data and represents a platform for studying the natural history of ADRD in a large group of participants with different subtypes of MCI (amnestic or not amnestic) or isolated SCCs. -TRIAL REGISTRATION: Clinicaltrials.gov, NCT01926249 . Registered on 16 August 2013.}, - language = {eng}, - number = {1}, - journal = {Alzheimer's Research \& Therapy}, - author = {Dufouil, Carole and Dubois, Bruno and Vellas, Bruno and Pasquier, Florence and Blanc, Frédéric and Hugon, Jacques and Hanon, Olivier and Dartigues, Jean-François and Harston, Sandrine and Gabelle, Audrey and Ceccaldi, Mathieu and Beauchet, Olivier and Krolak-Salmon, Pierre and David, Renaud and Rouaud, Olivier and Godefroy, Olivier and Belin, Catherine and Rouch, Isabelle and Auguste, Nicolas and Wallon, David and Benetos, Athanase and Pariente, Jérémie and Paccalin, Marc and Moreaud, Olivier and Hommet, Caroline and Sellal, François and Boutoleau-Bretonniére, Claire and Jalenques, Isabelle and Gentric, Armelle and Vandel, Pierre and Azouani, Chabha and Fillon, Ludovic and Fischer, Clara and Savarieau, Helen and Operto, Gregory and Bertin, Hugo and Chupin, Marie and Bouteloup, Vincent and Habert, Marie-Odile and Mangin, Jean-François and Chêne, Geneviève and {MEMENTO cohort Study Group}}, - month = aug, - year = {2017}, - pmid = {28851447}, - pmcid = {PMC5576287}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Pattern Recognition, Automated, Neuroimaging, Image Processing, Computer-Assisted, Female, Male, Neuropsychological Tests, Positron-Emission Tomography, Aged, Follow-Up Studies, Longitudinal Studies, Organ Size, Fluorodeoxyglucose F18, Cohort Studies, Cognitive Dysfunction, Radiopharmaceuticals, France, Cohort studies, Cognitive aging, Alzheimer’s disease, Diagnostic Self Evaluation, Natural history studies (prognosis), Research Design, Spinal Puncture}, - pages = {67}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YTGWZUTJ/Dufouil et al. - 2017 - Cognitive and imaging markers in non-demented subj.pdf:application/pdf}, -} - -@article{guevara_automatic_2015, - title = {Automatic segmentation of short association bundles using a new multi-subject atlas of the left hemisphere fronto-parietal brain connections}, - volume = {2015}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2015.7318390}, - abstract = {Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of the pathogenesis associated to it. In this work we developed a method for the automatic creation of a SWM bundle multi-subject atlas. The atlas generation method is based on a cortical parcellation for the extraction of fibers connecting two different gyri. Then, an intra-subject fiber clustering is applied, in order to divide each bundle into sub-bundles with similar shape. After that, a two-step inter-subject fiber clustering is used in order to find the correspondence between the sub-bundles across the subjects, fuse similar clusters and discard the outliers. The method was applied to 40 subjects of a high quality HARDI database, focused on the left hemisphere fronto-parietal and insula brain regions. We obtained an atlas composed of 44 bundles connecting 22 pair of ROIs. Then the atlas was used to automatically segment 39 new subjects from the database.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Guevara, M. and Seguel, D. and Roman, C. and Duclap, D. and Lebois, A. and Le Bihan, null and Mangin, J.-F. and Poupon, C. and Guevara, P.}, - year = {2015}, - pmid = {26736290}, - keywords = {Brain, Humans, Brain Mapping, Cluster Analysis}, - pages = {426--429}, -} - -@article{bouhali_anatomical_2014, - title = {Anatomical connections of the visual word form area}, - volume = {34}, - issn = {1529-2401}, - doi = {10.1523/JNEUROSCI.4918-13.2014}, - abstract = {The visual word form area (VWFA), a region systematically involved in the identification of written words, occupies a reproducible location in the left occipitotemporal sulcus in expert readers of all cultures. Such a reproducible localization is paradoxical, given that reading is a recent invention that could not have influenced the genetic evolution of the cortex. Here, we test the hypothesis that the VWFA recycles a region of the ventral visual cortex that shows a high degree of anatomical connectivity to perisylvian language areas, thus providing an efficient circuit for both grapheme-phoneme conversion and lexical access. In two distinct experiments, using high-resolution diffusion-weighted data from 75 human subjects, we show that (1) the VWFA, compared with the fusiform face area, shows higher connectivity to left-hemispheric perisylvian superior temporal, anterior temporal and inferior frontal areas; (2) on a posterior-to-anterior axis, its localization within the left occipitotemporal sulcus maps onto a peak of connectivity with language areas, with slightly distinct subregions showing preferential projections to areas respectively involved in grapheme-phoneme conversion and lexical access. In agreement with functional data on the VWFA in blind subjects, the results suggest that connectivity to language areas, over and above visual factors, may be the primary determinant of VWFA localization.}, - language = {eng}, - number = {46}, - journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, - author = {Bouhali, Florence and Thiebaut de Schotten, Michel and Pinel, Philippe and Poupon, Cyril and Mangin, Jean-François and Dehaene, Stanislas and Cohen, Laurent}, - month = nov, - year = {2014}, - pmid = {25392507}, - keywords = {Humans, Brain Mapping, Adult, Female, Male, Young Adult, Temporal Lobe, Middle Aged, Visual Cortex, Neural Pathways, Functional Laterality, Frontal Lobe, Diffusion magnetic resonance imaging, reading, visual word form area}, - pages = {15402--15414}, - annote = {The following values have no corresponding Zotero field:number: 46label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 25392507}, -} - -@article{worbe_altered_2015, - title = {Altered structural connectivity of cortico-striato-pallido-thalamic networks in {Gilles} de la {Tourette} syndrome}, - volume = {138}, - copyright = {All rights reserved}, - issn = {0006-8950}, - doi = {10.1093/brain/awu311}, - journal = {BRAIN}, - author = {Worbe, Yulia and Marrakchi-Kacem, Linda and Lecomte, Sophie and Valabregue, Romain and Poupon, Fabrice and Guevara, Pamela and Tucholka, Alan and Mangin, Jean-Francois and Vidailhet, Marie and Lehericy, Stephane and Hartmann, Andreas and Poupon, Cyril}, - month = feb, - year = {2015}, - keywords = {Humans, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Basal Ganglia, Anisotropy, Nerve Net, Thalamus, Tourette Syndrome, Globus Pallidus, Neostriatum, structural connectivity and tractography, Gilles de la Tourette syndrome, cortico-basal ganglia networks, Tics}, - pages = {472--482}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {Times Cited: 10}, - annote = {Unirs - UnatiPMID: 25392196}, -} - -@article{paillere-martinot_active_2017, - title = {Active and placebo transcranial magnetic stimulation effects on external and internal auditory hallucinations of schizophrenia}, - volume = {135}, - issn = {1600-0447}, - doi = {10.1111/acps.12680}, - abstract = {OBJECTIVE: Repetitive transcranial magnetic stimulation (rTMS) over the left temporo-parietal region has been proposed as a treatment for resistant auditory verbal hallucinations (AVH), but which patients are more likely to benefit from rTMS is still unclear. This study sought to assess the effects of rTMS on AVH, with a focus on hallucination phenomenology. -METHOD: Twenty-seven patients with schizophrenia and medication-resistant AVH participated to a randomized, double-blind, placebo-controlled, add-on rTMS study. The stimulation targeted a language-perception area individually determined using functional magnetic resonance imaging and a language recognition task. AVH were assessed using the hallucination subscale of the Scale for the Assessment of Positive Symptoms (SAPS). The spatial location of AVH was assessed using the Psychotic Symptom Rating Scales. -RESULTS: A significant improvement in SAPS hallucination subscale score was observed in both actively treated and placebo-treated groups with no difference between both modalities. Patients with external AVH were significantly more improved than patients with internal AVH, with both modalities. -CONCLUSIONS: A marked placebo effect of rTMS was observed in patients with resistant AVH. Patients with prominent external AVH may be more likely to benefit from both active and placebo interventions. Cortical effects related to non-magnetic stimulation of the auditory cortex are suggested.}, - language = {eng}, - number = {3}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Paillère-Martinot, M.-L. and Galinowski, A. and Plaze, M. and Andoh, J. and Bartrés-Faz, D. and Bellivier, F. and Lefaucheur, J.-P. and Rivière, D. and Gallarda, T. and Martinot, J.-L. and Artiges, E.}, - month = mar, - year = {2017}, - pmid = {27987221}, - keywords = {Humans, Adult, Female, Male, Young Adult, Hallucinations, Age of Onset, Treatment Outcome, functional magnetic resonance imaging, Double-Blind Method, Transcranial Magnetic Stimulation, auditory hallucinations, randomized placebo-controlled trial, repetitive transcranial magnetic stimulation}, - pages = {228--238}, -} - -@article{de_guio_study_2014, - title = {A study of cortical morphology in children with fetal alcohol spectrum disorders}, - volume = {35}, - issn = {1097-0193}, - doi = {10.1002/hbm.22327}, - abstract = {Prenatal alcohol exposure is responsible for a broad range of brain structural malformations, which can be studied using magnetic resonance imaging (MRI). Advanced MRI methods have emerged to characterize brain abnormalities, but the teratogenic effects of alcohol on cortical morphology have received little attention to date. Twenty-four 9-year-old children with fetal alcohol spectrum disorders (9 with fetal alcohol syndrome, 15 heavy exposed nonsyndromal children) and 16 age-matched controls were studied to assess the effect of alcohol consumption during pregnancy on cortical morphology. An automated method was applied to 3D T1-weighted images to assess cortical gyrification using global and regional sulcal indices and two region-based morphological measurements, mean sulcal depth and fold opening. Increasing levels of alcohol exposure were related to reduced cortical folding complexity, even among children with normal brain size, indicating a reduction of buried cortical surface. Fold opening was the strongest anatomical correlate of prenatal alcohol intake, indicating a widening of sulci in all regions that were examined. These data identify cortical morphology as a suitable marker for further investigation of brain damage associated with prenatal alcohol exposure.}, - language = {eng}, - number = {5}, - journal = {Human Brain Mapping}, - author = {De Guio, François and Mangin, Jean-François and Rivière, Denis and Perrot, Matthieu and Molteno, Christopher D. and Jacobson, Sandra W. and Meintjes, Ernesta M. and Jacobson, Joseph L.}, - month = may, - year = {2014}, - pmid = {23946151}, - keywords = {Humans, Brain Mapping, Image Processing, Computer-Assisted, Child, Female, Male, Cerebral Cortex, Pregnancy, Case-Control Studies, Analysis of Variance, Dose-Response Relationship, Drug, Fetal Alcohol Spectrum Disorders, cortical morphology, FAS, fold opening, Alcohols, Prenatal Exposure Delayed Effects, South Africa}, - pages = {2285--2296}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {Times Cited: 4}, - annote = {UnatiPMID: 23946151}, -} - -@article{brion_noise_2013, - title = {Noise correction for {HARDI} and {HYDI} data obtained with multi-channel coils and sum of squares reconstruction: an anisotropic extension of the {LMMSE}}, - volume = {31}, - issn = {1873-5894}, - shorttitle = {Noise correction for {HARDI} and {HYDI} data obtained with multi-channel coils and sum of squares reconstruction}, - doi = {10.1016/j.mri.2013.04.002}, - abstract = {Parallel magnetic resonance imaging (MRI) yields noisy magnitude data, described in most cases as following a noncentral χ distribution when the signals received by the coils are combined as the sum of their squares. One well-known case of this noncentral χ noise model is the Rician model, but it is only valid in the case of single-channel acquisition. Although the use of parallel MRI is increasingly common, most of the correction methods still perform Rician noise removal, yielding an erroneous result due to an incorrect noise model. Moreover, the existence of noise correlations in phased array systems renders noise nonstationary and further modifies the noise description in parallel MRI. However, the noncentral χ model has been demonstrated to work as a good approximation as long as effective voxelwise parameters are used. A good correction step, adapted to the right noise model, is of paramount importance, especially when working with diffusion-weighted MR data, whose signal-to-noise ratio is low. In this paper, we present a noise removal technique designed to be fast enough for integration into a real-time reconstruction system, thus offering the convenience of obtaining corrected data almost instantaneously during the MRI scan. Our method employs the noncentral χ noise model and uses a simplified method to account for noise correlations; this leads to an efficient and rapid correction. The method consists of an anisotropic extension of the Linear Minimum Mean Square Error estimator (LMMSE) that is a far better edge-preserving method than the traditional LMMSE and addresses noncentral χ distributions along with empirically computed global effective parameters. The results on simulated and real data demonstrate that this anisotropic extended LMMSE outperforms the original LMMSE on images corrupted by noncentral χ noise. Moreover, in comparison with the existing LMMSE technique incorporating the estimation of voxelwise effective parameters, our method yields improved results.}, - language = {eng}, - number = {8}, - journal = {Magnetic Resonance Imaging}, - author = {Brion, Véronique and Poupon, Cyril and Riff, Olivier and Aja-Fernández, Santiago and Tristán-Vega, Antonio and Mangin, Jean-François and Le Bihan, Denis and Poupon, Fabrice}, - month = oct, - year = {2013}, - pmid = {23659768}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Reproducibility of Results, Sensitivity and Specificity, Data Interpretation, Statistical, Nerve Fibers, Myelinated, Diffusion Tensor Imaging, Least-Squares Analysis, Artifacts, Equipment Design, Equipment Failure Analysis, HARDI, Signal-To-Noise Ratio, HYDI, LMMSE, Noise correction, Noncentral χ, Parallel MRI, Real-time}, - pages = {1360--1371}, -} - -@article{mangin_toward_2013, - title = {Toward global tractography}, - volume = {80}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2013.04.009}, - abstract = {Diffusion-based tractography is an ill-posed problem, because the step-by-step reconstruction of a fibre bundle trajectory cannot afford any serious mistake in the evaluation of the local fibre orientations. Such evaluation is difficult, however, because the myriad fibres passing through a single voxel follow different directions. Modelling tractography as a global inverse problem is a simple framework which addresses the ill-posed nature of the problem. The key idea is that the results of tractography in the neighbourhood of an ambiguous local diffusion profile can help to infer the local fibre directions. This paper provides an overview of past achievements of global tractography and proposes guidelines for a future research programme in the hope that the potential of the technique will increase the interest of the community.}, - language = {eng}, - journal = {Neuroimage}, - author = {Mangin, J.-F. and Fillard, P. and Cointepas, Y. and Le Bihan, D. and Frouin, V. and Poupon, C.}, - month = oct, - year = {2013}, - pmid = {23587688}, - keywords = {Brain, Humans, Image Interpretation, Computer-Assisted, Models, Neurological, Nerve Fibers, Myelinated, Animals, Diffusion Tensor Imaging, Nerve Net, Models, Anatomic, Connectome, Global tractography, Diffusion MRI}, - pages = {290--296}, -} - -@article{lefranc_groupwise_2016, - title = {Groupwise connectivity-based parcellation of the whole human cortical surface using watershed-driven dimension reduction}, - volume = {30}, - issn = {1361-8423}, - doi = {10.1016/j.media.2016.01.003}, - abstract = {Segregating the human cortex into distinct areas based on structural connectivity criteria is of widespread interest in neuroscience. This paper presents a groupwise connectivity-based parcellation framework for the whole cortical surface using a new high quality diffusion dataset of 79 healthy subjects. Our approach performs gyrus by gyrus to parcellate the whole human cortex. The main originality of the method is to compress for each gyrus the connectivity profiles used for the clustering without any anatomical prior information. This step takes into account the interindividual cortical and connectivity variability. To this end, we consider intersubject high density connectivity areas extracted using a surface-based watershed algorithm. A wide validation study has led to a fully automatic pipeline which is robust to variations in data preprocessing (tracking type, cortical mesh characteristics and boundaries of initial gyri), data characteristics (including number of subjects), and the main algorithmic parameters. A remarkable reproducibility is achieved in parcellation results for the whole cortex, leading to clear and stable cortical patterns. This reproducibility has been tested across non-overlapping subgroups and the validation is presented mainly on the pre- and postcentral gyri.}, - language = {eng}, - journal = {Medical Image Analysis}, - author = {Lefranc, Sandrine and Roca, Pauline and Perrot, Matthieu and Poupon, Cyril and Le Bihan, Denis and Mangin, Jean-François and Rivière, Denis}, - month = may, - year = {2016}, - pmid = {26849421}, - keywords = {Algorithms, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Female, Male, Young Adult, Diffusion Tensor Imaging, Nerve Net, Connectome, Clustering, Connectome, Clustering, Structural connectivity, Diffusion tensor imaging, Structural connectivity}, - pages = {11--29}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati}, -} - -@article{assaf_connect_2013, - title = {The {CONNECT} project: {Combining} macro- and micro-structure}, - volume = {80}, - issn = {1095-9572}, - shorttitle = {The {CONNECT} project}, - doi = {10.1016/j.neuroimage.2013.05.055}, - abstract = {In recent years, diffusion MRI has become an extremely important tool for studying the morphology of living brain tissue, as it provides unique insights into both its macrostructure and microstructure. Recent applications of diffusion MRI aimed to characterize the structural connectome using tractography to infer connectivity between brain regions. In parallel to the development of tractography, additional diffusion MRI based frameworks (CHARMED, AxCaliber, ActiveAx) were developed enabling the extraction of a multitude of micro-structural parameters (axon diameter distribution, mean axonal diameter and axonal density). This unique insight into both tissue microstructure and connectivity has enormous potential value in understanding the structure and organization of the brain as well as providing unique insights to abnormalities that underpin disease states. The CONNECT (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements. This paper summarizes the project and describes the perspective of using micro-structural measures to study the connectome.}, - language = {eng}, - journal = {Neuroimage}, - author = {Assaf, Yaniv and Alexander, Daniel C. and Jones, Derek K. and Bizzi, Albero and Behrens, Tim E. J. and Clark, Chris A. and Cohen, Yoram and Dyrby, Tim B. and Huppi, Petra S. and Knoesche, Thomas R. and Lebihan, Denis and Parker, Geoff J. M. and Poupon, Cyril and {CONNECT consortium} and Anaby, Debbie and Anwander, Alfred and Bar, Leah and Barazany, Daniel and Blumenfeld-Katzir, Tamar and De-Santis, Silvia and Duclap, Delphine and Figini, Matteo and Fischi, Elda and Guevara, Pamela and Hubbard, Penny and Hofstetter, Shir and Jbabdi, Saad and Kunz, Nicolas and Lazeyras, Francois and Lebois, Alice and Liptrot, Matthew G. and Lundell, Henrik and Mangin, Jean-François and Dominguez, David Moreno and Morozov, Darya and Schreiber, Jan and Seunarine, Kiran and Nava, Simone and Poupon, Cyril and Riffert, Till and Sasson, Efrat and Schmitt, Benoit and Shemesh, Noam and Sotiropoulos, Stam N. and Tavor, Ido and Zhang, Hui Gary and Zhou, Feng-Lei}, - month = oct, - year = {2013}, - pmid = {23727318}, - keywords = {Brain, Humans, Image Enhancement, Models, Neurological, Diffusion Tensor Imaging, Nerve Net, Models, Anatomic, Connectome}, - pages = {273--282}, -} - -@inproceedings{auzias_model-driven_2015-1, - title = {Model-driven parameterization of fetal cortical surfaces}, - isbn = {978-1-4799-2374-8}, - doi = {10.1109/ISBI.2015.7164103}, - booktitle = {12th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2015, {Brooklyn}, {NY}, {USA}, {April} 16-19, 2015}, - publisher = {IEEE}, - author = {Auzias, Guillaume and Guio, F. De and Pepe, A. and Rousseau, François and Mangin, Jean-Francois and Girard, Nadine and Lefèvre, Julien and Coulon, Olivier}, - year = {2015}, - pages = {1260--1263}, -} - -@inproceedings{lebenberg_clustering_2015, - title = {Clustering the infant brain tissues based on microstructural properties and maturation assessment using multi-parametric {MRI}}, - isbn = {978-1-4799-2374-8}, - doi = {10.1109/ISBI.2015.7163837}, - booktitle = {12th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2015, {Brooklyn}, {NY}, {USA}, {April} 16-19, 2015}, - publisher = {IEEE}, - author = {Lebenberg, Jessica and Poupon, Cyril and Thirion, Bertrand and Leroy, François and Mangin, Jean-Francois and Dehaene-Lambertz, Ghislaine and Dubois, Jessica}, - year = {2015}, - pages = {148--151}, -} - -@inproceedings{teillac_novel_2017, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {A {Novel} {Anatomically}-{Constrained} {Global} {Tractography} {Approach} to {Monitor} {Sharp} {Turns} in {Gyri}}, - volume = {10433}, - isbn = {978-3-319-66181-0}, - doi = {10.1007/978-3-319-66182-7_61}, - booktitle = {Medical {Image} {Computing} and {Computer} {Assisted} {Intervention} - {MICCAI} 2017 - 20th {International} {Conference}, {Quebec} {City}, {QC}, {Canada}, {September} 11-13, 2017, {Proceedings}, {Part} {I}}, - publisher = {Springer}, - author = {Teillac, Achille and Beaujoin, Justine and Poupon, Fabrice and Mangin, Jean-Francois and Poupon, Cyril}, - editor = {Descoteaux, Maxime and Maier-Hein, Lena and Franz, Alfred M. and Jannin, Pierre and Collins, D. Louis and Duchesne, Simon}, - year = {2017}, - pages = {532--539}, -} - -@inproceedings{guen_regional_2017, - title = {Regional study of the genetic influence on the sulcal pits}, - isbn = {978-1-5090-1172-8}, - doi = {10.1109/ISBI.2017.7950472}, - booktitle = {14th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2017, {Melbourne}, {Australia}, {April} 18-21, 2017}, - publisher = {IEEE}, - author = {Guen, Yann Le and Auzias, Guillaume and Dehaene-Lambertz, Ghislaine and Leroy, François and Mangin, Jean-Francois and Duchesnay, Edouard and Coulon, Olivier and Frouin, Vincent}, - year = {2017}, - keywords = {Brain, Biomarkers, Additives, Correlation, cortical structures, genetic control, genetic influence, genomics, imaging-genetic, Junctions, Olfactory, Organizations, sulcal depth, sulcal pits}, - pages = {77--80}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QJPSNRWG/7950472.html:text/html}, -} - -@inproceedings{lefevre_surface_2013-1, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {Surface {Smoothing}: {A} {Way} {Back} in {Early} {Brain} {Morphogenesis}}, - volume = {8149}, - isbn = {978-3-642-40810-6}, - shorttitle = {Surface {Smoothing}}, - doi = {10.1007/978-3-642-40811-3_74}, - booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention} - {MICCAI} 2013 - 16th {International} {Conference}, {Nagoya}, {Japan}, {September} 22-26, 2013, {Proceedings}, {Part} {I}}, - publisher = {Springer}, - author = {Lefèvre, Julien and Intwali, Victor and Hertz-Pannier, Lucie and Hüppi, Petra S. and Mangin, Jean-François and Dubois, Jessica and Germanaud, David}, - editor = {Mori, Kensaku and Sakuma, Ichiro and Sato, Yoshinobu and Barillot, Christian and Navab, Nassir}, - year = {2013}, - pages = {590--597}, -} - -@inproceedings{lefranc_validation_2014, - title = {Validation of consistent inter-subject connectivity-based parcellation}, - isbn = {978-1-4673-1961-4}, - doi = {10.1109/ISBI.2014.6868022}, - booktitle = {{IEEE} 11th {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2014, {April} 29 - {May} 2, 2014, {Beijing}, {Chin}, {Beijing}, {China}}, - publisher = {IEEE}, - author = {Lefranc, Sandrine and Roca, Pauline and Perrot, Matthieu and Poupon, Cyril and Coulon, Olivier and Bihan, Denis Le and Hertz-Pannier, Lucie and Mangin, Jean-Francois and Rivière, Denis}, - year = {2014}, - pages = {923--926}, -} - -@inproceedings{balbastre_quantitative_2015, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {A {Quantitative} {Approach} to {Characterize} {MR} {Contrasts} with {Histology}}, - volume = {9556}, - isbn = {978-3-319-30857-9}, - doi = {10.1007/978-3-319-30858-6_10}, - booktitle = {Brainlesion: {Glioma}, {Multiple} {Sclerosis}, {Stroke} and {Traumatic} {Brain} {Injuries} - {First} {International} {Workshop}, {Brainles} 2015, {Held} in {Conjunction} with {MICCAI} 2015, {Munich}, {Germany}, {October} 5, 2015, {Revised} {Selected} {Papers}}, - publisher = {Springer}, - author = {Balbastre, Yaël and Vandenberghe, Michel E. and Hérard, Anne-Sophie and Gipchtein, Pauline and Jan, Caroline and Perrier, Anselme L. and Hantraye, Philippe and Aron-Badin, Romina and Mangin, Jean-François and Delzescaux, Thierry}, - editor = {Crimi, Alessandro and Menze, Bjoern H. and Maier, Oskar and Reyes, Mauricio and Handels, Heinz}, - year = {2015}, - pages = {104--115}, -} - -@inproceedings{lefranc_concomitant_2015, - title = {Concomitant variability of the central sulcus morphology and adjacent connectivity patterns}, - isbn = {978-1-4799-2374-8}, - doi = {10.1109/ISBI.2015.7163907}, - booktitle = {12th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2015, {Brooklyn}, {NY}, {USA}, {April} 16-19, 2015}, - publisher = {IEEE}, - author = {Lefranc, Sandrine and Sun, Zhong Yi and Roca, Pauline and Poupon, Cyril and Bihan, Denis Le and Mangin, Jean-Francois and Rivière, Denis}, - year = {2015}, - pages = {445--448}, -} - -@inproceedings{dubois_exploring_2016, - title = {Exploring the successive waves of cortical folding in the developing brain using {MRI} and spectral analysis of gyrification}, - isbn = {978-1-4799-2349-6}, - doi = {10.1109/ISBI.2016.7493259}, - booktitle = {13th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2016, {Prague}, {Czech} {Republic}, {April} 13-16, 2016}, - publisher = {IEEE}, - author = {Dubois, Jessica and Germanaud, David and Angleys, Hugo and Leroy, François and Fischer, Clara and Lebenberg, Jessica and Lazeyras, François and Dehaene-Lambertz, Ghislaine and Hertz-Pannier, Lucie and Mangin, Jean-François and Hüppi, Petra S. and Lefèvre, Julien}, - year = {2016}, - pages = {261--264}, -} - -@inproceedings{leprince_combined_2015, - title = {Combined {Laplacian}-equivolumic model for studying cortical lamination with ultra high field {MRI} (7 {T})}, - isbn = {978-1-4799-2374-8}, - doi = {10.1109/ISBI.2015.7163940}, - booktitle = {12th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2015, {Brooklyn}, {NY}, {USA}, {April} 16-19, 2015}, - publisher = {IEEE}, - author = {Leprince, Yann and Poupon, Fabrice and Delzescaux, Thierry and Hasboun, Dominique and Poupon, Cyril and Rivière, Denis}, - year = {2015}, - pages = {580--583}, -} - -@article{hopkins_evolution_2014, - title = {Evolution of the {Central} {Sulcus} {Morphology} in {Primates}}, - volume = {84}, - copyright = {All rights reserved}, - issn = {0006-8977}, - doi = {10.1159/000362431}, - number = {1}, - journal = {Brain Behavior and Evolution}, - author = {Hopkins, William D. and Meguerditchian, Adrien and Coulon, Olivier and Bogart, Stephanie and Mangin, Jean-Francois and Sherwood, Chet C. and Grabowski, Mark W. and Bennett, Allyson J. and Pierre, Peter J. and Fears, Scott and Woods, Roger and Hof, Patrick R. and Vauclair, Jacques}, - year = {2014}, - pages = {19--30}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 25139259}, -} - -@inproceedings{roman_short_2016, - title = {Short association bundle atlas based on inter-subject clustering from {HARDI} data}, - volume = {2016}, - doi = {10.1109/EMBC.2016.7591983}, - abstract = {This paper is focused on the study of short brain association fibers. We present an automatic method to identify short bundles of the superficial white matter based on inter-subject hierarchical clustering. Our method finds clusters of similar fibers, belonging to the different subjects, according to a distance measure between fibers. First, the algorithm obtains representative bundles and subsequently we perform an automatic labeling based on the anatomy, of the most stable connections. The analysis was applied to two independent groups of 37 subjects. Results between the two groups were compared, in order to keep reproducible connections for the atlas creation. The method was applied using linear and non-linear registration, where the non-linear registration showed significantly better results. A final atlas with 35 bundles in the left hemisphere and 27 in the right hemisphere from the whole brain was obtained. Finally results were validated using the atlas to segment 26 new subjects from another HARDI database.}, - language = {eng}, - booktitle = {Conference proceedings: ... {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society}. {IEEE} {Engineering} in {Medicine} and {Biology} {Society}. {Annual} {Conference}}, - author = {Roman, C. and Guevara, M. and Duclap, D. and Lebois, A. and Poupon, C. and Mangin, J.-F. and Guevara, P.}, - year = {2016}, - pmid = {28269513}, - keywords = {Algorithms, Brain, Humans, Reproducibility of Results, Image Processing, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Databases, Factual, White Matter, Cluster Analysis, Connectome, Diffusion magnetic resonance imaging}, - pages = {5545--5549}, - annote = {The following values have no corresponding Zotero field:label: ACTI}, - annote = {UnirsPMID: 28269513}, -} - -@article{balbastre_validation_2018, - title = {A validation dataset for {Macaque} brain {MRI} segmentation}, - volume = {16}, - issn = {2352-3409}, - doi = {10.1016/j.dib.2017.11.008}, - abstract = {Validation data for segmentation algorithms dedicated to preclinical images is fiercely lacking, especially when compared to the large number of databases of Human brain images and segmentations available to the academic community. Not only is such data essential for validating methods, it is also needed for objectively comparing concurrent algorithms and detect promising paths, as segmentation challenges have shown for clinical images. The dataset we present here is a first step in this direction. It comprises 10 T2-weighted MRIs of healthy adult macaque brains, acquired on a 7 T magnet, along with corresponding manual segmentations into 17 brain anatomic labelled regions spread over 5 hierarchical levels based on a previously published macaque atlas (Calabrese et al., 2015) [1]. By giving access to this unique dataset, we hope to provide a reference needed by the non-human primate imaging community. This dataset was used in an article presenting a new primate brain morphology analysis pipeline, Primatologist (Balbastre et al., 2017) [2]. Data is available through a NITRC repository (https://www.nitrc.org/projects/mircen\_macset).}, - language = {eng}, - journal = {Data in Brief}, - author = {Balbastre, Yaël and Rivière, Denis and Souedet, Nicolas and Fischer, Clara and Hérard, Anne-Sophie and Williams, Susannah and Vandenberghe, Michel E. and Flament, Julien and Aron-Badin, Romina and Hantraye, Philippe and Mangin, Jean-François and Delzescaux, Thierry}, - month = feb, - year = {2018}, - pmid = {29167818}, - pmcid = {PMC5686468}, - pages = {37--42}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CJBRQKIG/Balbastre et al. - 2018 - A validation dataset for Macaque brain MRI segment.pdf:application/pdf}, -} - -@article{moon_associations_2017, - title = {Associations between white matter hyperintensities and cognitive decline over three years in non-dementia older adults with memory complaints}, - volume = {379}, - issn = {1878-5883}, - doi = {10.1016/j.jns.2017.06.031}, - abstract = {We investigated whether the baseline level and overtime changes of white matter hyperintensities (WMH) would be associated with cognitive decline over three years in non-demented older adults with memory complaints. 109 participants with baseline magnetic resonance imaging (MRI) and follow-up cognitive assessments up to 3-year were included; among them, 82 also had a follow-up MRI assessment over three years. WMH volume was obtained by an automated segmentation algorithm. Baseline WMH volumes and change between baseline and follow-up WMH were related to cognitive scores over time using mixed-effect linear regressions. Secondary stratified analyses according to Clinical Dementia Rating (CDR) status, APOE4 status, and presence of amyloid in the brain were conducted using similar regression models. Change in WMH volume overtime was associated with declines in COWAT (β=-0.239; 95\% CI=-0.381, -0.096, p=0.001). Baseline WMH was not associated to any of the cognitive tests. Secondary analysis found that baseline WMH was associated to declines in TMT-A in APOE4 non-carriers (β=0.343; 95\% CI=0.121, 0.564, p=0.003) and CDR 0 groups (β=0.307; 95\% CI=0.095, 0.519, p=0.005); in CDR 0 group, overtime changes in WMH was associated to declines on both TMT-A (β=0.698; 95\% CI=0.270, 1.126, p=0.002) and TMT-B (β=2.573; 95\% CI=1.200, 3.947, p{\textless}0.001). Changes in WMH volume are associated with declines in information processing speed and executive function in non-demented older adults with memory complaints. Overtime changes in WMH volume is probably a better determinant of cognitive function in the elderly than baseline WMH volume.}, - language = {eng}, - journal = {Journal of the Neurological Sciences}, - author = {Moon, So Young and de Souto Barreto, Philipe and Chupin, Marie and Mangin, Jean François and Bouyahia, Ali and Fillon, Ludovic and Andrieu, Sandrine and Vellas, Bruno and {MAPT/DSA group}}, - month = aug, - year = {2017}, - pmid = {28716257}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Neuroimaging, Female, Male, Neuropsychological Tests, Aged, Cognition, White Matter, Time Factors, White matter hyperintensities, Cognitive Dysfunction, Memory Disorders, Amyloid, Apolipoprotein E4, Longitudinal}, - pages = {266--270}, -} - -@article{balbastre_primatologist:_2017, - title = {Primatologist: {A} modular segmentation pipeline for macaque brain morphometry}, - volume = {162}, - issn = {1095-9572}, - shorttitle = {Primatologist}, - doi = {10.1016/j.neuroimage.2017.09.007}, - abstract = {Because they bridge the genetic gap between rodents and humans, non-human primates (NHPs) play a major role in therapy development and evaluation for neurological disorders. However, translational research success from NHPs to patients requires an accurate phenotyping of the models. In patients, magnetic resonance imaging (MRI) combined with automated segmentation methods has offered the unique opportunity to assess in vivo brain morphological changes. Meanwhile, specific challenges caused by brain size and high field contrasts make existing algorithms hard to use routinely in NHPs. To tackle this issue, we propose a complete pipeline, Primatologist, for multi-region segmentation. Tissue segmentation is based on a modular statistical model that includes random field regularization, bias correction and denoising and is optimized by expectation-maximization. To deal with the broad variety of structures with different relaxing times at 7 T, images are segmented into 17 anatomical classes, including subcortical regions. Pre-processing steps insure a good initialization of the parameters and thus the robustness of the pipeline. It is validated on 10 T2-weighted MRIs of healthy macaque brains. Classification scores are compared with those of a non-linear atlas registration, and the impact of each module on classification scores is thoroughly evaluated.}, - language = {eng}, - journal = {NeuroImage}, - author = {Balbastre, Yaël and Rivière, Denis and Souedet, Nicolas and Fischer, Clara and Hérard, Anne-Sophie and Williams, Susannah and Vandenberghe, Michel E. and Flament, Julien and Aron-Badin, Romina and Hantraye, Philippe and Mangin, Jean-François and Delzescaux, Thierry}, - year = {2017}, - pmid = {28899745}, - keywords = {Algorithms, Brain, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Software, MRI, Neuroimaging, Image Processing, Computer-Assisted, Animals, Segmentation, Atlases as Topic, Expectation-maximization, Macaque, Primatologist, Macaca}, - pages = {306--321}, -} - -@article{sarrazin_neurodevelopmental_2018, - title = {Neurodevelopmental subtypes of bipolar disorder are related to cortical folding patterns: {An} international multicenter study}, - issn = {1399-5618}, - shorttitle = {Neurodevelopmental subtypes of bipolar disorder are related to cortical folding patterns}, - doi = {10.1111/bdi.12664}, - abstract = {OBJECTIVES: Brain sulcation is an indirect marker of neurodevelopmental processes. Studies of the cortical sulcation in bipolar disorder have yielded mixed results, probably due to high variability in clinical phenotype. We investigated whole-brain cortical sulcation in a large sample of selected patients with high neurodevelopmental load. -METHODS: A total of 263 patients with bipolar disorder I and 320 controls were included in a multicentric magnetic resonance imaging (MRI) study. All subjects underwent high-resolution T1-weighted brain MRI. Images were processed with an automatized pipeline to extract the global sulcal index (g-SI) and the local sulcal indices (l-SIs) from 12 a priori determined brain regions covering the whole brain. We compared l-SI and g-SI between patients with and without early-onset bipolar disorder and between patients with and without a positive history of psychosis, adjusting for age, gender and handedness. -RESULTS: Patients with early-onset bipolar disorder had a higher l-SI in the right prefrontal dorsolateral region. Patients with psychotic bipolar disorder had a decreased l-SI in the left superior parietal cortex. No group differences in g-SI or l-SI were found between healthy subjects and the whole patient cohort. We could replicate the early-onset finding in an independent cohort. -CONCLUSIONS: Our work suggests that bipolar disorder is not associated with generalized abnormalities of sulcation, but rather with localized changes of cortical folding restricted to patients with a heavy neurodevelopmental loading. These findings support the hypothesis that bipolar disorder is heterogeneous but may be disentangled using MRI, and suggest the need for investigations into neurodevelopmental deviations in the disorder.}, - language = {eng}, - journal = {Bipolar Disorders}, - author = {Sarrazin, Samuel and Cachia, Arnaud and Hozer, Franz and McDonald, Colm and Emsell, Louise and Cannon, Dara M. and Wessa, Michele and Linke, Julia and Versace, Amelia and Hamdani, Nora and D'Albis, Marc-Antoine and Delavest, Marine and Phillips, Mary L. and Brambilla, Paolo and Bellani, Marcella and Polosan, Mircea and Favre, Pauline and Leboyer, Marion and Mangin, Jean-François and Houenou, Josselin}, - month = jul, - year = {2018}, - pmid = {29981196}, - keywords = {neurodevelopment, psychosis, bipolar disorder, magnetic resonance imaging, early-onset, sulcation}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZGD8IKUZ/bdi.html:text/html;Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HSX9VKYF/Sarrazin et al. - 2018 - Neurodevelopmental subtypes of bipolar disorder ar.pdf:application/pdf}, -} - -@article{dalbis_local_2018, - title = {Local structural connectivity is associated with social cognition in autism spectrum disorder}, - volume = {141}, - issn = {1460-2156}, - doi = {10.1093/brain/awy275}, - abstract = {The current theory implying local, short-range overconnectivity in autism spectrum disorder, contrasting with long-range underconnectivity, is based on heterogeneous results, on limited data involving functional connectivity studies, on heterogeneous paediatric populations and non-specific methodologies. In this work, we studied short-distance structural connectivity in a homogeneous population of males with high-functioning autism spectrum disorder and used a novel methodology specifically suited for assessing U-shaped short-distance tracts, including a recently developed tractography-based atlas of the superficial white matter fibres. We acquired diffusion-weighted MRI for 58 males (27 subjects with high-functioning autism spectrum disorder and 31 control subjects) and extracted the mean generalized fractional anisotropy of 63 short-distance tracts. Neuropsychological evaluation included Wechsler Adult Intelligence Scale IV (WAIS-IV), Communication Checklist-Adult, Empathy Quotient, Social Responsiveness Scale and Behaviour Rating Inventory of Executive Function-Adult (BRIEF-A). In contradiction with the models of short-range over-connectivity in autism spectrum disorder, we found that patients with autism spectrum disorder had a significantly decreased anatomical connectivity in a component comprising 13 short tracts compared to controls. Specific short-tract atypicalities in temporal lobe and insula were significantly associated with clinical manifestations of autism spectrum disorder such as social awareness, language structure, pragmatic skills and empathy, emphasizing their importance in social dysfunction. Short-range decreased anatomical connectivity may thus be an important substrate of social deficits in autism spectrum disorder, in contrast with current models.}, - language = {eng}, - number = {12}, - journal = {Brain: A Journal of Neurology}, - author = {d'Albis, Marc-Antoine and Guevara, Pamela and Guevara, Miguel and Laidi, Charles and Boisgontier, Jennifer and Sarrazin, Samuel and Duclap, Delphine and Delorme, Richard and Bolognani, Federico and Czech, Christian and Bouquet, Céline and Ly-Le Moal, Myriam and Holiga, Stefan and Amestoy, Anouck and Scheid, Isabelle and Gaman, Alexandru and Leboyer, Marion and Poupon, Cyril and Mangin, Jean-François and Houenou, Josselin}, - month = dec, - year = {2018}, - pmid = {30423029}, - pages = {3472--3481}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/K95RIQ4J/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3PQZ935H/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8Z5Y4QS7/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf}, -} - -@inproceedings{leprince_optimization_2015, - address = {Toronto, ON, Canada, Poster}, - title = {Optimization of sample preparation for {MRI} of formaldehyde-fixed brains}, - author = {Leprince, Y. and Schmitt, B. and Chaillou, E. and Destrieux, C. and Barantin, L. and Vignaud, A. and Riviere, D. and Poupon, C.}, - year = {2015}, - pages = {3616}, - annote = {The following values have no corresponding Zotero field:pub-location: Toronto, Canadalabel: ACTI}, - annote = {Unirs - MetricHAL }, -} - -@article{rodrigo_uncinate_2007, - title = {Uncinate fasciculus fiber tracking in mesial temporal lobe epilepsy. {Initial} findings}, - volume = {17}, - issn = {0938-7994}, - doi = {10.1007/s00330-006-0558-x}, - abstract = {In temporal lobe epilepsy (TLE) due to hippocampal sclerosis (HS), ictal discharge spread to the frontal and insulo-perisylvian cortex is commonly observed. The implication of white matter pathways in this propagation has not been investigated. We compared diffusion tensor imaging (DTI) measurements along the uncinate fasciculus (UF), a major tract connecting the frontal and temporal lobes, in patients and controls. Ten right-handed patients referred for intractable TLE due to a right HS were investigated on a 1.5-T MR scanner including a DTI sequence. All patients had interictal fluorodeoxyglucose PET showing an ipsilateral temporal hypometabolism associated with insular and frontal or perisylvian hypometabolism. The controls consisted of ten right-handed healthy subjects. UF fiber tracking was performed, and its fractional anisotropy (FA) values were compared between patients and controls, separately for the right and left UF. The left-minus-right FA UF asymmetry index was computed to test for intergroup differences. Asymmetries were found in the control group with right-greater-than-left FA. This asymmetrical pattern was lost in the patient group. Right FA values were lower in patients with right HS versus controls. Although preliminary, these findings may be related to the preferential pathway of seizure spread from the mesial temporal lobe to frontal and insulo-perisylvian areas.}, - language = {eng}, - number = {7}, - journal = {European Radiology}, - author = {Rodrigo, S. and Oppenheim, C. and Chassoux, F. and Golestani, N. and Cointepas, Y. and Poupon, C. and Semah, F. and Mangin, J.-F. and Le Bihan, D. and Meder, J.-F.}, - month = jul, - year = {2007}, - pmid = {17219141}, - keywords = {Humans, Imaging, Three-Dimensional, Image Processing, Computer-Assisted, Reference Values, Adult, Adolescent, Female, Male, Temporal Lobe, Anisotropy, Diffusion Magnetic Resonance Imaging, Nerve Fibers, Myelinated, Neural Pathways, Dominance, Cerebral, Hippocampus, Frontal Lobe, Energy Metabolism, Epilepsy, Temporal Lobe, Sclerosis}, - pages = {1663--1668}, - annote = {Journal articleEur Radiol. 2007 Jul;17(7):1663-1668. Epub 2007 Jan 12.}, - annote = {The following values have no corresponding Zotero field:auth-address: Departement d'Imagerie Morphologique et Fonctionnelle, Universite Paris-Descartes, Faculte de Medecine, Centre Hospitalier Sainte-Anne, 75674, Paris, France, c.oppenheim@ch-sainte-anne.fr.number: 7edition: 2007/01/16accession-num: 17219141label: ACLcustom1: NEUROSPIN}, -} - -@article{duchesnay_classification_2007, - title = {Classification based on cortical folding patterns}, - volume = {26}, - issn = {0278-0062}, - doi = {10.1109/TMI.2007.892501}, - abstract = {We describe here a classification system based on automatically identified cortical sulci. Multivariate recognition methods are required for the detection of complex brain patterns with a spatial distribution. However, such methods may face the well-known issue of the curse of dimensionality-the risk of overfitting the training dataset in high-dimensional space. We overcame this problem, using a classifier pipeline with one- or two-stage of descriptor selection based on machine-learning methods, followed by a support vector machine classifier or linear discriminant analysis. We compared alternative designs of the pipeline on two different datasets built from the same database corresponding to 151 brains. The first dataset dealt with cortex asymmetry and the second dealt with the effect of the subject's sex. Our system successfully (98\%) distinguished between the left and right hemispheres on the basis of sulcal shape (size, depth, etc.). The sex of the subject could be determined with a success rate of 85\%. These results highlight the attractiveness of multivariate recognition models combined with appropriate descriptor selection. The sulci selected by the pipeline are consistent with previous whole-brain studies on sex effects and hemispheric asymmetries.}, - language = {eng}, - number = {4}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Duchesnay, Edouard and Cachia, Arnaud and Roche, Alexis and Rivière, Denis and Cointepas, Yann and Papadopoulos-Orfanos, Dimitri and Zilbovicius, Monica and Martinot, Jean-Luc and Régis, Jean and Mangin, Jean-François}, - month = apr, - year = {2007}, - pmid = {17427742}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Cerebral Cortex, Numerical Analysis, Computer-Assisted, Classification,Sulci,Anatomy,brainvisa}, - pages = {553--565}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - http://brainvisa.info/pdf/duchesnay-TMI07.pdfarticle}, -} - -@article{el_kouby_mr_2005, - title = {{MR} diffusion-based inference of a fiber bundle model from a population of subjects}, - volume = {8}, - abstract = {This paper proposes a method to infer a high level model of the white matter organization from a population of subjects using MR diffusion imaging. This method takes as input for each subject a set of trajectories stemming from any tracking algorithm. Then the inference results from two nested clustering stages. The first clustering converts each individual set of trajectories into a set of bundles supposed to represent large white matter pathways. The second clustering matches these bundles across subjects in order to provide a list of candidates for the bundle model. The method is applied on a population of eleven subjects and leads to the inference of 17 such candidates.}, - language = {eng}, - number = {Pt 1}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {El Kouby, V. and Cointepas, Y. and Poupon, C. and Rivière, D. and Golestani, N. and Poline, J. B. and Le Bihan, D. and Mangin, J. F.}, - year = {2005}, - pmid = {16685846}, - keywords = {Algorithms, Artificial Intelligence, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Diffusion Magnetic Resonance Imaging, Nerve Fibers, Myelinated, Spatial normalization, human brain, propagation, tracking}, - pages = {196--204}, - annote = {The following values have no corresponding Zotero field:auth-address: CEA, Serv Hosp Frederic Joliot, F-91401 Orsay, France. INSERM U562, Orsay, France. Inst Fed Rech 49 Imagerie Neurofonctionnelle, Paris, France.accession-num: ISI:000233337000025label: ACLcustom1: NeuroSpin}, - annote = {Unati - ISI Document Delivery No.: BDG20Times Cited: 3Cited Reference Count: 20LECTURE NOTES IN COMPUTER SCIENCEEnglishProceedings Paper0302-9743}, -} - -@article{perrin_connectivity-based_2008, - title = {Connectivity-based parcellation of the cortical mantle using q-ball diffusion imaging}, - volume = {2008}, - issn = {1687-4188}, - doi = {10.1155/2008/368406}, - abstract = {This paper exploits the idea that each individual brain region has a specific connection profile to create parcellations of the cortical mantle using MR diffusion imaging. The parcellation is performed in two steps. First, the cortical mantle is split at a macroscopic level into 36 large gyri using a sulcus recognition system. Then, for each voxel of the cortex, a connection profile is computed using a probabilistic tractography framework. The tractography is performed from q fields using regularized particle trajectories. Fiber ODF are inferred from the q-balls using a sharpening process focusing the weight around the q-ball local maxima. A sophisticated mask of propagation computed from a T1-weighted image perfectly aligned with the diffusion data prevents the particles from crossing the cortical folds. During propagation, the particles father child particles in order to improve the sampling of the long fascicles. For each voxel, intersection of the particle trajectories with the gyri lead to a connectivity profile made up of only 36 connection strengths. These profiles are clustered on a gyrus by gyrus basis using a K-means approach including spatial regularization. The reproducibility of the results is studied for three subjects using spatial normalization.}, - language = {eng}, - journal = {International Journal of Biomedical Imaging}, - author = {Perrin, Muriel and Cointepas, Yann and Cachia, Arnaud and Poupon, Cyril and Thirion, Bertrand and Rivière, Denis and Cathier, Pascal and El Kouby, Vincent and Constantinesco, André and Le Bihan, Denis and Mangin, Jean-François}, - year = {2008}, - pmid = {18401457}, - pmcid = {PMC2288697}, - pages = {368406}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - articleMH212867}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/V7E6EEAV/Perrin et al. - 2008 - Connectivity-based parcellation of the cortical ma.pdf:application/pdf}, -} - -@article{operto_cati:_2016, - title = {{CATI}: {A} {Large} {Distributed} {Infrastructure} for the {Neuroimaging} of {Cohorts}}, - volume = {14}, - issn = {1559-0089}, - shorttitle = {{CATI}}, - doi = {10.1007/s12021-016-9295-8}, - abstract = {This paper provides an overview of CATI, a platform dedicated to multicenter neuroimaging. Initiated by the French Alzheimer's plan (2008-2012), CATI is a research project called on to provide service to other projects like an industrial partner. Its core mission is to support the neuroimaging of large populations, providing concrete solutions to the increasing complexity involved in such projects by bringing together a service infrastructure, the know-how of its expert academic teams and a large-scale, harmonized network of imaging facilities. CATI aims to make data sharing across studies easier and promotes sharing as much as possible. In the last 4 years, CATI has assisted the clinical community by taking charge of 35 projects so far and has emerged as a recognized actor at the national and international levels.}, - language = {eng}, - number = {3}, - journal = {Neuroinformatics}, - author = {Operto, Grégory and Chupin, Marie and Batrancourt, Bénédicte and Habert, Marie-Odile and Colliot, Olivier and Benali, Habib and Poupon, Cyril and Champseix, Catherine and Delmaire, Christine and Marie, Sullivan and Rivière, Denis and Pélégrini-Issac, Mélanie and Perlbarg, Vincent and Trebossen, Régine and Bottlaender, Michel and Frouin, Vincent and Grigis, Antoine and Orfanos, Dimitri Papadopoulos and Dary, Hugo and Fillon, Ludovic and Azouani, Chabha and Bouyahia, Ali and Fischer, Clara and Edward, Lydie and Bouin, Mathilde and Thoprakarn, Urielle and Li, Jinpeng and Makkaoui, Leila and Poret, Sylvain and Dufouil, Carole and Bouteloup, Vincent and Chételat, Gaël and Dubois, Bruno and Lehéricy, Stéphane and Mangin, Jean-François and Cointepas, Yann and {CATI Consortium}}, - year = {2016}, - pmid = {27066973}, - keywords = {Humans, Neuroimaging, Information Dissemination, Data sharing, Computational Biology, Large-scale studies, Multicenter protocols, Multicenter Studies as Topic, Neuroimaging biomarkers, Workflow, Data Mining, Data mining}, - pages = {253--264}, - annote = {The following values have no corresponding Zotero field:number: 3}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QWHI6VJG/Operto et al. - 2016 - CATI A Large Distributed Infrastructure for the N.pdf:application/pdf}, -} - -@article{gesierich_features_2016, - title = {Features and {Determinants} of {Lacune} {Shape}: {Relationship} {With} {Fiber} {Tracts} and {Perforating} {Arteries}}, - volume = {47}, - issn = {1524-4628}, - shorttitle = {Features and {Determinants} of {Lacune} {Shape}}, - doi = {10.1161/STROKEAHA.116.012779}, - abstract = {BACKGROUND AND PURPOSE: Lacunes are a major manifestation of cerebral small vessel disease. Although still debated, the morphological features of lacunes may offer mechanistic insights. We systematically analyzed the shape of incident lacunes in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, a genetically defined small vessel disease. -METHODS: A total of 88 incident lacunes from 57 patients were segmented from 3-dimensional T1 magnetic resonance images and 3 dimensionally reconstructed. Anatomic location, diameter, volume, surface area, and compactness of lacunes were assessed. The shape was analyzed using a size, orientation, and position invariant spectral shape descriptor. We further investigated the relationship with perforating arteries and fiber tracts. -RESULTS: Lacunes were most abundant in the centrum semiovale and the basal ganglia. Diameter, volume, and surface area of lacunes in the basal ganglia and centrum semiovale were larger than in other brain regions. The spectral shape descriptor revealed a continuum of shapes with no evidence for distinct classes of lacunes. Shapes varied mostly in elongation and planarity. The main axis and plane of lacunes were found to align with the orientation of perforating arteries but not with fiber tracts. -CONCLUSIONS: Elongation and planarity are the primary shape principles of lacunes. Their main axis and plane align with perforating arteries. Our findings add to current concepts on the mechanisms of lacunes.}, - language = {eng}, - number = {5}, - journal = {Stroke}, - author = {Gesierich, Benno and Duchesnay, Edouard and Jouvent, Eric and Chabriat, Hugues and Schmidt, Reinhold and Mangin, Jean-Francois and Duering, Marco and Dichgans, Martin}, - year = {2016}, - pmid = {27048698}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Basal Ganglia, Middle Aged, Aged, CADASIL, White Matter, cerebral small vessel diseases, neuroimaging, magnetic resonance imaging, Aftercare}, - pages = {1258--1264}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JF7ZBKIR/Gesierich et al. - 2016 - Features and Determinants of Lacune Shape Relatio.pdf:application/pdf}, -} - -@article{jouvent_prediction_2016, - title = {Prediction of 3-year clinical course in {CADASIL}}, - volume = {87}, - issn = {1526-632X}, - doi = {10.1212/WNL.0000000000003252}, - abstract = {OBJECTIVE: To obtain simple models predicting disease evolution at 3 years for a given patient with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). -METHODS: Based on data obtained in a prospective study of 236 patients, we built and validated models predicting, at the individual level, 3-year changes in Mini-Mental State Examination (MMSE), Mattis Dementia Rating Scale (MDRS), Trail Making Test version B (TMTB), and modified Rankin Scale (mRS). These models were based on different sets of predictors obtained at baseline, including either clinical data (epidemiologic data and cardiovascular risk factors) or clinical data and quantitative MRI markers (volume of lacunes [LLV], volume of white matter hyperintensities, normalized brain volume [BPF], number of microbleeds). The Bayesian information criterion (BIC) and the coefficient of determination (R2) were used to determine models with the highest predictive ability and the lowest numbers of predictors. -RESULTS: We obtained validated models with a demonstrated ability to predict, for a given patient, 3-year changes in MMSE, MDRS, TMTB, and mRS (R2 on independent samples: 0.22, 0.12, 0.09, and 0.17, respectively). In all cases, the best models according to R2 and BIC values included only the baseline values of the outcome, of BPF, and of LLV. Inclusion of other potential predictors always led to a loss of generalizability. -CONCLUSIONS: The prediction of 3-year changes in MMSE, MDRS, TMTB, and mRS for a given patient with CADASIL can be obtained using simple models relying only on the initial values of the considered score, BPF, and LLV.}, - language = {eng}, - number = {17}, - journal = {Neurology}, - author = {Jouvent, Eric and Duchesnay, Edouard and Hadj-Selem, Foued and De Guio, François and Mangin, Jean-François and Hervé, Dominique and Duering, Marco and Ropele, Stefan and Schmidt, Reinhold and Dichgans, Martin and Chabriat, Hugues}, - month = oct, - year = {2016}, - pmid = {27694265}, - pmcid = {PMC5089530}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Neuropsychological Tests, Predictive Value of Tests, Young Adult, Middle Aged, Linear Models, Aged, CADASIL, Disease Progression, Longitudinal Studies, Retrospective Studies, Severity of Illness Index, Bayes Theorem, France, Germany, Mental Status Schedule}, - pages = {1787--1795}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DE3KY35Q/Jouvent et al. - 2016 - Prediction of 3-year clinical course in CADASIL.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CEUKXX7Z/1787.html:text/html;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EG77RT9X/1787.html:text/html}, -} - -@article{reiner_sulcal_2012, - title = {Sulcal span in {Azheimer}'s disease, amnestic mild cognitive impairment, and healthy controls}, - volume = {29}, - issn = {1875-8908}, - doi = {10.3233/JAD-2012-111622}, - abstract = {Differences of cortical morphology between healthy controls (HC), amnestic mild cognitive impairment (MCI), and Alzheimer's disease (AD) have been repeatedly investigated using voxel-based morphometry (VBM). However, the results obtained using mainly VBM remain difficult to interpret as they can be explained by various mechanisms. The aim of the present study was to evaluate the differences of cortical morphology between HC, MCI, and AD patients using a new post-processing method based on reconstruction and identification of cortical sulci. Thirty HC, 33 MCI, and 30 AD patients were randomly selected from the ADNI database. For each subject, cortical sulci were reconstructed and automatically identified using Brainvisa software. Depth and fold opening of nine large sulci were compared between HC, MCI, and AD patients. Fold opening of parietaloccipital fissure and intraparietal sulcus on both sides strongly differed between the 3 groups, with gradual increase from HC to MCI of about 1 mm and from MCI to AD of about 2 mm (right intraparietal: p = 0.005; left intraparietal: p = 0.004; right parietaloccipital: p = 0.003; left parietaloccipital: p = 0.0009). Results were left unchanged after adjustment for age, gender, and level of education. These variables were also strongly linked to neuropsychological scores, independent of age, gender, and level of education. In the present study, we found important regional differences of cortical morphology with gradual deterioration from HC to MCI to AD. The most important differences were found in parietaloccipital fissure and intraparietal sulcus. Further studies are needed to understand the involved underlying mechanisms.}, - language = {eng}, - number = {3}, - journal = {Journal of Alzheimer's disease: JAD}, - author = {Reiner, Peggy and Jouvent, Eric and Duchesnay, Edouard and Cuingnet, Rémi and Mangin, Jean-François and Chabriat, Hugues and {Alzheimer's Disease Neuroimaging Initiative}}, - year = {2012}, - pmid = {22297645}, - keywords = {Humans, Magnetic Resonance Imaging, Brain Mapping, Image Processing, Computer-Assisted, Alzheimer Disease, Female, Male, Neuropsychological Tests, Cerebral Cortex, Middle Aged, Aged, Aged, 80 and over, Mild Cognitive Impairment, Educational Status, Cognitive Dysfunction}, - pages = {605--613}, -} - -@article{jouvent_shape_2016, - title = {Shape of the {Central} {Sulcus} and {Disability} {After} {Subcortical} {Stroke}: {A} {Motor} {Reserve} {Hypothesis}}, - volume = {47}, - issn = {1524-4628}, - shorttitle = {Shape of the {Central} {Sulcus} and {Disability} {After} {Subcortical} {Stroke}}, - doi = {10.1161/STROKEAHA.115.012562}, - abstract = {BACKGROUND AND PURPOSE: Both brain and cognitive reserves modulate the clinical impact of chronic brain diseases. Whether a motor reserve also modulates the relationships between stroke and disability is unknown. We aimed to determine whether the shape of the central sulcus, a marker of the development of underlying motor connections, is independently associated with disability in patients with a positive history of small subcortical ischemic stroke. -METHODS: Shapes of central sulci were reconstructed from high-resolution magnetic resonance imaging and ordered without supervision according to a validated algorithm in 166 patients with a positive history of small subcortical ischemic stroke caused by CADASIL (Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy), a severe monogenic cerebral small vessel disease affecting young patients. Ordinal logistic regression modeling was used to test the relationships between modified Rankin scale, a disability scale strongly weighted toward motor disability, and sulcal shape. -RESULTS: Modified Rankin scale was strongly associated with sulcal shape, independent of age, sex, and level of education (proportional odds ratio =1.19, 95\% confidence interval =1.06-1.35; P=0.002). Results remained significant after further adjustment for brain atrophy, volume of lacunes, and volume of white matter hyperintensities of presumed vascular origin. -CONCLUSIONS: The severity of disability in patients with a positive history of small subcortical ischemic stroke caused by a severe cerebral small vessel disease is related to the shape of the central sulcus, independently of the main determinants of disability. These results support the concept of a motor reserve that could modulate the clinical severity in patients with a positive history of small subcortical ischemic stroke.}, - language = {eng}, - number = {4}, - journal = {Stroke}, - author = {Jouvent, Eric and Sun, Zhong Yi and De Guio, François and Duchesnay, Edouard and Duering, Marco and Ropele, Stefan and Dichgans, Martin and Mangin, Jean-François and Chabriat, Hugues}, - month = apr, - year = {2016}, - pmid = {26941259}, - keywords = {Algorithms, Humans, Magnetic Resonance Imaging, Brain Mapping, Image Processing, Computer-Assisted, Adult, Female, Male, Cerebral Cortex, Middle Aged, Aged, Atrophy, CADASIL, White Matter, central sulcus, motor reserve, stroke, Stroke, Recovery of Function, cerebral cortex}, - pages = {1023--1029}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/MVY5J3R3/1023.html:text/html}, -} - -@article{duchesnay_different_2018, - title = {Different {Types} of {White} {Matter} {Hyperintensities} in {CADASIL}}, - volume = {9}, - issn = {1664-2295}, - doi = {10.3389/fneur.2018.00526}, - abstract = {Objective: In CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), white matter hyperintensities (WMH) are considered to result from hypoperfusion. We hypothesized that in fact the burden of WMH results from the combination of several regional populations of WMH with different mechanisms and clinical consequences. Methods: To identify regional WMH populations, we used a 4-step approach. First, we used an unsupervised principal component algorithm to determine, without a priori knowledge, the main sources of variation of the global spatial pattern of WMH. Thereafter, to determine whether these sources are likely to include relevant information regarding regional populations of WMH, we tested their relationships with: (1) MRI markers of the disease; (2) the clinical severity assessed by the Mattis Dementia Rating scale (MDRS) (cognitive outcome) and the modified Rankin's score (disability outcome). Finally, through careful interpretation of all the results, we tried to identify different regional populations of WMH. Results: The unsupervised principal component algorithm identified 3 main sources of variation of the global spatial pattern of WMH, which showed significant and sometime inverse relationships with MRI markers and clinical scores. The models predicting clinical severity based on these sources outperformed those evaluating WMH by their volume (MDRS, coefficient of determination of 39.0 vs. 35.3\%, p = 0.01; modified Rankin's score, 43.7 vs. 38.1\%, p = 0.001). By carefully interpreting the visual aspect of these sources as well as their relationships with MRI markers and clinical severity, we found strong arguments supporting the existence of different regional populations of WMH. For instance, in multivariate analyses, larger extents of WMH in anterior temporal poles and superior frontal gyri were associated with better outcomes, while larger extents of WMH in pyramidal tracts were associated with worse outcomes, which could not be explained if WMH in these different areas shared the same mechanisms. Conclusion: The results of the present study support the hypothesis that the whole extent of WMH results from a combination of different regional populations of WMH, some of which are associated, for yet undetermined reasons, with milder forms of the disease.}, - language = {eng}, - journal = {Frontiers in Neurology}, - author = {Duchesnay, Edouard and Hadj Selem, Fouad and De Guio, François and Dubois, Mathieu and Mangin, Jean-François and Duering, Marco and Ropele, Stefan and Schmidt, Reinhold and Dichgans, Martin and Chabriat, Hugues and Jouvent, Eric}, - year = {2018}, - pmid = {30042721}, - pmcid = {PMC6048276}, - keywords = {CADASIL, cerebral small vessel disease, white matter hyperintensities, Cerebral Small Vessel Diseases, brain atrophy, lacunes, white matter hyperintensities (WMH), White Matter Integrity, clinical severity, white matter changes}, - pages = {526}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YCRAGYJM/Duchesnay et al. - 2018 - Different Types of White Matter Hyperintensities i.pdf:application/pdf}, -} - -@article{borne_automatic_2020, - title = {Automatic labeling of cortical sulci using patch- or {CNN}-based segmentation techniques combined with bottom-up geometric constraints}, - volume = {62}, - issn = {1361-8415}, - url = {https://www.sciencedirect.com/science/article/pii/S1361841520300189}, - doi = {10.1016/j.media.2020.101651}, - abstract = {The extreme variability of the folding pattern of the human cortex makes the recognition of cortical sulci, both automatic and manual, particularly challenging. Reliable identification of the human cortical sulci in its entirety, is extremely difficult and is practiced by only a few experts. Moreover, these sulci correspond to more than a hundred different structures, which makes manual labeling long and fastidious and therefore limits access to large labeled databases to train machine learning. Here, we seek to improve the current model proposed in the Morphologist toolbox, a widely used sulcus recognition toolbox included in the BrainVISA package. Two novel approaches are proposed: patch-based multi-atlas segmentation (MAS) techniques and convolutional neural network (CNN)-based approaches. Both are currently applied for anatomical segmentations because they embed much better representations of inter-subject variability than approaches based on a single template atlas. However, these methods typically focus on voxel-wise labeling, disregarding certain geometrical and topological properties of interest for sulcus morphometry. Therefore, we propose to refine these approaches with domain specific bottom-up geometric constraints provided by the Morphologist toolbox. These constraints are utilized to provide a single sulcus label to each topologically elementary fold, the building blocks of the pattern recognition problem. To eliminate the shortcomings associated with the Morphologist’s pre-segmentation into elementary folds, we complement this regularization scheme using a top-down perspective which triggers an additional cleavage of the elementary folds when required. All the newly proposed models outperform the current Morphologist model, the most efficient being a CNN U-Net-based approach which carries out sulcus recognition within a few seconds.}, - urldate = {2024-02-28}, - journal = {Medical Image Analysis}, - author = {Borne, Léonie and Rivière, Denis and Mancip, Martial and Mangin, Jean-François}, - month = may, - year = {2020}, - keywords = {Convolutional neural network, Cortical sulci labeling, Multi-atlas segmentation}, - pages = {101651}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NUHX6KJT/Borne et al. - 2020 - Automatic labeling of cortical sulci using patch- .pdf:application/pdf}, -} - -@article{guillon_identification_2024, - title = {Identification of rare cortical folding patterns using unsupervised deep learning}, - volume = {2}, - url = {https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00084/119130}, - urldate = {2024-02-28}, - journal = {Imaging Neuroscience}, - author = {Guillon, Louise and Chavas, Joël and Bénézit, Audrey and Moutard, Marie-Laure and Roca, Pauline and Mellerio, Charles and Oppenheim, Catherine and Rivière, Denis and Mangin, Jean-François}, - year = {2024}, - note = {Publisher: MIT Press One Broadway, 12th Floor, Cambridge, Massachusetts 02142, USA …}, - pages = {1--27}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/KPDXLXWK/Guillon et al. - 2024 - Identification of rare cortical folding patterns u.pdf:application/pdf}, -} - -@article{de_vareilles_development_2023, - title = {Development of cortical folds in the human brain: {An} attempt to review biological hypotheses, early neuroimaging investigations and functional correlates}, - volume = {61}, - issn = {1878-9293}, - shorttitle = {Development of cortical folds in the human brain}, - url = {https://www.sciencedirect.com/science/article/pii/S1878929323000543}, - doi = {10.1016/j.dcn.2023.101249}, - abstract = {The folding of the human brain mostly takes place in utero, making it challenging to study. After a few pioneer studies looking into it in post-mortem foetal specimen, modern approaches based on neuroimaging have allowed the community to investigate the folding process in vivo, its normal progression, its early disturbances, and its relationship to later functional outcomes. In this review article, we aimed to first give an overview of the current hypotheses on the mechanisms governing cortical folding. After describing the methodological difficulties raised by its study in fetuses, neonates and infants with magnetic resonance imaging (MRI), we reported our current understanding of sulcal pattern emergence in the developing brain. We then highlighted the functional relevance of early sulcal development, through recent insights about hemispheric asymmetries and early factors influencing this dynamic such as prematurity. Finally, we outlined how longitudinal studies have started to relate early folding markers and the child’s sensorimotor and cognitive outcome. Through this review, we hope to raise awareness on the potential of studying early sulcal patterns both from a fundamental and clinical perspective, as a window into early neurodevelopment and plasticity in relation to growth in utero and postnatal environment of the child.}, - urldate = {2024-02-28}, - journal = {Developmental Cognitive Neuroscience}, - author = {de Vareilles, H. and Rivière, D. and Mangin, JF and Dubois, J.}, - month = jun, - year = {2023}, - keywords = {MRI, Gyrification, Prematurity, Fetuses, Neonates, Sulcus}, - pages = {101249}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LJBIPQPW/S1878929323000543.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/XHTRBKJ8/de Vareilles et al. - 2023 - Development of cortical folds in the human brain .pdf:application/pdf}, -} - -@inproceedings{pizzagalli_sulcal-based_2018, - title = {Sulcal-based morphometry in {Parkinson}’s disease: a study of reliability and disease effects}, - volume = {10975}, - shorttitle = {Sulcal-based morphometry in {Parkinson}’s disease}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10975/109750T/Sulcal-based-morphometry-in-Parkinsons-disease--a-study-of/10.1117/12.2511590.full}, - doi = {10.1117/12.2511590}, - abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder in which patients show progressively worsening motor symptoms, often followed by cognitive impairment and dementia. Brain MRI can be used to identify patterns of neurodegeneration that are characteristic of PD, but the spatial pattern of brain abnormalities is still not well understood. “Sulcus-based morphometry” provides measures of the cortical fissures of the brain that reflect degenerative changes in relation to neuropsychiatric disease. Extracting sulci requires good contrast between the gray matter and the CSF, and less well-defined sulci may be difficult to extract reliably. Before embarking on a study of sulcal abnormalities in PD, we set out to determine the reliability of measures from 123 sulci, defined by an existing atlas, using publicly available test-retest data from 8 cohorts. Of the 123 atlas-defined sulci, several major sulci were broken down into smaller regions (e.g., the superior temporal sulcus was divided into the main STS, the anterior terminal ascending branch of STS and the posterior terminal ascending branch of STS); we assessed reliability in each individually, and after merging the portions of the sulci together, in a newly defined, concatenated atlas. For 467 subjects from the PPMI cohort (http://www.ppmiinfo. org ;age range: 61.5 \± 10.1 years), we segmented and labeled major sulci and extracted 4 shape descriptors for each: length, depth, surface area, and width. We then aimed to establish the profile of case-control differences for 3 candidate sulci of interest: the central sulcus, superior temporal sulcus and the calcarine fissure. These sulci were among the more robust in terms of reproducibility; we found that the calcarine width was associated with PD, offering new features for genetic and interventional studies of PD.}, - urldate = {2024-02-28}, - booktitle = {14th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Pizzagalli, Fabrizio and Auzias, Guillaume and Amini, Armand and Faskowitz, Joshua and Rashid, Faisal and Moyer, Daniel and Kochunov, Peter and Rivière, Denis and Mangin, Jean-François and Thompson, Paul M. and Jahanshad, Neda}, - month = dec, - year = {2018}, - pages = {246--255}, -} - -@inproceedings{de_vareilles_folding_2019, - title = {Folding dynamics of the {Central} {Sulcus}: a longitudinal study on preterms {Authors}: {Introduction}}, - shorttitle = {Folding dynamics of the {Central} {Sulcus}}, - url = {https://hal.science/hal-02876130/file/HeloiseOHBM.pdf}, - urldate = {2024-02-28}, - author = {de Vareilles, Héloïse and yi Sun, Zhong and Benders, Manon and Fischer, Clara and Leroy, François and de Vries, Linda and Groenendaal, Floris and Rivière, Denis and Dubois, Jessica and Mangin, Jean-François}, - year = {2019}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/US3IZCLW/de Vareilles et al. - 2019 - Folding dynamics of the Central Sulcus a longitud.pdf:application/pdf}, -} - -@inproceedings{guevara_identification_2019, - address = {Cham}, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {Identification of {U}-{Bundles} {Based} on {Sulcus} {Morphology}}, - isbn = {978-3-030-13835-6}, - doi = {10.1007/978-3-030-13835-6_1}, - abstract = {It is a fact that the brain cortical folding pattern morphology is specific to each human being. Neuroanatomists think that the folding pattern is strongly related to brain connectivity [1]. As each folding variation implies a specific rearrangement of the different white matter bundles, it also impacts the position of functional regions. This particularity raises an issue for precise brain spatial normalization, as nobody knows how to align brains with different folding patterns. For this reason, in the field of brain segmentation, old fashion approaches relying on a single model, often generated from a single subject or a group’s average, cannot overcome the folding variability. Therefore, modern strategies are often built from a multi-subject atlas, which has proven to be a very efficient solution to overcome this difficulty [2]. In order to design an analogous solution for brain mapping, it was recently proposed to restrict statistical analysis to groups of subjects with compatible folding pattern [3], which has been experimented to deal with the impact of the central sulcus morphology on fMRI-based activation maps [4]. Differences in the cortical folding have been proved to be associated with differences in the localization of functional areas. Therefore, we need to understand better how to relate to each other brains with different folding patterns. In this abstract, we propose a new step in this direction: we performed a first attempt to observe an effect of a simple morphological polymorphism related to central sulcus on the underlying U-fiber organization.}, - language = {en}, - booktitle = {Processing and {Analysis} of {Biomedical} {Information}}, - publisher = {Springer International Publishing}, - author = {Guevara, M. and Sun, Z. Y. and Guevara, P. and Rivière, D. and Poupon, C. and Mangin, J.-F.}, - editor = {Lepore, Natasha and Brieva, Jorge and Romero, Eduardo and Racoceanu, Daniel and Joskowicz, Leo}, - year = {2019}, - pages = {3--7}, -} - -@inproceedings{rolland_exploring_2019, - title = {Exploring {Microstructure} {Asymmetries} in the {Infant} {Brain} {Cortex}: {A} {Methodological} {Framework} {Combining} {Structural} and {Diffusion} {Mri}}, - shorttitle = {Exploring {Microstructure} {Asymmetries} in the {Infant} {Brain} {Cortex}}, - url = {https://ieeexplore.ieee.org/abstract/document/8759421}, - doi = {10.1109/ISBI.2019.8759421}, - abstract = {The development of the human brain is a complex process that starts during early pregnancy and extends until the end of adolescence. In parallel to morphological changes in brain size and gyrification, several microstructural changes occur in the cortex, such as the development of dendritic arborization, synaptogenesis and pruning, and fiber myelination. Magnetic Resonance Imaging (MRI) can provide indirect markers of these mechanisms through the mapping of quantitative parameters. Here, we used a dedicated methodological framework to perform reliable voxel-wise analyses over the infant cortex. The examination of hemispheric asymmetries in microstructure required careful alignment of morphological asymmetries through registration of native and flipped brains using a 2-step matching strategy of sulci (DISCO approach) and cortical ribbon (DAR℡ approach). We tested the potential of this approach in 1-to-5-month-old infants, with a focus on cortical longitudinal diffusivity from Diffusion Tensor Imaging (DTI). This enabled us to unravel different microstructural evolution patterns of specific sensorimotor and language regions in the left and right hemispheres.}, - urldate = {2024-02-28}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Rolland, C. and Lebenberg, J. and Leroy, F. and Moulton, E. and Adibpour, P. and Rivière, D. and Poupon, C. and Hertz-Pannier, L. and Mangin, J.-F. and Dehaene-Lambertz, G. and Dubois, J.}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {structural MRI, Reliability, Artificial intelligence, Diffusion tensor imaging, Microstructure, Pediatrics, diffusion tensor imaging DTI, cortical maturation, Developing brain, infants, Surface morphology}, - pages = {426--429}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UXMS7YIH/8759421.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/99P92Z8V/Rolland et al. - 2019 - Exploring Microstructure Asymmetries in the Infant.pdf:application/pdf}, -} - -@inproceedings{de_vareilles_longitudinal_2019, - address = {Cham}, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {A {Longitudinal} {Study} of the {Evolution} of the {Central} {Sulcus}’ {Shape} in {Preterm} {Infants} {Using} {Manifold} {Learning}}, - isbn = {978-3-030-32875-7}, - doi = {10.1007/978-3-030-32875-7_16}, - abstract = {Cortical folding in humans is different for every individual, and is associated with functional specificities. It forms mainly during the last trimester of pregnancy, hence its development lacks description, especially in a longitudinal way. To cope with this issue, this study focused on the evolution of the central sulcus’ variability of 71 preterm infants studied longitudinally with MRI at 30 and 40 weeks (w) postmenstrual age (PMA). Our aim was to investigate the main shape characteristics and whether they are encoded early on or appear closer to term birth. We captured shape dissimilarity between the sulci using a distance matrix after pairwise co-registration using an Iterative Closest Point algorithm. We applied non-linear dimensionality reduction to this matrix using the Isomap algorithm in order to capture the most discriminative shape features among the central sulci. We characterized the three most discriminative features over the group, and found that the sulci evolved consistently from a given feature at 30w PMA to the 40w PMA equivalent feature. We incidentally captured a feature that could coincide with the most discriminative adult feature, both visually and by its asymmetry in left and right sulcal distribution. These results captured the main shape features of the central sulcus in preterm infants and suggest that they are already encoded at 30w PMA.}, - language = {en}, - booktitle = {Smart {Ultrasound} {Imaging} and {Perinatal}, {Preterm} and {Paediatric} {Image} {Analysis}}, - publisher = {Springer International Publishing}, - author = {de Vareilles, Héloïse and Sun, Zhongyi and Benders, Manon and Fischer, Clara and Leroy, François and de Vries, Linda and Groenendaal, Floris and Rivière, Denis and Dubois, Jessica and Mangin, Jean-François}, - editor = {Wang, Qian and Gomez, Alberto and Hutter, Jana and McLeod, Kristin and Zimmer, Veronika and Zettinig, Oliver and Licandro, Roxane and Robinson, Emma and Christiaens, Daan and Turk, Esra Abaci and Melbourne, Andrew}, - year = {2019}, - keywords = {Brain MRI, Preterm infants, Central sulcus, Cortical development}, - pages = {143--152}, -} - -@inproceedings{borne_combining_2019, - title = {Combining {3D} {U}-{Net} and bottom-up geometric constraints for automatic cortical sulci recognition}, - url = {https://openreview.net/forum?id=ryl0VTZCtV}, - abstract = {While the limits of deep learning are still to be clarified, some problems may benefit from a mixed approach combining CNNs with traditional strategies. For instance, bottom-up representations embedding domain-specific knowledge could help to regularise a voxelwise segmentation. In this paper, we propose such an approach dedicated to the automatic recognition of the human cortical sulci, designed as the labelling of the voxels of a skeleton of the fluid surrounding the brain. Deep learning is used to provide a top-down perspective to a classical bottom-up pattern recognition system. Our original approach is compared with the approach proposed in the BrainVISA package (www.brainvisa.info), the most used sulcus recognition toolbox. As far as we know, this is the first time that CNNs is used for sulcus recognition. We show that our approach outperforms the BrainVISA method.}, - language = {en}, - urldate = {2024-02-28}, - author = {Borne, Léonie and Rivière, Denis and Mangin, Jean-François}, - month = apr, - year = {2019}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FIVNUT6R/Borne et al. - 2019 - Combining 3D U-Net and bottom-up geometric constra.pdf:application/pdf}, -} - -@article{lizarazu_neural_2021, - title = {Neural entrainment to speech and nonspeech in dyslexia: {Conceptual} replication and extension of previous investigations}, - volume = {137}, - issn = {0010-9452}, - shorttitle = {Neural entrainment to speech and nonspeech in dyslexia}, - url = {https://www.sciencedirect.com/science/article/pii/S0010945221000265}, - doi = {10.1016/j.cortex.2020.12.024}, - abstract = {Whether phonological deficits in developmental dyslexia are associated with impaired neural sampling of auditory information is still under debate. Previous findings suggested that dyslexic participants showed atypical neural entrainment to slow and/or fast temporal modulations in speech, which might affect prosodic/syllabic and phonemic processing respectively. However, the large methodological variations across these studies do not allow us to draw clear conclusions on the nature of the entrainment deficit in dyslexia. Using magnetoencephalography, we measured neural entrainment to nonspeech and speech in both groups. We first aimed to conceptually replicate previous studies on auditory entrainment in dyslexia, using the same measurement methods as in previous studies, and also using new measurement methods (cross-correlation analyses) to better characterize the synchronization between stimulus and brain response. We failed to observe any of the significant group differences that had previously been reported in delta, theta and gamma frequency bands, whether using speech or nonspeech stimuli. However, when analyzing amplitude cross-correlations between noise stimuli and brain responses, we found that control participants showed larger responses than dyslexic participants in the delta range in the right hemisphere and in the gamma range in the left hemisphere. Overall, our results are weakly consistent with the hypothesis that dyslexic individuals show an atypical entrainment to temporal modulations. Our attempt at replicating previously published results highlights the multiple weaknesses of this research area, particularly low statistical power due to small sample size, and the lack of methodological standards inducing considerable heterogeneity of measurement and analysis methods across studies.}, - urldate = {2024-02-28}, - journal = {Cortex}, - author = {Lizarazu, Mikel and Scotto di Covella, Lou and van Wassenhove, Virginie and Rivière, Denis and Mizzi, Raphael and Lehongre, Katia and Hertz-Pannier, Lucie and Ramus, Franck}, - month = apr, - year = {2021}, - keywords = {Magnetoencephalography, Dyslexia, Auditory processing, Neural oscillations, Speech}, - pages = {160--178}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/N55AEZ35/S0010945221000265.html:text/html;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AC55TRE5/Lizarazu et al. - 2021 - Neural entrainment to speech and nonspeech in dysl.pdf:application/pdf}, -} - -@inproceedings{guillon_detection_2021, - address = {Cham}, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {Detection of {Abnormal} {Folding} {Patterns} with {Unsupervised} {Deep} {Generative} {Models}}, - isbn = {978-3-030-87586-2}, - doi = {10.1007/978-3-030-87586-2_7}, - abstract = {Although the main structures of cortical folding are present in each human brain, the folding pattern is unique to each individual. Because of this large normal variability, the identification of abnormal patterns associated to developmental disorders is a complex open challenge. In this paper, we tackle this problem as an anomaly detection task and explore the potential of deep generative models using benchmarks made up of synthetic anomalies. To focus learning on the folding geometry, brain MRI are preprocessed first to deal only with a skeleton-based negative cast of the cortex. A variational auto-encoder is trained to get a representation of the regional variability of the folding pattern of the general population. Then several synthetic benchmark datasets of abnormalities are designed. The latent space expressivity is assessed through classification experiments between control’s and abnormal’s latent codes. Finally, the properties encoded in the latent space are analyzed through perturbation of specific latent dimensions and observation of the resulting modification of the reconstructed images. The results have shown that the latent representation is rich enough to distinguish subtle differences like asymmetries between the right and left hemispheres.}, - language = {en}, - booktitle = {Machine {Learning} in {Clinical} {Neuroimaging}}, - publisher = {Springer International Publishing}, - author = {Guillon, Louise and Cagna, Bastien and Dufumier, Benoit and Chavas, Joël and Rivière, Denis and Mangin, Jean-François}, - editor = {Abdulkadir, Ahmed and Kia, Seyed Mostafa and Habes, Mohamad and Kumar, Vinod and Rondina, Jane Maryam and Tax, Chantal and Wolfers, Thomas}, - year = {2021}, - keywords = {Cortical folding, Anomaly detection, Anomaly benchmark, Brain architecture, Variational autoencoder}, - pages = {63--72}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/2C3GKHKT/Guillon et al. - 2021 - Detection of Abnormal Folding Patterns with Unsupe.pdf:application/pdf}, -} - -@article{balzeau_a_2024, - title = {À la recherche des particularités du cerveau d’{Homo} neanderthalensis et d’{Homo} sapiens}, - volume = {36}, - copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, - issn = {0037-8984}, - url = {https://journals.openedition.org/bmsap/12394}, - doi = {10.4000/bmsap.12394}, - abstract = {Étudier le cerveau des humains préhistoriques est complexe du fait de la non fossilisation de cet organe. Des empreintes sur la surface interne du crâne permettent la reconstruction de ce que nous nommons l’endocrâne (le moulage de cette surface). Sur cette base, nous ne disposons que d’un reflet partiel de la morphologie et des dimensions du cerveau, puisque le détail de la correspondance entre cerveau et endocrâne demeure faiblement documenté. C’est l’objectif principal du projet PaleoBrain...}, - language = {fr}, - number = {(s)}, - urldate = {2024-02-28}, - journal = {Bulletins et mémoires de la Société d’Anthropologie de Paris. BMSAP}, - author = {Balzeau, Antoine and Bardinet, Éric and Didier, Mélanie and Giolland, Victor and Labra, Nicole and Leprince, Yann and Mangin, Jean-François and Mounier, Aurélien and Prima, Sylvain and Rivière, Denis and Santin, Mathieu and Filippo, Andréa}, - month = jan, - year = {2024}, - note = {Number: (s) -Publisher: Société d'anthropologie de Paris}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IBDXT7IE/Balzeau et al. - 2024 - À la recherche des particularités du cerveau d’Hom.pdf:application/pdf}, -} - -@article{labra_what_2024, - title = {What do brain endocasts tell us? {A} comparative analysis of the accuracy of sulcal identification by experts and perspectives in palaeoanthropology}, - volume = {244}, - copyright = {© 2023 The Authors. Journal of Anatomy published by John Wiley \& Sons Ltd on behalf of Anatomical Society.}, - issn = {1469-7580}, - shorttitle = {What do brain endocasts tell us?}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.13966}, - doi = {10.1111/joa.13966}, - abstract = {Palaeoneurology is a complex field as the object of study, the brain, does not fossilize. Studies rely therefore on the (brain) endocranial cast (often named endocast), the only available and reliable proxy for brain shape, size and details of surface. However, researchers debate whether or not specific marks found on endocasts correspond reliably to particular sulci and/or gyri of the brain that were imprinted in the braincase. The aim of this study is to measure the accuracy of sulcal identification through an experiment that reproduces the conditions that palaeoneurologists face when working with hominin endocasts. We asked 14 experts to manually identify well-known foldings in a proxy endocast that was obtained from an MRI of an actual in vivo Homo sapiens head. We observe clear differences in the results when comparing the non-corrected labels (the original labels proposed by each expert) with the corrected labels. This result illustrates that trying to reconstruct a sulcus following the very general known shape/position in the literature or from a mean specimen may induce a bias when looking at an endocast and trying to follow the marks observed there. We also observe that the identification of sulci appears to be better in the lower part of the endocast compared to the upper part. The results concerning specific anatomical traits have implications for highly debated topics in palaeoanthropology. Endocranial description of fossil specimens should in the future consider the variation in position and shape of sulci in addition to using models of mean brain shape. Moreover, it is clear from this study that researchers can perceive sulcal imprints with reasonably high accuracy, but their correct identification and labelling remains a challenge, particularly when dealing with extinct species for which we lack direct knowledge of the brain.}, - language = {en}, - number = {2}, - urldate = {2024-02-28}, - journal = {Journal of Anatomy}, - author = {Labra, Nicole and Mounier, Aurélien and Leprince, Yann and Rivière, Denis and Didier, Mélanie and Bardinet, Eric and Santin, Mathieu D. and Mangin, Jean François and Filippo, Andréa and Albessard-Ball, Lou and Beaudet, Amélie and Broadfield, Douglas and Bruner, Emiliano and Carlson, Kristian J. and Cofran, Zachary and Falk, Dean and Gilissen, Emmanuel and Gómez-Robles, Aida and Neubauer, Simon and Pearson, Alannah and Röding, Carolin and Zhang, Yameng and Balzeau, Antoine}, - year = {2024}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/joa.13966}, - keywords = {brain endocast, brain evolution, palaeoneurology, sulcal identification}, - pages = {274--296}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TX6E9643/Labra et al. - 2024 - What do brain endocasts tell us A comparative ana.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EJIRKF87/joa.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8PMYIVZ2/Labra et al. - 2024 - What do brain endocasts tell us A comparative ana.pdf:application/pdf}, -} - -@inproceedings{mendoza_superficial_2023, - address = {Valparaíso, Chile}, - title = {Superficial white matter shape characterization using hierarchical clustering and a multi-subject bundle atlas}, - isbn = {978-1-5106-6254-4 978-1-5106-6255-1}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/2669738/Superficial-white-matter-shape-characterization-using-hierarchical-clustering-and-a/10.1117/12.2669738.full}, - doi = {10.1117/12.2669738}, - urldate = {2024-02-27}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Mendoza, Cristobal and Román, Claudio and Molina, Joaquín and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - editor = {Linguraru, Marius G. and Rittner, Letícia and Lepore, Natasha and Romero Castro, Eduardo and Brieva, Jorge and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {9}, -} - -@article{haeger_imaging_2020, - title = {Imaging the aging brain: study design and baseline findings of the {SENIOR} cohort}, - volume = {12}, - issn = {1758-9193}, - shorttitle = {Imaging the aging brain}, - url = {https://alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1}, - doi = {10.1186/s13195-020-00642-1}, - abstract = {Abstract - - Background - Current demographic trends point towards an aging society entailing increasing occurrence and burden of neurodegenerative diseases. In this context, understanding physiological aging and its turning point into neurodegeneration is essential for the development of possible biomarkers and future therapeutics of brain disease. - - - Methods - The SENIOR study represents a longitudinal, observational study including cognitively healthy elderlies aged between 50 and 70 years old at the time of inclusion, being followed annually over 10 years. Our multimodal protocol includes structural, diffusion, functional, and sodium magnetic resonance imaging (MRI) at 3 T and 7 T, positron emission tomography (PET), blood samples, genetics, audiometry, and neuropsychological and neurological examinations as well as assessment of neuronal risk factors. - - - Results - One hundred forty-two participants (50\% females) were enrolled in the SENIOR cohort with a mean age of 60 (SD 6.3) years at baseline. Baseline results with multiple regression analyses reveal that cerebral white matter lesions can be predicted by cardiovascular and cognitive risk factors and age. Cardiovascular risk factors were strongly associated with juxtacortical and periventricular lesions. Intra-subject across-test variability as a measure of neuropsychological test performance and possible cognitive marker predicts white matter volume and is significantly associated with risk profile. Division of the cohort into subjects with a higher and lower risk profile shows significant differences in intra-subject across-test variability and volumes as well as cortical thickness of brain regions of the temporal lobe. There is no difference between the lower- and higher-risk groups in amyloid load using PET data from a subset of 81 subjects. - - - Conclusions - We here describe the study protocol and baseline findings of the SENIOR observational study which aim is the establishment of integrated, multiparametric maps of normal aging and the identification of early biomarkers for neurodegeneration. We show that intra-subject across-test variability as a marker of neuropsychological test performance as well as age, gender, and combined risk factors influence neuronal decline as represented by decrease in brain volume, cortical thickness, and increase in white matter lesions. Baseline findings will be used as underlying basis for the further implications of aging and neuronal degeneration as well as examination of brain aging under different aspects of brain pathology versus physiological aging.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {Alzheimer's Research \& Therapy}, - author = {Haeger, Alexa and Mangin, Jean-François and Vignaud, Alexandre and Poupon, Cyril and Grigis, Antoine and Boumezbeur, Fawzi and Frouin, Vincent and Deverre, Jean-Robert and Sarazin, Marie and Hertz-Pannier, Lucie and Bottlaender, Michel and {the SENIOR team} and Baron, Christine and Berland, Valérie and Blancho, Nathalie and Desmidt, Séverine and Doublé, Christine and Ginisty, Chantal and Joly-Testault, Véronique and Laurier, Laurence and Lecomte, Yann and Leroy, Claire and Manciot, Christine and Marchand, Stephanie and Mediouni, Gaelle and Millot, Xavier and Monassier, Ludivine and Roger, Séverine and Vuillemard, Catherine}, - month = dec, - year = {2020}, - keywords = {Imaging, Aging, Biomarker, Prevention, Dementia, Neurodegenerative disease, Alzheimer’s disease, Cognitive decline, Intra-person across-test variability}, - pages = {77}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AMRXRWZU/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf;PubMed Central Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/STJTPBIP/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf}, -} - -@article{vazquez_automatic_2020, - title = {Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information}, - volume = {19}, - issn = {1475-925X}, - url = {https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-020-00786-z}, - doi = {10.1186/s12938-020-00786-z}, - abstract = {Abstract - - Background - Diffusion MRI is the preferred non-invasive in vivo modality for the study of brain white matter connections. Tractography datasets contain 3D streamlines that can be analyzed to study the main brain white matter tracts. Fiber clustering methods have been used to automatically group similar fibers into clusters. However, due to inter-subject variability and artifacts, the resulting clusters are difficult to process for finding common connections across subjects, specially for superficial white matter. - - - Methods - We present an automatic method for labeling of short association bundles on a group of subjects. The method is based on an intra-subject fiber clustering that generates compact fiber clusters. Posteriorly, the clusters are labeled based on the cortical connectivity of the fibers, taking as reference the Desikan–Killiany atlas, and named according to their relative position along one axis. Finally, two different strategies were applied and compared for the labeling of inter-subject bundles: a matching with the Hungarian algorithm, and a well-known fiber clustering algorithm, called QuickBundles. - - - Results - Individual labeling was executed over four subjects, with an execution time of 3.6 min. An inspection of individual labeling based on a distance measure showed good correspondence among the four tested subjects. Two inter-subject labeling were successfully implemented and applied to 20 subjects and compared using a set of distance thresholds, ranging from a conservative value of 10 mm to a moderate value of 21 mm. Hungarian algorithm led to a high correspondence, but low reproducibility for all the thresholds, with 96 s of execution time. QuickBundles led to better correspondence, reproducibility and short execution time of 9 s. Hence, the whole processing for the inter-subject labeling over 20 subjects takes 1.17 h. - - - Conclusion - We implemented a method for the automatic labeling of short bundles in individuals, based on an intra-subject clustering and the connectivity of the clusters with the cortex. The labels provide useful information for the visualization and analysis of individual connections, which is very difficult without any additional information. Furthermore, we provide two fast inter-subject bundle labeling methods. The obtained clusters could be used for performing manual or automatic connectivity analysis in individuals or across subjects.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {BioMedical Engineering OnLine}, - author = {Vázquez, Andrea and López-López, Narciso and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Ladra, Susana and Guevara, Pamela}, - month = dec, - year = {2020}, - keywords = {Clustering, Tractography, Fiber bundle, Superficial white matter, Fiber labeling}, - pages = {42}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/89DX6DK5/Vázquez et al. - 2020 - Automatic group-wise whole-brain short association.pdf:application/pdf}, -} - -@article{osorio_abrainvis_2021, - title = {{ABrainVis}: an android brain image visualization tool}, - volume = {20}, - issn = {1475-925X}, - shorttitle = {{ABrainVis}}, - url = {https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-021-00909-0}, - doi = {10.1186/s12938-021-00909-0}, - abstract = {Abstract - - Background - The visualization and analysis of brain data such as white matter diffusion tractography and magnetic resonance imaging (MRI) volumes is commonly used by neuro-specialist and researchers to help the understanding of brain structure, functionality and connectivity. As mobile devices are widely used among users and their technology shows a continuous improvement in performance, different types of applications have been designed to help users in different work areas. - - - Results - We present, ABrainVis, an Android mobile tool that allows users to visualize different types of brain images, such as white matter diffusion tractographies, represented as fibers in 3D, segmented fiber bundles, MRI 3D images as rendered volumes and slices, and meshes. The tool enables users to choose and combine different types of brain imaging data to provide visual anatomical context for specific visualization needs. ABrainVis provides high performance over a wide range of Android devices, including tablets and cell phones using medium and large tractography datasets. Interesting visualizations including brain tumors and arteries, along with fiber, are given as examples of case studies using ABrainVis. - - - Conclusions - The functionality, flexibility and performance of ABrainVis tool introduce an improvement in user experience enabling neurophysicians and neuroscientists fast visualization of large tractography datasets, as well as the ability to incorporate other brain imaging data such as MRI volumes and meshes, adding anatomical contextual information.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {BioMedical Engineering OnLine}, - author = {Osorio, Ignacio and Guevara, Miguel and Bonometti, Danilo and Carrasco, Diego and Descoteaux, Maxime and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = dec, - year = {2021}, - keywords = {Brain imaging, 3D rendering, Mobile visualization}, - pages = {72}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UGZD27KA/Osorio et al. - 2021 - ABrainVis an android brain image visualization to.pdf:application/pdf}, -} - -@inproceedings{deman_intranat_2017, - title = {{INTRANAT} {ELECTRODES}: {A} {FREE} {SOFTWARE} {TO} {VISUALIZE} {SEEG} {DATA} {IN} {PATIENT} {REFERENTIAL} {AND} {INITIATE} {GROUP} {STUDIES}}, - volume = {58}, - shorttitle = {{INTRANAT} {ELECTRODES}}, - url = {https://scholar.google.com/scholar?cluster=11665156421866533739&hl=en&oi=scholarr}, - urldate = {2024-02-28}, - booktitle = {{EPILEPSIA}}, - publisher = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, - author = {Deman, P. and Bhattacharjee, M. and Trebaul, L. and Riviere, D. and Cointepas, Y. and Kahane, P. and David, O.}, - year = {2017}, - pages = {S21--S22}, -} - -@inproceedings{sun_new_2018, - title = {New {Anatomical} {Characterizations} of the {Posterior} {Sylvian} {Fissure} using the {Human} {Connectome} {Project} {Database}}, - url = {https://hal.science/hal-02876125/file/SunHBM2018abstract.pdf}, - urldate = {2024-02-28}, - author = {Sun, Z. Y. and Rivière, D. and Fischer, C. and Mangin, Jean-François}, - year = {2018}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/4DFS7NEI/Sun et al. - 2018 - New Anatomical Characterizations of the Posterior .pdf:application/pdf}, -} - -@article{bouteloup_p2-277_2018, - title = {P2-277: {Cortical} {Sulci} {Width} and {Incident} {Dementia} in {Outpatients} {Attending} {French} {Memory} {Clinics}: {The} {Memento} {Cohort}}, - volume = {14}, - copyright = {© 2018 The Alzheimer's Association}, - issn = {1552-5279}, - shorttitle = {P2-277}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1016/j.jalz.2018.06.966}, - doi = {10.1016/j.jalz.2018.06.966}, - language = {en}, - number = {7S\_Part\_14}, - urldate = {2024-02-28}, - journal = {Alzheimer's \& Dementia}, - author = {Bouteloup, Vincent and Mangin, Jean-Francois and Dubois, Bruno and Ousset, Pierre Jean and Pasquier, Florence and Fischer, Clara and Rivière, Denis and yi Sun, Zhong and Azouani, Chabha and Paquet, Claire and Blanc, Frederic and Chupin, Marie and Belliard, Serge and Chêne, Geneviève and Dufouil, Carole and Group, Memento Study}, - year = {2018}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1016/j.jalz.2018.06.966}, - pages = {P784--P785}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HN2ESGFK/Bouteloup et al. - 2018 - P2-277 Cortical Sulci Width and Incident Dementia.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5RSHN2YL/j.jalz.2018.06.html:text/html}, -} - -@article{deman_intranat_2018, - title = {{IntrAnat} {Electrodes}: {A} {Free} {Database} and {Visualization} {Software} for {Intracranial} {Electroencephalographic} {Data} {Processed} for {Case} and {Group} {Studies}}, - volume = {12}, - issn = {1662-5196}, - shorttitle = {{IntrAnat} {Electrodes}}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2018.00040}, - abstract = {In some cases of pharmaco-resistant and focal epilepsies, intracranial recordings performed epidurally (electrocorticography, ECoG) and/or in depth (stereoelectroencephalography, SEEG) can be required to locate the seizure onset zone and the eloquent cortex before surgical resection. In SEEG, each electrode contact records brain’s electrical activity in a spherical volume of 3 mm diameter approximately. The spatial coverage is around 1\% of the brain and differs between patients because the implantation of electrodes is tailored for each case. Group studies thus need a large number of patients to reach a large spatial sampling, which can be achieved more easily using a multicentric approach such as implemented in our F-TRACT project (f-tract.eu). To facilitate group studies, we developed a software—IntrAnat Electrodes—that allows to perform virtual electrode implantation in patients’ neuroanatomy and to overlay results of epileptic and functional mapping, as well as resection masks from the surgery. IntrAnat Electrodes is based on a patient database providing multiple search criteria to highlight various group features. For each patient, the anatomical processing is based on a series of software publicly available. Imaging modalities (Positron Emission Tomography (PET), anatomical MRI pre-implantation, post-implantation and post-resection, functional MRI, diffusion MRI, Computed Tomography (CT) with electrodes) are coregistered. The 3D T1 pre-implantation MRI gray/white matter is segmented and spatially normalized to obtain a series of cortical parcels using different neuroanatomical atlases. On post-implantation images, the user can position 3D models of electrodes defined by their geometry. Each electrode contact is then labeled according to its position in the anatomical atlases, to the class of tissue (gray or white matter, cerebro-spinal fluid) and to its presence inside or outside the resection mask. Users can add more functionally informed labels on contact, such as clinical responses after electrical stimulation, cortico-cortical evoked potentials, gamma band activity during cognitive tasks or epileptogenicity. IntrAnat Electrodes software thus provides a means to visualize multimodal data. The contact labels allow to search for patients in the database according to multiple criteria representing almost all available data, which is to our knowledge unique in current SEEG software. IntrAnat Electrodes will be available in the forthcoming release of BrainVisa software and tutorials can be found on the F-TRACT webpage.}, - urldate = {2024-02-28}, - journal = {Frontiers in Neuroinformatics}, - author = {Deman, Pierre and Bhattacharjee, Manik and Tadel, François and Job, Anne-Sophie and Rivière, Denis and Cointepas, Yann and Kahane, Philippe and David, Olivier}, - year = {2018}, - keywords = {database and tools development, epilepsy surgery, multimodal neuroimaging, Python software, stereoelectroencephalography}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QTDCZP75/Deman et al. - 2018 - IntrAnat Electrodes A Free Database and Visualiza.pdf:application/pdf}, -} - -@inproceedings{sun_manifold-based_2020, - title = {Manifold-based exploration of the links between precentral sulcus interruptions and language-associated area 55b}, - author = {Sun, ZY and Fischer, C and Grigis, A and Rivière, D and Mangin, Jean-François}, - year = {2020}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/ADRFLNLB/Sun et al. - 2020 - Manifold-based exploration of the links between pr.pdf:application/pdf}, -} - -@inproceedings{sun_manifold-based_2019, - title = {Manifold-based exploration of the links between cortical morphology and functional architecture}, - author = {Sun, Zhong Yi and Rivière, Denis and Fischer, Clara and Grigis, Antoine and Poupon, Cyril and Mangin, Jean-François}, - year = {2019}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/69TL6MRQ/Sun et al. - 2019 - Manifold-based exploration of the links between co.pdf:application/pdf}, -} - -@inproceedings{cachia_sulcus-based_2005, - address = {Toronto, Canada}, - title = {Sulcus-based morphometry of heteromodal cortex in schizophrenia patients with resistant auditory hallucinations.}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Proc. 11th {HBM} {CD}-{Rom} {Neuroimage} vol 26 (1)}, - author = {Cachia, A. and Duchesnay, E. and Plaze, M. and Paillère-Martinot, M.-L. and Januel, D. and Bellivier, F. and Galinowski, A. and Andoh, J. and Bartrés-Faz, D. and De Beaurepaire, R. and Artiges, E. and Rivière, D. and Mangin, J.-F. and Martinot, J.-L.}, - year = {2005}, - keywords = {anatomy, conference, Anatomy, Sulci, sulci}, -} - -@inproceedings{duchesnay_guessing_2004, - title = {Guessing the {Sex} from the {Shapes} of {Cortical} {Folds}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {{HBM}, {Budapest}}, - author = {Duchesnay, Edouard and Roche, Alexis and Rivière, Denis and Papadopoulos-Orfanos, Dimitri and Cointepas, Yann and Mangin, Jean-Francois}, - year = {2004}, - keywords = {conference}, - pages = {164}, -} - -@inproceedings{duchesnay_population_2004, - address = {Arlington, VA, USA}, - title = {Population {Classification} {Based} on {Structural} {Morphometry} of {Cortical} {Sulci}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {International {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Duchesnay, Edouard and Roche, Alexis and Rivière, Denis and Papadopoulos-Orfanos, Dimitri and Cointepas, Yann and Mangin, Jean-Francois}, - year = {2004}, - keywords = {biomedical MRI, pattern classification, Support vector machine classification, Support vector machines, Neuroimaging, conference, support vector machines, brain, neurophysiology, artificial neuroanatomist, Automatic testing, brains, cortical sulci, Diseases, Image databases, iterative feature selection loop, leave-one-out procedure, medical computing, Performance analysis, population classification, shape measurement, Shape measurement, Spatial databases, structural morphometry, sulcus recognition system, support vector machine classifier, System testing}, - pages = {1276--1279}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6F4ZY2VL/1398776.html:text/html}, -} - -@article{cachia_cortical_2008, - title = {Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations}, - volume = {39}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2007.08.049}, - abstract = {Gray matter volume and functional abnormalities have been reported in language-related cortex in schizophrenia patients with auditory hallucinations. Such abnormalities might denote abnormal cortical folding development, which can now be investigated using gyrification measures. Anatomic magnetic resonance images (MRIs) were obtained from 30 schizophrenia patients screened for resistant auditory hallucinations and 28 control subjects. We searched for overall gyrification abnormalities in the whole cortex as well as localized abnormalities in language-related cortex, assuming that gyrification is associated with brain sulcation. A fully automated method was applied to MRIs to extract, label and measure the sulcus area in the whole cortex. Gyrification was assessed using both global and local sulcal indices, respectively the ratio between total sulcal area, or area of each labeled sulcus, and outer cortex area. For both hemispheres, the patients had a lower global sulcal index. The local sulcal index decrease was not homogeneous across the whole cortex. It was more significant in the superior temporal sulcus bilaterally, in the left middle frontal sulcus and in the diagonal branch of left sylvian fissure (Broca's area). Findings suggest abnormalities in cortical gyrification in these patients. Sulcal abnormalities in language-related cortex might underlie these patients' particular vulnerability to hallucinations.}, - language = {eng}, - number = {3}, - journal = {NeuroImage}, - author = {Cachia, Arnaud and Paillère-Martinot, Marie-Laure and Galinowski, André and Januel, Dominique and de Beaurepaire, Renaud and Bellivier, Frank and Artiges, Eric and Andoh, Jamila and Bartrés-Faz, David and Duchesnay, Edouard and Rivière, Denis and Plaze, Marion and Mangin, Jean-Francois and Martinot, Jean-Luc}, - month = feb, - year = {2008}, - pmid = {17988891}, - keywords = {Humans, Magnetic Resonance Imaging, Schizophrenia, Image Processing, Computer-Assisted, Adult, Female, Male, Cerebral Cortex, Middle Aged, Linear Models, Functional Laterality, Antipsychotic Agents, Hallucinations, Psychiatric Status Rating Scales, Sulci,Anatomy,brainvisa}, - pages = {927--935}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Cachia-NI08.pdf}, -} - -@article{duchesnay_feature_2011, - series = {Special {Issue}: {Educational} {Neuroscience}}, - title = {Feature selection and classification of imbalanced datasets: {Application} to {PET} images of children with autistic spectrum disorders}, - volume = {57}, - copyright = {All rights reserved}, - issn = {1053-8119}, - shorttitle = {Feature selection and classification of imbalanced datasets}, - url = {http://www.sciencedirect.com/science/article/pii/S105381191100499X}, - doi = {10.1016/j.neuroimage.2011.05.011}, - abstract = {Learning with discriminative methods is generally based on minimizing the misclassification of training samples, which may be unsuitable for imbalanced datasets where the recognition might be biased in favor of the most numerous class. This problem can be addressed with a generative approach, which typically requires more parameters to be determined leading to reduced performances in high dimension. In such situations, dimension reduction becomes a crucial issue. We propose a feature selection/classification algorithm based on generative methods in order to predict the clinical status of a highly imbalanced dataset made of PET scans of forty-five low-functioning children with autism spectrum disorders (ASD) and thirteen non-ASD low functioning children. ASDs are typically characterized by impaired social interaction, narrow interests, and repetitive behaviors, with a high variability in expression and severity. The numerous findings revealed by brain imaging studies suggest that ASD is associated with a complex and distributed pattern of abnormalities that makes the identification of a shared and common neuroimaging profile a difficult task. In this context, our goal is to identify the rest functional brain imaging abnormalities pattern associated with ASD and to validate its efficiency in individual classification. The proposed feature selection algorithm detected a characteristic pattern in the ASD group that included a hypoperfusion in the right Superior Temporal Sulcus (STS) and a hyperperfusion in the contralateral postcentral area. Our algorithm allowed for a significantly accurate (88\%), sensitive (91\%) and specific (77\%) prediction of clinical category. For this imbalanced dataset, with only 13 control scans, the proposed generative algorithm outperformed other state-of-the-art discriminant methods. The high predictive power of the characteristic pattern, which has been automatically identified on whole brains without any priors, confirms previous findings concerning the role of STS in ASD. This work offers exciting possibilities for early autism detection and/or the evaluation of treatment response in individual patients.}, - language = {en}, - number = {3}, - urldate = {2021-01-04}, - journal = {NeuroImage}, - author = {Duchesnay, Edouard and Cachia, Arnaud and Boddaert, Nathalie and Chabane, Nadia and Mangin, Jean-Franois and Martinot, Jean-Luc and Brunelle, Francis and Zilbovicius, Monica}, - month = aug, - year = {2011}, - keywords = {Feature selection, Autism, Dimension reduction, Multivariate classification}, - pages = {1003--1014}, - annote = {The following values have no corresponding Zotero field:number: 3accession-num: WOS:000292717900034label: ACLcustom1: Neurospin}, - annote = {Unati1053-8119SI}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B36T2GS2/S105381191100499X.html:text/html}, -} - -@article{favre_widespread_2019, - title = {Widespread white matter microstructural abnormalities in bipolar disorder: evidence from mega- and meta-analyses across 3033 individuals}, - copyright = {2019 The Author(s), under exclusive licence to American College of Neuropsychopharmacology}, - issn = {1740-634X}, - shorttitle = {Widespread white matter microstructural abnormalities in bipolar disorder}, - url = {https://www.nature.com/articles/s41386-019-0485-6}, - doi = {10.1038/s41386-019-0485-6}, - abstract = {Fronto-limbic white matter (WM) abnormalities are assumed to lie at the heart of the pathophysiology of bipolar disorder (BD); however, diffusion tensor imaging (DTI) studies have reported heterogeneous results and it is not clear how the clinical heterogeneity is related to the observed differences. This study aimed to identify WM abnormalities that differentiate patients with BD from healthy controls (HC) in the largest DTI dataset of patients with BD to date, collected via the ENIGMA network. We gathered individual tensor-derived regional metrics from 26 cohorts leading to a sample size of N = 3033 (1482 BD and 1551 HC). Mean fractional anisotropy (FA) from 43 regions of interest (ROI) and average whole-brain FA were entered into univariate mega- and meta-analyses to differentiate patients with BD from HC. Mega-analysis revealed significantly lower FA in patients with BD compared with HC in 29 regions, with the highest effect sizes observed within the corpus callosum (R2 = 0.041, Pcorr {\textless} 0.001) and cingulum (right: R2 = 0.041, left: R2 = 0.040, Pcorr {\textless} 0.001). Lithium medication, later onset and short disease duration were related to higher FA along multiple ROIs. Results of the meta-analysis showed similar effects. We demonstrated widespread WM abnormalities in BD and highlighted that altered WM connectivity within the corpus callosum and the cingulum are strongly associated with BD. These brain abnormalities could represent a biomarker for use in the diagnosis of BD. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.}, - language = {en}, - urldate = {2019-08-21}, - journal = {Neuropsychopharmacology}, - author = {Favre, Pauline and Pauling, Melissa and Stout, Jacques and Hozer, Franz and Sarrazin, Samuel and Abé, Christoph and Alda, Martin and Alloza, Clara and Alonso-Lana, Silvia and Andreassen, Ole A. and Baune, Bernhard T. and Benedetti, Francesco and Busatto, Geraldo F. and Canales-Rodríguez, Erick J. and Caseras, Xavier and Chaim-Avancini, Tiffany Moukbel and Ching, Christopher R. K. and Dannlowski, Udo and Deppe, Michael and Eyler, Lisa T. and Fatjo-Vilas, Mar and Foley, Sonya F. and Grotegerd, Dominik and Hajek, Tomas and Haukvik, Unn K. and Howells, Fleur M. and Jahanshad, Neda and Kugel, Harald and Lagerberg, Trine V. and Lawrie, Stephen M. and Linke, Julia O. and McIntosh, Andrew and Melloni, Elisa M. T. and Mitchell, Philip B. and Polosan, Mircea and Pomarol-Clotet, Edith and Repple, Jonathan and Roberts, Gloria and Roos, Annerine and Rosa, Pedro G. P. and Salvador, Raymond and Sarró, Salvador and Schofield, Peter R. and Serpa, Mauricio H. and Sim, Kang and Stein, Dan J. and Sussmann, Jess E. and Temmingh, Henk S. and Thompson, Paul M. and Verdolini, Norma and Vieta, Eduard and Wessa, Michele and Whalley, Heather C. and Zanetti, Marcus V. and Leboyer, Marion and Mangin, Jean-François and Henry, Chantal and Duchesnay, Edouard and Houenou, Josselin}, - month = aug, - year = {2019}, - pmid = {31527792}, - note = {tex.ids: favre\_correction\_2019}, - keywords = {Translational research, Diagnostic markers}, - pages = {1--11}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UCEC66DU/Favre et al. - 2019 - Correction Widespread white matter microstructura.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BCH8G2RS/Favre et al. - 2019 - Widespread white matter microstructural abnormalit.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/44P2C76Q/s41386-019-0485-6.html:text/html}, -} - -@article{jouvent_longitudinal_2012, - title = {Longitudinal changes of cortical morphology in {CADASIL}}, - volume = {33}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1558-1497}, - doi = {10.1016/j.neurobiolaging.2011.09.013}, - abstract = {In CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leucoencephalopathy), a genetic model of subcortical ischemic vascular dementia (SIVD), clinical status was previously found related to cortex morphology. In the present report, alterations of cortex morphology and their links to clinical worsening were investigated in 190 CADASIL patients followed during 24.4 months. Linear models were used to test relationships between: (1) clinical worsening and changes of depth of cortical sulci and of cortical thickness; (2) alterations of cortical morphology and changes of volume of white matter hyperintensities (WMH(v)) and of lacunar lesions (LL(v)). Reduction of sulcal depth was independently associated with increased time to complete trail making test A and B (p {\textless} 0.0001 and p = 0.004) and that of cortical thickness to increased disability (modified Rankin's scale, p = 0.008), while brain atrophy was only related to global cognitive worsening (Mattis dementia rating scale, p = 0.002). The impact of volume of lacunar lesions on cortical alterations was larger than that of volume of white matter hyperintensities. Cortical alterations, mainly related to lacunar lesions, evolve parallel to clinical worsening. These results further support the eventual role of cortical alterations in subcortical ischemic vascular dementia.}, - language = {eng}, - number = {5}, - journal = {Neurobiology of Aging}, - author = {Jouvent, Eric and Mangin, Jean-François and Duchesnay, Edouard and Porcher, Raphael and Düring, Marco and Mewald, Yvonne and Guichard, Jean-Pierre and Hervé, Dominique and Reyes, Sonia and Zieren, Nikola and Dichgans, Martin and Chabriat, Hugues}, - month = may, - year = {2012}, - pmid = {22000857}, - keywords = {Humans, Magnetic Resonance Imaging, Models, Neurological, Adult, Female, Male, Cerebral Cortex, Middle Aged, Nerve Fibers, Myelinated, Aged, Aged, 80 and over, Atrophy, CADASIL, Dementia, Vascular, Disease Progression, Follow-Up Studies, Longitudinal Studies}, - pages = {1002.e29--36}, - annote = {Times Cited: 0}, -} - -@article{mangin_brain_2004, - title = {Brain morphometry using {3D} moment invariants}, - volume = {8}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1361-8415}, - doi = {10.1016/j.media.2004.06.016}, - abstract = {This paper advocates the use of shape descriptors based on moments of 3D coordinates for morphometry of the cortical sulci. These descriptors, which have been introduced more than a decade ago, are invariant relatively to rotations, translations and scale and can be computed for any topology. A rapid insight into the derivation of these invariants is proposed first. Then, their potential to characterize shapes is shown from a principal component analysis of the 12 first invariants computed for 12 different deep brain structures manually drawn for 7 different brains. Finally, these invariants are used to find some correlates of handedness and sex among the shapes of 116 different cortical sulci automatically identified in each of 142 brains of the ICBM database.}, - language = {eng}, - number = {3}, - journal = {Medical Image Analysis}, - author = {Mangin, J.-F. and Poupon, F. and Duchesnay, E. and Rivière, D. and Cachia, A. and Collins, D. L. and Evans, A. C. and Régis, J.}, - month = sep, - year = {2004}, - pmid = {15450214}, - keywords = {Algorithms, Humans, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Female, Male, Cerebral Cortex, Computer Simulation, Functional Laterality, Models, Biological}, - pages = {187--196}, -} - -@article{mangin_framework_2004, - title = {A framework to study the cortical folding patterns}, - volume = {23 Suppl 1}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2004.07.019}, - abstract = {This paper describes a decade-long research program focused on the variability of the cortical folding patterns. The program has developed a framework of using artificial neuroanatomists that are trained to identify sulci from a database. The framework relies on a renormalization of the brain warping problem, which consists in matching the cortices at the scale of the folds. Another component of the program is the search for the alphabet of the folding patterns, namely, a list of indivisible elementary sulci. The search relies on the study of the cortical folding process using antenatal imaging and on backward simulations of morphogenesis aimed at revealing traces of the embryologic dimples in the mature cortical surface. The importance of sulcal-based morphometry is illustrated by a simple study of the correlates of handedness on asymmetry indices. The study shows for instance that the central sulcus is larger in the dominant hemisphere.}, - language = {eng}, - journal = {NeuroImage}, - author = {Mangin, J.-F. and Rivière, D. and Cachia, A. and Duchesnay, E. and Cointepas, Y. and Papadopoulos-Orfanos, D. and Scifo, P. and Ochiai, T. and Brunelle, F. and Régis, J.}, - year = {2004}, - pmid = {15501082}, - keywords = {Humans, Brain Mapping, Image Processing, Computer-Assisted, Female, Cerebral Cortex, Computer Simulation, Databases, Factual, Dominance, Cerebral, Pregnancy, Terminology as Topic}, - pages = {S129--138}, -} - -@article{aczel_consensus-based_2021, - title = {Consensus-based guidance for conducting and reporting multi-analyst studies}, - volume = {10}, - issn = {2050-084X}, - url = {https://doi.org/10.7554/eLife.72185}, - doi = {10.7554/eLife.72185}, - abstract = {Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.}, - urldate = {2024-03-12}, - journal = {eLife}, - author = {Aczel, Balazs and Szaszi, Barnabas and Nilsonne, Gustav and van den Akker, Olmo R and Albers, Casper J and van Assen, Marcel ALM and Bastiaansen, Jojanneke A and Benjamin, Daniel and Boehm, Udo and Botvinik-Nezer, Rotem and Bringmann, Laura F and Busch, Niko A and Caruyer, Emmanuel and Cataldo, Andrea M and Cowan, Nelson and Delios, Andrew and van Dongen, Noah NN and Donkin, Chris and van Doorn, Johnny B and Dreber, Anna and Dutilh, Gilles and Egan, Gary F and Gernsbacher, Morton Ann and Hoekstra, Rink and Hoffmann, Sabine and Holzmeister, Felix and Huber, Juergen and Johannesson, Magnus and Jonas, Kai J and Kindel, Alexander T and Kirchler, Michael and Kunkels, Yoram K and Lindsay, D Stephen and Mangin, Jean-Francois and Matzke, Dora and Munafò, Marcus R and Newell, Ben R and Nosek, Brian A and Poldrack, Russell A and van Ravenzwaaij, Don and Rieskamp, Jörg and Salganik, Matthew J and Sarafoglou, Alexandra and Schonberg, Tom and Schweinsberg, Martin and Shanks, David and Silberzahn, Raphael and Simons, Daniel J and Spellman, Barbara A and St-Jean, Samuel and Starns, Jeffrey J and Uhlmann, Eric Luis and Wicherts, Jelte and Wagenmakers, Eric-Jan}, - editor = {Rodgers, Peter}, - month = nov, - year = {2021}, - note = {Publisher: eLife Sciences Publications, Ltd}, - keywords = {analytical variability, expert consensus, metascience, multi-analyst, science forum, statistical practice}, - pages = {e72185}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3J7MEECC/Aczel et al. - 2021 - Consensus-based guidance for conducting and report.pdf:application/pdf}, -} - -@article{lu_associations_2021, - title = {Associations {Between} {Nutritional} {Deficits} and {Physical} {Performance} in {Community}-{Dwelling} {Older} {Adults}}, - volume = {8}, - issn = {2296-861X}, - url = {https://www.frontiersin.org/articles/10.3389/fnut.2021.771470}, - doi = {10.3389/fnut.2021.771470}, - abstract = {Background - Whether multiple nutritional deficiencies have a synergic effect on mobility loss remains unknown. This study aims to evaluate associations between multi-nutritional deficits and physical performance evolution among community-dwelling older adults. Methods - We included 386 participants from the Multidomain Alzheimer Preventive Trial (MAPT) (75.6 ± 4.5 years) not receiving omega-3 polyunsaturated fatty acid (PUFA) supplementation and who had available data on nutritional deficits. Baseline nutritional deficits were defined as: plasma 25 hydroxyvitamin D 14 μmol/L, or erythrocyte omega-3 PUFA index ≤4.87\% (lower quartile). The Short Physical Performance Battery (SPPB), gait speed and chair rise time were used to assess physical performance at baseline and after 6, 12, 24, 36, 48 and 60 months. We explored if the nutrition-physical performance associations varied according to the presence of low-grade inflammation (LGI) and brain imaging indicators. Results - Within-group comparisons showed physical function (decreased SPPB and gait speed; increased chair rise time) worsened over time, particularly in participants with ≥2 nutritional deficits; however, no between-group differences were observed when comparing individuals without deficit and those with either one or ≥2 deficits. Our exploratory analysis on nutritional deficits-LGI interactions showed that, among people ≥2 deficits, chair rise time was increased over time in participants with LGI (adjusted mean difference: 3.47; 95\% CI: 1.03, 5.91; p=0.017), compared to non-LGI individuals. Conclusions - Accumulated deficits on vitamin D, homocysteine and omega-3 PUFA was not associated with physical performance evolution in older adults, but they determined declined chair rise performance in subjects with low-grade inflammation.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Nutrition}, - author = {Lu, Wan-Hsuan and Giudici, Kelly Virecoulon and Rolland, Yves and Guyonnet, Sophie and Mangin, Jean-François and Vellas, Bruno and de Souto Barreto, Philipe}, - month = nov, - year = {2021}, - note = {Publisher: Frontiers}, - keywords = {Inflammation, Vitamin D, Homocysteine, Omega - 3 fatty acids, physical performace}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GMSPL2CH/Lu et al. - 2021 - Associations Between Nutritional Deficits and Phys.pdf:application/pdf}, -} - -@article{coarelli_safety_2022, - title = {Safety and efficacy of riluzole in spinocerebellar ataxia type 2 in {France} ({ATRIL}): a multicentre, randomised, double-blind, placebo-controlled trial}, - volume = {21}, - issn = {1474-4422, 1474-4465}, - shorttitle = {Safety and efficacy of riluzole in spinocerebellar ataxia type 2 in {France} ({ATRIL})}, - url = {https://www.thelancet.com/journals/laneur/article/PIIS1474-4422(21)00457-9/abstract}, - doi = {10.1016/S1474-4422(21)00457-9}, - language = {English}, - number = {3}, - urldate = {2024-03-12}, - journal = {The Lancet Neurology}, - author = {Coarelli, Giulia and Heinzmann, Anna and Ewenczyk, Claire and Fischer, Clara and Chupin, Marie and Monin, Marie-Lorraine and Hurmic, Hortense and Calvas, Fabienne and Calvas, Patrick and Goizet, Cyril and Thobois, Stéphane and Anheim, Mathieu and Nguyen, Karine and Devos, David and Verny, Christophe and Ricigliano, Vito A. G. and Mangin, Jean-François and Brice, Alexis and Montcel, Sophie Tezenas du and Durr, Alexandra}, - month = mar, - year = {2022}, - pmid = {35063116}, - note = {Publisher: Elsevier}, - pages = {225--233}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FBJ7BBF7/Coarelli et al. - 2022 - Safety and efficacy of riluzole in spinocerebellar.pdf:application/pdf}, -} - -@article{riviere_browsing_2022, - title = {Browsing {Multiple} {Subjects} {When} the {Atlas} {Adaptation} {Cannot} {Be} {Achieved} via a {Warping} {Strategy}}, - volume = {16}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2022.803934}, - doi = {10.3389/fninf.2022.803934}, - abstract = {Brain mapping studies often need to identify brain structures or functional circuits into a set of individual brain. To this end, multiple atlases have been published to represent such structures, based on different modalities, subject sets, and techniques. The mainstream approach to exploit these atlases consists in spatially deforming each individual data onto a given atlas using dense deformation fields, which supposes the existence of a continuous mapping between atlases and individuals. However this continuity is not always verified, and this “iconic” approach has limits. We present in this paper an alternative, complementary, “structural” approach, which consists in extracting structures from the individual data, and comparing them without deformation. A “structural atlas” is thus a collection of annotated individual data with a common structure nomenclature. It may be used to characterize structure shape variability across individuals or species, or to train machine learning systems. This paper exhibits Anatomist, a powerful structural 3D visualization software dedicated to building, exploring, and editing structural atlases involving a large number of subjects. It has been developed primarily to decipher the cortical folding variability: cortical sulci vary enormously in both size and shape, some may be missing, or have various topologies, which makes iconic approaches inefficient to study them. We therefore had to build structural atlases for cortical sulci, and use them to train sulci identification algorithms. Anatomist can display multiple subjects data in multiple views, supports all kinds of neuroimaging data including compound structural object graphs, handles arbitrary coordinate transformation chains between data, and has multiple display features. It is designed as a programming library in both C++ and Python languages, and may be extended or used to build dedicated custom applications. Its generic design makes all the display and structural aspects used to explore the variability of the cortical folding pattern work in other applications, for instance to browse axonal fiber bundles, deep nuclei, functional activations, or other kinds of cortical parcellations. Multimodal, multi-individual, or inter-species display is supported, and adaptations to large scale screen walls have been developed. These very original features makes it a unique viewer for structural atlas browsing.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {Rivière, Denis and Leprince, Yann and Labra, Nicole and Vindas, Nabil and Foubet, Ophélie and Cagna, Bastien and Loh, Kep Kee and Hopkins, William and Balzeau, Antoine and Mancip, Martial and Lebenberg, Jessica and Cointepas, Yann and Coulon, Olivier and Mangin, Jean-François}, - month = mar, - year = {2022}, - note = {Publisher: Frontiers}, - keywords = {3D, Brain Atlas, Inter-subject, Parcellation atlas, Structural approach, visualization}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FAWUB5WT/Rivière et al. - 2022 - Browsing Multiple Subjects When the Atlas Adaptati.pdf:application/pdf}, -} - -@article{cachia_mapping_2022, - title = {Mapping the human brain from the prenatal period to infancy using {3D} magnetic reonance imaging}, - url = {https://books.google.com/books?hl=en&lr=&id=zhhdEAAAQBAJ&oi=fnd&pg=PA50&dq=info:7CC4s-ZEMSoJ:scholar.google.com&ots=qbsUayXZdg&sig=vTKl0d3BqK4iZ-bIQsYrOovHCPo}, - urldate = {2024-03-12}, - journal = {The Cambridge Handbook of Congitive Development}, - author = {Cachia, Arnaud and Mangin, Jean-François and Dubois, Jessica}, - year = {2022}, - note = {Publisher: Cambridge Univerity Press}, - pages = {50}, -} - -@article{regy_association_2022, - title = {Association of \textit{{APOE}} ε4 with cerebral gray matter volumes in non-demented older adults: {The} {MEMENTO} cohort study}, - volume = {250}, - issn = {1053-8119}, - shorttitle = {Association of \textit{{APOE}} ε4 with cerebral gray matter volumes in non-demented older adults}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922000957}, - doi = {10.1016/j.neuroimage.2022.118966}, - abstract = {Data on 2,045 non-demented individuals with memory complaints were drawn from the Memento cohort study to examine the association between Apolipoprotein E ε4 allele (APOE4) and regional brain gray matter volumes. Linear regression was used to examine the association of APOE4 and measures of regional gray matter volumes in cross-sectional analysis and change therein using longitudinal analyses based on two brain MRI performed at baseline and at two-year follow-up. Overall, in analyses adjusted for age, sex, and intracranial volume, the presence of APOE4 was associated with lower total gray matter volume at baseline and with a higher atrophy rate over the follow-up. The hippocampus and entorhinal cortex were the two gray matter regions most associated with APOE4. Further adjustment for cardiovascular risk factors had little impact on these associations. There was an interaction between age, APOE4 status and total brain volume atrophy rate, with evidence of an earlier age at onset of atrophy in hippocampal volume in APOE4 carriers compared to non-carriers. Those results are in accordance with the role of medial temporal structures in the greater risk of dementia observed in people carrying the APOE4 allele.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Régy, Mélina and Dugravot, Aline and Sabia, Séverine and Fayosse, Aurore and Mangin, Jean-Francois and Chupin, Marie and Fischer, Clara and Bouteloup, Vincent and Dufouil, Carole and Chêne, Geneviève and Paquet, Claire and Hanseeuw, Bernard and Singh-Manoux, Archana and Dumurgier, Julien}, - month = apr, - year = {2022}, - keywords = {MRI, Longitudinal analysis}, - pages = {118966}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QY5H8I6A/Régy et al. - 2022 - Association of APOE ε4 with cerebral gray m.pdf:application/pdf}, -} - -@article{de_vareilles_shape_2022, - title = {Shape variability of the central sulcus in the developing brain: {A} longitudinal descriptive and predictive study in preterm infants}, - volume = {251}, - issn = {1053-8119}, - shorttitle = {Shape variability of the central sulcus in the developing brain}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921011083}, - doi = {10.1016/j.neuroimage.2021.118837}, - abstract = {Despite growing evidence of links between sulcation and function in the adult brain, the folding dynamics, occurring mostly before normal-term-birth, is vastly unknown. Looking into the development of cortical sulci in infants can give us keys to address fundamental questions: what is the sulcal shape variability in the developing brain? When are the shape features encoded? How are these morphological parameters related to further functional development? In this study, we aimed to investigate the shape variability of the developing central sulcus, which is the frontier between the primary somatosensory and motor cortices. We studied a cohort of 71 extremely preterm infants scanned twice using MRI – once around 30 weeks post-menstrual age (w PMA) and once at term-equivalent age, around 40w PMA –, in order to quantify the sulcus's shape variability using manifold learning, regardless of age-group or hemisphere. We then used these shape descriptors to evaluate the sulcus's variability at both ages and to assess hemispheric and age-group specificities. This led us to propose a description of ten shape features capturing the variability in the central sulcus of preterm infants. Our results suggested that most of these features (8/10) are encoded as early as 30w PMA. We unprecedentedly observed hemispheric asymmetries at both ages, and the one captured at term-equivalent age seems to correspond with the asymmetry pattern previously reported in adults. We further trained classifiers in order to explore the predictive value of these shape features on manual performance at 5 years of age (handedness and fine motor outcome). The central sulcus's shape alone showed a limited but relevant predictive capacity in both cases. The study of sulcal shape features during early neurodevelopment may participate to a better comprehension of the complex links between morphological and functional organization of the developing brain.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {de Vareilles, Héloïse and Rivière, Denis and Sun, Zhong-Yi and Fischer, Clara and Leroy, François and Neumane, Sara and Stopar, Nuša and Eijsermans, Rian and Ballu, Marin and Tataranno, Maria-Luisa and Benders, Manon and Mangin, Jean-François and Dubois, Jessica}, - month = may, - year = {2022}, - keywords = {Brain morphological development, cortical folding, fine motor outcome, hemispheric asymmetries, lateralization, manual dexterity, outcome prediction, prematurity}, - pages = {118837}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SNAPTR2K/de Vareilles et al. - 2022 - Shape variability of the central sulcus in the dev.pdf:application/pdf}, -} - -@article{mortamais_sulcal_2022, - title = {Sulcal morphology as cognitive decline predictor in older adults with memory complaints}, - volume = {113}, - issn = {0197-4580}, - url = {https://www.sciencedirect.com/science/article/pii/S0197458022000240}, - doi = {10.1016/j.neurobiolaging.2022.02.003}, - abstract = {To determine whether sulcal morphology can predict changes in cognition, we investigated the relationship between width of 20 cerebral sulci and cognitive decline. Sulcal width was measured in T1-weighted MRI images at baseline in 433 adults aged ≥70 years with memory complaints from the MRI-Multidomain Alzheimer Preventive Trial study. Cognition was evaluated at baseline, 6, 12, 24, and 36 months of follow-up with a composite Z score. The composite score variations over time relative to the baseline sulcal width were assessed using linear mixed regression models. We observed a positive association between a greater decline in cognitive composite score and the width of the superior and the anterior inferior temporal sulci, and the cingulate anterior sulcus of the left hemisphere. Sulcal widening in the lateral temporal and the cingulate anterior areas might predict cognitive decline in individuals with memory complaints.}, - urldate = {2024-03-12}, - journal = {Neurobiology of Aging}, - author = {Mortamais, Marion and Gutierrez, Laure-Anne and Balem, Marianne and Bars, Emmanuelle Le and de Champfleur, Nicolas Menjot and Bouyahia, Ali and Chupin, Marie and Perus, Lisa and Fisher, Clara and Vellas, Bruno and Andrieu, Sandrine and Mangin, Jean-François and Berr, Claudine and Gabelle, Audrey}, - month = may, - year = {2022}, - keywords = {Neuroimaging biomarkers, Cerebral sulci, Cognitive decline, Older adults}, - pages = {84--94}, -} - -@article{schirner_brain_2022, - title = {Brain simulation as a cloud service: {The} {Virtual} {Brain} on {EBRAINS}}, - volume = {251}, - issn = {1053-8119}, - shorttitle = {Brain simulation as a cloud service}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922001021}, - doi = {10.1016/j.neuroimage.2022.118973}, - abstract = {The Virtual Brain (TVB) is now available as open-source services on the cloud research platform EBRAINS (ebrains.eu). It offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability, and clinical translation.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Schirner, Michael and Domide, Lia and Perdikis, Dionysios and Triebkorn, Paul and Stefanovski, Leon and Pai, Roopa and Prodan, Paula and Valean, Bogdan and Palmer, Jessica and Langford, Chloê and Blickensdörfer, André and van der Vlag, Michiel and Diaz-Pier, Sandra and Peyser, Alexander and Klijn, Wouter and Pleiter, Dirk and Nahm, Anne and Schmid, Oliver and Woodman, Marmaduke and Zehl, Lyuba and Fousek, Jan and Petkoski, Spase and Kusch, Lionel and Hashemi, Meysam and Marinazzo, Daniele and Mangin, Jean-François and Flöel, Agnes and Akintoye, Simisola and Stahl, Bernd Carsten and Cepic, Michael and Johnson, Emily and Deco, Gustavo and McIntosh, Anthony R. and Hilgetag, Claus C. and Morgan, Marc and Schuller, Bernd and Upton, Alex and McMurtrie, Colin and Dickscheid, Timo and Bjaalie, Jan G. and Amunts, Katrin and Mersmann, Jochen and Jirsa, Viktor and Ritter, Petra}, - month = may, - year = {2022}, - keywords = {Neuroimaging, Connectome, Reproducibility, Brain modelling, Cloud, Data protection, High performance computing, Network model}, - pages = {118973}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WCGZST9E/Schirner et al. - 2022 - Brain simulation as a cloud service The Virtual B.pdf:application/pdf}, -} - -@article{grasset_explaining_2022, - title = {Explaining the association between social and lifestyle factors and cognitive functions: a pathway analysis in the {Memento} cohort}, - volume = {14}, - issn = {1758-9193}, - shorttitle = {Explaining the association between social and lifestyle factors and cognitive functions}, - url = {https://doi.org/10.1186/s13195-022-01013-8}, - doi = {10.1186/s13195-022-01013-8}, - abstract = {This work aimed to investigate the potential pathways involved in the association between social and lifestyle factors, biomarkers of Alzheimer’s disease and related dementia (ADRD), and cognition.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Alzheimer's Research \& Therapy}, - author = {Grasset, Leslie and Proust-Lima, Cécile and Mangin, Jean-François and Habert, Marie-Odile and Dubois, Bruno and Paquet, Claire and Hanon, Olivier and Gabelle, Audrey and Ceccaldi, Mathieu and Annweiler, Cédric and David, Renaud and Jonveaux, Therese and Belin, Catherine and Julian, Adrien and Rouch-Leroyer, Isabelle and Pariente, Jérémie and Locatelli, Maxime and Chupin, Marie and Chêne, Geneviève and Dufouil, Carole and {on behalf of the Memento Cohort Study group}}, - month = may, - year = {2022}, - keywords = {Brain markers, Cognitive function, Lifestyle factors, Pathology, Pathways, Social factors}, - pages = {68}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7E79Z2VK/Grasset et al. - 2022 - Explaining the association between social and life.pdf:application/pdf}, -} - -@article{angioni_biomarkers_2022, - title = {Biomarkers of {Age}-{Related} {Frailty} and {Frailty} {Related} to {Diseases}: {An} {Exploratory}, {Cross}-{Sectional} {Analysis} from the {MAPT} {Study}}, - volume = {26}, - issn = {1279-7707}, - shorttitle = {Biomarkers of {Age}-{Related} {Frailty} and {Frailty} {Related} to {Diseases}}, - url = {https://www.sciencedirect.com/science/article/pii/S1279770723008448}, - doi = {10.1007/s12603-022-1793-9}, - abstract = {Background -Frailty may in most cases result from two main causes: the aging process (age-related frailty) and diseases (evolving chronic conditions or acute medical illnesses — disease-related frailty). The biological determinants characterizing these two main causes of frailty may be different. -Objectives -The aim of this study is to compare the biological and neuroimaging profile of people without frailty, those with age-related frailty, and subjects with disease-related frailty in community-dwelling older adults. -Material and Methods -We performed a secondary, cross-sectional analysis from the Multidomain Alzheimer Preventive Trial (MAPT). We included 1199 subjects without frailty throughout the 5-year follow-up, 82 subjects with incident age-related frailty, and 53 with incident disease-related frailty. Available blood biomarkers involved nutritional (eg, vitamin D, omega-3 fatty acids), inflammatory-related (IL-6, TNFR1, GDF15), neurodegenerative (eg, beta-amyloid, neurofilament light chain) and neuroimaging markers (MRI, Amyloid-PET). -Results -Although not statistically significant, the results of the unadjusted model showed increasing gradients for inflammatory markers (GDF15, TNFR1) and decreasing gradients for nutritional and neuroimaging markers (omega 3 index, hippocampal volume) from age-related frailty participants to individuals with disease-related frailty. Considering the linear models we observed higher GDF15 values in disease-related frailty group compared to age-related frailty individuals [β = 242.8 (49.5, 436.2)]. We did not find any significant difference between subjects without frailty and those with age-related frailty. Subjects with disease-related frailty compared to subjects without frailty had lower values of DHA [β = −2.42 (−4.76, −0.08)], Omega 3 Index [β = −0.50 (−0.95, −0.06)] and hippocampal volume [β = −0.22 (−0.42,−0.02)]. They also had higher values of GDF15 [β = 246.1 (88.9, 403.4)] and TNFR1 [β = 157.5 (7.8, 307.2)]. -Conclusion -Age-related frailty and disease-related frailty may represent different degrees of frailty severity on a biological level. Further research is needed to identify biomarkers potentially able to distinguish these classifications of frailty.}, - number = {6}, - urldate = {2024-03-12}, - journal = {The Journal of nutrition, health and aging}, - author = {Angioni, D. and Lu, W. H. and Sourdet, S. and Macaron, T. and Takeda, C. and Guyonnet, S. and Mangin, J. F. and Rolland, Y. and de Souto Barreto, P. and Vellas, B.}, - month = jun, - year = {2022}, - keywords = {biomarkers, age-related frailty, Frailty related to diseases, geroscience}, - pages = {545--551}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/S5W4CN3N/Angioni et al. - 2022 - Biomarkers of Age-Related Frailty and Frailty Rela.pdf:application/pdf}, -} - -@article{angioni_neuroimaging_2022, - title = {Neuroimaging correlates of persistent fatigue in older adults: {A} secondary analysis from the {Multidomain} {Alzheimer} {Preventive} {Trial} ({MAPT}) trial}, - volume = {26}, - issn = {1360-7863}, - shorttitle = {Neuroimaging correlates of persistent fatigue in older adults}, - url = {https://doi.org/10.1080/13607863.2021.1932737}, - doi = {10.1080/13607863.2021.1932737}, - abstract = {Fatigue has been suggested as a marker of biological aging. It seems plausible that this symptom might be associated with changes in brain health. The objective of this study was to examine the associations between persistent fatigue and neuroimaging correlates in a non-disease-specific population of community-dwelling older adults. We performed a cross-sectional analysis using data from The Multidomain Alzheimer Preventive Trial (MAPT). We included 458 subjects. Persistent fatigue was defined as meeting exhaustion criterion of Fried frailty phenotype in two consecutive clinical visits six months apart between study baseline and one year. Brain imaging correlates, assessed by magnetic resonance imaging (MRI), were the outcomes. The associations between persistent fatigue and brain correlates were explored using mixed model linear regressions with random effect at the center level. The mean age of the participants was 74.8 ± 4 years old, and 63\% of the subjects were women. Forty-seven participants (10\%) exhibited a persistent fatigue profile. People with persistent fatigue were older compared to subjects without persistent fatigue (76.2 years ± 4.3 vs.74.7 ± 3.9 p = 0.009). Persistent fatigue was associated with higher white matter hyperintensity volume in the fully adjusted analysis. We did not find any cross-sectional association between persistent fatigue and sub-cortical volumes and global and regional cortical thickness. Persistent fatigue was cross-sectionnally associated with higher white matter hyperintensity volume in older adults. Further longitudinal studies, using an assessment tool specifically designed and validated for measuring fatigue, are needed to confirm our findings.}, - number = {8}, - urldate = {2024-03-12}, - journal = {Aging \& Mental Health}, - author = {Angioni, Davide and Cesari, Matteo and Raffin, Jeremy and Virecoulon Giudici, Kelly and Mangin, Jean François and Bouyahia, Ali and Chupin, Marie and Fischer, Clara and Gourieux, Emmanuelle and Rolland, Yves and De Breucker, Sandra and Vellas, Bruno and de Souto Barreto, Philipe}, - month = jul, - year = {2022}, - pmid = {34082625}, - note = {Publisher: Routledge -\_eprint: https://doi.org/10.1080/13607863.2021.1932737}, - keywords = {cortical thickness, brain health, Fatigue, older adults, sub-cortical volumes, white matter hyperintensity volume}, - pages = {1654--1660}, -} - -@article{guevara_disentangling_2022, - title = {Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification}, - volume = {255}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922003214}, - doi = {10.1016/j.neuroimage.2022.119197}, - abstract = {Each variation of the cortical folding pattern implies a particular rearrangement of the geometry of the fibers of the underlying white matter. While this rearrangement only impacts the ends of the long pathways, it may affect most of the trajectory of the short bundles. Therefore, mapping the short fibers of the human brain using diffusion-based tractography requires a dedicated strategy to overcome the variability of the folding patterns. In this paper, we propose a fiber-based stratification strategy splitting the population into homogeneous groups for disentangling the superficial white matter bundle organization. This strategy introduces a new refined fiber distance which includes angular considerations for inferring fine-grained atlases of the short bundles surrounding a specific sulcus and a subtractogram distance that quantifies the similitude between fiber sets of two different subjects. The stratification splits the population into groups with similar regional fiber organization using manifold learning. We first successfully test the hypothesis that the main source of variability of the regional fiber organization is the variability of the regional folding pattern. Then, in each group, we proceed with the automatic identification of the most stable bundles, at a higher granularity level than what can be achieved with the non-stratified whole population, enabling the disentanglement of the very variable configuration of the short fibers. Finally, the method searches for bundle correspondence across groups to build a population level atlas. As a proof of concept, the atlas refinement achieved by this strategy is illustrated for the fibers that surround the central sulcus and the superior temporal sulcus using the HCP dataset.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Sun, Zhong-Yi and Guevara, Pamela and Rivière, Denis and Grigis, Antoine and Poupon, Cyril and Mangin, Jean-François}, - month = jul, - year = {2022}, - keywords = {Tractography, Short association fibers, Diffusion-weighted imaging, Cortical variability, Superficial white matter, U-fibers, White matter bundle}, - pages = {119197}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EWUQUNGE/S1053811922003214.html:text/html}, -} - -@article{de_vareilles_exploring_2023, - title = {Exploring the emergence of morphological asymmetries around the brain’s {Sylvian} fissure: a longitudinal study of shape variability in preterm infants}, - volume = {33}, - issn = {1047-3211}, - shorttitle = {Exploring the emergence of morphological asymmetries around the brain’s {Sylvian} fissure}, - url = {https://doi.org/10.1093/cercor/bhac533}, - doi = {10.1093/cercor/bhac533}, - abstract = {Brain folding patterns vary within the human species, but some folding properties are common across individuals, including the Sylvian fissure’s inter-hemispheric asymmetry. Contrarily to the other brain folds (sulci), the Sylvian fissure develops through the process of opercularization, with the frontal, parietal, and temporal lobes growing over the insular lobe. Its asymmetry may be related to the leftward functional lateralization for language processing, but the time course of these asymmetries’ development is still poorly understood. In this study, we investigated refined shape features of the Sylvian fissure and their longitudinal development in 71 infants born extremely preterm (mean gestational age at birth: 26.5 weeks) and imaged once before and once at term-equivalent age (TEA). We additionally assessed asymmetrical sulcal patterns at TEA in the perisylvian and inferior frontal regions, neighbor to the Sylvian fissure. While reproducing renowned strong asymmetries in the Sylvian fissure, we captured an early encoding of its main asymmetrical shape features, and we observed global asymmetrical shape features representative of a more pronounced opercularization in the left hemisphere, contrasting with the previously reported right hemisphere advance in sulcation around birth. This added novel insights about the processes governing early-life brain folding mechanisms, potentially linked to the development of language-related capacities.}, - number = {11}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {De Vareilles, Héloïse and Rivière, Denis and Pascucci, Marco and Sun, Zhong-Yi and Fischer, Clara and Leroy, François and Tataranno, Maria-Luisa and Benders, Manon J and Dubois, Jessica and Mangin, Jean-François}, - month = jun, - year = {2023}, - pages = {6667--6680}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/C9B6Z5JX/7005629.html:text/html;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7XEB2EWI/De Vareilles et al. - 2023 - Exploring the emergence of morphological asymmetri.pdf:application/pdf}, -} - -@article{blanc_prodromal_2022, - title = {Prodromal characteristics of dementia with {Lewy} bodies: baseline results of the {MEMENTO} memory clinics nationwide cohort}, - volume = {14}, - issn = {1758-9193}, - shorttitle = {Prodromal characteristics of dementia with {Lewy} bodies}, - url = {https://doi.org/10.1186/s13195-022-01037-0}, - doi = {10.1186/s13195-022-01037-0}, - abstract = {Isolated subjective cognitive impairment (SCI) and mild cognitive impairment (MCI) are the prodromal phases of dementia with Lewy bodies (DLB). MEMENTO is a nationwide study of patients with SCI and MCI with clinic, neuropsychology, biology, and brain imaging data. We aimed to compare SCI and MCI patients with symptoms of prodromal DLB to others in this study at baseline.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Alzheimer's Research \& Therapy}, - author = {Blanc, Frederic and Bouteloup, Vincent and Paquet, Claire and Chupin, Marie and Pasquier, Florence and Gabelle, Audrey and Ceccaldi, Mathieu and de Sousa, Paulo Loureiro and Krolak-Salmon, Pierre and David, Renaud and Fischer, Clara and Dartigues, Jean-François and Wallon, David and Moreaud, Olivier and Sauvée, Mathilde and Belin, Catherine and Harston, Sandrine and Botzung, Anne and Albasser, Timothée and Demuynck, Catherine and Namer, Izzie and Habert, Marie-Odile and Kremer, Stéphane and Bousiges, Olivier and Verny, Marc and Muller, Candice and Philippi, Nathalie and Chene, Geneviève and Cretin, Benjamin and Mangin, Jean-François and Dufouil, Carole}, - month = jul, - year = {2022}, - keywords = {Mild cognitive impairment, Prodromal, Dementia with Lewy bodies, Lewy body disease, Mild neurocognitive impairment, Subjective cognitive impairment}, - pages = {96}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/G8CTPVB9/Blanc et al. - 2022 - Prodromal characteristics of dementia with Lewy bo.pdf:application/pdf}, -} - -@inproceedings{chavas_unsupervised_2022, - address = {Cham}, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {Unsupervised {Representation} {Learning} of {Cingulate} {Cortical} {Folding} {Patterns}}, - isbn = {978-3-031-16431-6}, - doi = {10.1007/978-3-031-16431-6_8}, - abstract = {The human cerebral cortex is folded, making sulci and gyri over the whole cortical surface. Folding presents a very high inter-subject variability, and some neurodevelopmental disorders are correlated to local folding structures, named folding patterns. However, it is tough to characterize these patterns manually or semi-automatically using geometric distances. Here, we propose a new methodology to identify typical folding patterns. We focus on the cingulate region, known to have a clinical interest, using so-called skeletons (3D representation of folding patterns). We compare two models, \$\${\textbackslash}beta -VAE\$\$β-VAEand SimCLR, in an unsupervised setting to learn a relevant representation of these patterns. We add a decoder to SimCLR to be able to analyse latent space. Specifically, we leverage the data augmentations used in SimCLR to propose a novel kind of augmentations based on folding topology. We then apply a clustering on the latent space. Cluster folding averages, interpolation in the latent space and reconstructions reveal new pattern structures. This structured representation shows that unsupervised learning can help in the discovery of still unknown patterns. We will gain further insights into folding patterns by using new priors in the unsupervised algorithms and integrating other brain data modalities. Code and experiments are available at github.com/neurospin-projects/2021\_jchavas\_lguillon\_deepcingulate.}, - language = {en}, - booktitle = {Medical {Image} {Computing} and {Computer} {Assisted} {Intervention} – {MICCAI} 2022}, - publisher = {Springer Nature Switzerland}, - author = {Chavas, Joël and Guillon, Louise and Pascucci, Marco and Dufumier, Benoît and Rivière, Denis and Mangin, Jean-François}, - editor = {Wang, Linwei and Dou, Qi and Fletcher, P. Thomas and Speidel, Stefanie and Li, Shuo}, - year = {2022}, - keywords = {Folding pattern, Cortex, beta-VAE, Contrastive learning, SimCLR}, - pages = {77--87}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/97NRZ9PE/Chavas et al. - 2022 - Unsupervised Representation Learning of Cingulate .pdf:application/pdf}, -} - -@article{roman_superficial_2022, - title = {Superficial white matter bundle atlas based on hierarchical fiber clustering over probabilistic tractography data}, - volume = {262}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922006656}, - doi = {10.1016/j.neuroimage.2022.119550}, - abstract = {The study of short association fibers is still an incomplete task due to their higher inter-subject variability and the smaller size of this kind of fibers in comparison to known long association bundles. However, their description is essential to understand human brain dysfunction and better characterize the human brain connectome. In this work, we present a multi-subject atlas of short association fibers, which was computed using a superficial white matter bundle identification method based on fiber clustering. To create the atlas, we used probabilistic tractography from one hundred subjects from the HCP database, aligned with non-linear registration. The method starts with an intra-subject clustering of short fibers (30-85 mm). Based on a cortical atlas, the intra-subject cluster centroids from all subjects are segmented to identify the centroids connecting each region of interest (ROI) of the atlas. To reduce computational load, the centroids from each ROI group are randomly separated into ten subgroups. Then, an inter-subject hierarchical clustering is applied to each centroid subgroup, followed by a second level of clustering to select the most-reproducible clusters across subjects for each ROI group. Finally, the clusters are labeled according to the regions that they connect, and clustered to create the final bundle atlas. The resulting atlas is composed of 525 bundles of superficial short association fibers along the whole brain, with 384 bundles connecting pairs of different ROIs and 141 bundles connecting portions of the same ROI. The reproducibility of the bundles was verified using automatic segmentation on three different tractogram databases. Results for deterministic and probabilistic tractography data show high reproducibility, especially for probabilistic tractography in HCP data. In comparison to previous work, our atlas features a higher number of bundles and greater cortical surface coverage.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Román, Claudio and Hernández, Cecilia and Figueroa, Miguel and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela}, - month = nov, - year = {2022}, - keywords = {dMRI, Hierarchical clustering, Superficial white matter, Human Connectome Project, Short association bundles}, - pages = {119550}, -} - -@article{perus_effects_2022, - title = {Effects of preventive interventions on neuroimaging biomarkers in subjects at-risk to develop {Alzheimer}'s disease: {A} systematic review}, - volume = {14}, - issn = {1663-4365}, - shorttitle = {Effects of preventive interventions on neuroimaging biomarkers in subjects at-risk to develop {Alzheimer}'s disease}, - url = {https://www.frontiersin.org/articles/10.3389/fnagi.2022.1014559}, - doi = {10.3389/fnagi.2022.1014559}, - abstract = {Alzheimer’s Disease (AD) is a multifactorial and complex neurodegenerative disorder. Some modifiable risk factors have been associated with an increased risk of appearance of the disease and/or cognitive decline. Preventive clinical trials aiming at reducing one or combined risk factors have been implemented and their potential effects assessed on cognitive trajectories and on AD biomarkers. However, the effect of interventions on surrogate markers, in particular imaging biomarkers, remains poorly understood. We conducted a review of the literature and analyzed forty-three interventional studies that included physical exercise, nutrition, cognitive training or multidomain interventions, and assessed various brain imaging biomarkers, to determine the effects of preventive interventions on imaging biomarkers for subjects at-risk to develop AD. Deciphering the global and regional brain effect of each and combined interventions will help to better understand the interplay relationship between multimodal interventions, cognition, surrogate brain markers and to better design primary and secondary outcomes for future preventive clinical trials. Those studies were pondered using generally-admitted quality criteria to reveal that interventions may affect the brain of patients with cognitive impairment rather than those without cognitive impairment thus indicating that particular care should be taken when selecting individuals for interventions. Additionally, a majority of the studies concurred on the effect of the interventions and particularly onto the frontal brain areas.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Aging Neuroscience}, - author = {Perus, Lisa and Busto, Germain U. and Mangin, Jean-François and Le Bars, Emmanuelle and Gabelle, Audrey}, - month = nov, - year = {2022}, - note = {Publisher: Frontiers}, - keywords = {Alzheimer's disease, prevention, Multidomain intervention, brain imaging, biomarkers, cognitive training, nutrition, physical exercise}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QNM6HD9B/Perus et al. - 2022 - Effects of preventive interventions on neuroimagin.pdf:application/pdf}, -} - -@article{devos_trial_2022, - title = {Trial of {Deferiprone} in {Parkinson}’s {Disease}}, - volume = {387}, - issn = {0028-4793}, - url = {https://doi.org/10.1056/NEJMoa2209254}, - doi = {10.1056/NEJMoa2209254}, - number = {22}, - urldate = {2024-03-12}, - journal = {New England Journal of Medicine}, - author = {Devos, David and Labreuche, Julien and Rascol, Olivier and Corvol, Jean-Christophe and Duhamel, Alain and Guyon Delannoy, Pauline and Poewe, Werner and Compta, Yaroslau and Pavese, Nicola and Růžička, Evžen and Dušek, Petr and Post, Bart and Bloem, Bastiaan R. and Berg, Daniela and Maetzler, Walter and Otto, Markus and Habert, Marie-Odile and Lehericy, Stéphane and Ferreira, Joaquim and Dodel, Richard and Tranchant, Christine and Eusebio, Alexandre and Thobois, Stéphane and Marques, Ana-Raquel and Meissner, Wassilios G. and Ory-Magne, Fabienne and Walter, Uwe and de Bie, Rob M.A. and Gago, Miguel and Vilas, Dolores and Kulisevsky, Jaime and Januario, Cristina and Coelho, Miguel V.S. and Behnke, Stefanie and Worth, Paul and Seppi, Klaus and Ouk, Thavarak and Potey, Camille and Leclercq, Céline and Viard, Romain and Kuchcinski, Gregory and Lopes, Renaud and Pruvo, Jean-Pierre and Pigny, Pascal and Garçon, Guillaume and Simonin, Ophélie and Carpentier, Jessica and Rolland, Anne-Sophie and Nyholm, Dag and Scherfler, Christoph and Mangin, Jean-François and Chupin, Marie and Bordet, Régis and Dexter, David T. and Fradette, Caroline and Spino, Michael and Tricta, Fernando and Ayton, Scott and Bush, Ashley I. and Devedjian, Jean-Christophe and Duce, James A. and Cabantchik, Ioav and Defebvre, Luc and Deplanque, Dominique and Moreau, Caroline}, - month = dec, - year = {2022}, - pmid = {36449420}, - note = {Publisher: Massachusetts Medical Society -\_eprint: https://doi.org/10.1056/NEJMoa2209254}, - pages = {2045--2055}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WP2H8PI9/Devos et al. - 2022 - Trial of Deferiprone in Parkinson’s Disease.pdf:application/pdf}, -} - -@article{gonzalez-bautista_development_2023, - title = {Development and {Validation} of a {Cutoff} for the {Chair} {Stand} {Test} as a {Screening} for {Mobility} {Impairment} in the {Context} of the {Integrated} {Care} for {Older} {People} {Program}}, - volume = {78}, - issn = {1758-535X}, - url = {https://doi.org/10.1093/gerona/glac055}, - doi = {10.1093/gerona/glac055}, - abstract = {The 5-repetition chair stand test (CST) is increasingly being used to assess locomotion capacity in older adults. However, there is a lack of age-stratified cutoffs for adults aged ≥70 validated against a higher risk of functional loss.We used 2 population-based studies (Study on global AGEing and adult health in Mexico [SAGE Mexico] and Toledo Study for Healthy Aging [TSHA]) and receiver operating characteristic (ROC) analyses to develop and cross-validate age-stratified chair stand cutoffs with activities of daily living (ADL) disability as the outcome. Then, we used data from an randomized controlled trial (RCT) (Multidomain Alzheimer Preventive Trial [MAPT]) and a frailty day-hospital for external validation with cross-sectional and longitudinal measures of ADL disability. The merged sample of SAGE Mexico and TSHA was n = 1 595; sample sizes for external validation were: MAPT n = 1 573 and Frailty day-hospital n = 2 434. The Cox models for incident disability in MAPT had a mean follow-up of 58.6 months.Cutoffs obtained were 14 second (ages 70–79) and 16 second (ages 80+). Those cutoffs identified older adults at higher odds of incident ADL disability odds ratio (OR) = 1.72 (95\% confidence interval [CI] 1.06; 2.78) for ages 70–79 and odds ratio (OR) = 2.27 (95\% CI 1.07; 4.80) in those aged 80+. Being a slow chair stander according to the cut points was associated with ADL disability in cross-sectional and longitudinal measures.Fourteen- and 16-second cut points for the CST are suitable to identify people at higher risk of functional decline among older adults in Mexico and Toledo, Spain. Adjusting the cut point from 14 to 16 second generally improved the psychometric properties of the test. The validation of these cutoffs can facilitate the screening for limited mobility and the implementation of the Integrated Care for Older People program.}, - number = {1}, - urldate = {2024-03-12}, - journal = {The Journals of Gerontology: Series A}, - author = {Gonzalez-Bautista, Emmanuel and de Souto Barreto, Philipe and Salinas-Rodriguez, Aaron and Manrique-Espinoza, Betty and Sourdet, Sandrine and Rolland, Yves and Rodríguez-Mañas, Leocadio and Andrieu, Sandrine and Vellas, Bruno and {MAPT/DSA Group}}, - month = jan, - year = {2023}, - pages = {104--110}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CHL2PZDE/Gonzalez-Bautista et al. - 2023 - Development and Validation of a Cutoff for the Cha.pdf:application/pdf}, -} - -@article{perus_impact_2023, - title = {Impact of multidomain preventive strategies on functional brain connectivity in older adults with cognitive complaint: {Subset} from the {Montpellier} center of the ancillary {MAPT}-{MRI} study}, - volume = {14}, - issn = {1663-4365}, - shorttitle = {Impact of multidomain preventive strategies on functional brain connectivity in older adults with cognitive complaint}, - url = {https://www.frontiersin.org/articles/10.3389/fnagi.2022.971220}, - doi = {10.3389/fnagi.2022.971220}, - abstract = {The impact of multi-domain preventive interventions on older adults and, in particular on those with higher risk to develop Alzheimer’s disease (AD), could be beneficial, as it may delay brain cognitive decline. However, the precise mechanism of such positive impact is not fully understood and may involve brain reserve and adaptability of brain functional connectivity (FC) adaptability. To determine the effect of multidomain interventions (involving physical activity, cognitive training, nutritional counseling alone or in combination with omega-3 fatty acid supplementation and versus a placebo) on the brain, longitudinal FC changes were assessed after 36 months of intervention in on 100 older adults {\textgreater}(above 70 years’ year-old) and with subjective cognitive complaints. No global change in FC was detected after uni or multidomain preventive interventions. However, an effect of omega-3 fatty acid supplementation dependent on cognitive decline status was underlined for frontoparietal, salience, visual and sensorimotor networks FC. These findings were independent of the cortical thickness and vascular burden. These results emphasize the importance of patient stratification, based on risk factors, preventive interventions.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Aging Neuroscience}, - author = {Perus, Lisa and Mangin, Jean-François and Deverdun, Jérémy and Gutierrez, Laure-Anne and Gourieux, Emmanuelle and Fischer, Clara and Van Dokkum, Liesjet E. H. and Manesco, Clara and Busto, Germain and Guyonnet, Sophie and Vellas, Bruno and Gabelle, Audrey and Le Bars, Emmanuelle and Group, The MAPT/DSA and Vellas, Bruno and Guyonnet, Sophie and Carrié, Isabelle and Brigitte, Lauréne and Faisant, Catherine and Lala, Françoise and Delrieu, Julien and Villars, Hélène and Combrouze, Emeline and Badufle, Carole and Zueras, Audrey and Andrieu, Sandrine and Cantet, Christelle and Morin, Christophe and Van Kan, Gabor Abellan and Dupuy, Charlotte and Rolland, Yves and Caillaud, Céline and Ousset, Pierre-Jean and Lala, Françoise and Willis, Sherry and Belleville, Sylvie and Gilbert, Brigitte and Fontaine, Francine and Dartigues, Jean-François and Marcet, Isabelle and Delva, Fleur and Foubert, Alexandra and Cerda, Sandrine and Marie-Noëlle-Cuffi and Costes, Corinne and Rouaud, Olivier and Manckoundia, Patrick and Quipourt, Valérie and Marilier, Sophie and Franon, Evelyne and Bories, Lawrence and Pader, Marie-Laure and Basset, Marie-France and Lapoujade, Bruno and Faure, Valérie and Tong, Michael Li Yung and Malick-Loiseau, Christine and Cazaban-Campistron, Evelyne and Desclaux, Françoise and Blatge, Colette and Dantoine, Thierry and Laubarie-Mouret, Cécile and Saulnier, Isabelle and Clément, Jean-Pierre and Picat, Marie-Agnès and Bernard-Bourzeix, Laurence and Willebois, Stéphanie and Désormais, Iléana and Cardinaud, Noëlle and Bonnefoy, Marc and Livet, Pierre and Rebaudet, Pascale and Gédéon, Claire and Burdet, Catherine and Terracol, Flavien and Pesce, Alain and Roth, Stéphanie and Chaillou, Sylvie and Louchart, Sandrine and Sudres, Kristel and Lebrun, Nicolas and Barro-Belaygues, Nadège and Touchon, Jacques and Bennys, Karim and Gabelle, Audrey and Romano, Aurélia and Touati, Lynda and Marelli, Cécilia and Pays, Cécile and Robert, Philippe and Le Duff, Franck and Gervais, Claire and Gonfrier, Sébastien and Gasnier, Yannick and Bordes, Serge and Begorre, Danièle and Carpuat, Christian and Khales, Khaled and Lefebvre, Jean-François and Misbah El Idrissi, Samira and Skolil, Pierre and Salles, Jean-Pierre and Dufouil, Carole and Lehéricy, Stéphane and Chupin, Marie and Mangin, Jean-François and Bouhayia, Ali and Allard, Michèle and Ricolfi, Frédéric and Dubois, Dominique and Bonceour Martel, Marie Paule and Cotton, François and Bonafé, Alain and Chanalet, Stéphane and Hugon, Françoise and Bonneville, Fabrice and Cognard, Christophe and Chollet, François and Payoux, Pierre and Voisin, Thierry and Delrieu, Julien and Peiffer, Sophie and Hitzel, Anne and Allard, Michèle and Zanca, Michel and Monteil, Jacques and Darcourt, Jacques and Molinier, Laurent and Derumeaux, Hélène and Costa, Nadège and Perret, Bertrand and Vinel, Claire and Caspar-Bauguil, Sylvie and Olivier-Abbal, Pascale and Andrieu, Sandrine and Cantet, Christelle and Coley, Nicola}, - month = jan, - year = {2023}, - note = {Publisher: Frontiers}, - keywords = {Multidomain intervention, cognitive training, Exercise, magnetic resonance imaging (MRI), Omega-3 fatty Acids, Resting-state functional MRI (fMRI)}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AFRSA6UB/Perus et al. - 2023 - Impact of multidomain preventive strategies on fun.pdf:application/pdf}, -} - -@article{labra_comparative_2023, - title = {Comparative study of manual identification of brain foldings in a living human brain using a proxy-endocast obtained from {MRI}}, - volume = {35}, - copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, - issn = {0037-8984}, - url = {https://journals.openedition.org/bmsap/11242}, - doi = {10.4000/bmsap.11242}, - abstract = {The use of virtual endocasts allows investigation of the folding configurations of the cerebral cortex of extinct species. However, is that really possible? Our goal is to help answer this question by qualifying and quantifying the subjective identifications of the foldings on endocasts compared to their real configurations on the brain. We invited 14 paleoneurologists to manually reconstruct the foldings they could recognize in a proxy-endocast obtained from an in-vivo MRI. MRI data were obt...}, - language = {gb}, - number = {(s)}, - urldate = {2024-03-12}, - journal = {Bulletins et mémoires de la Société d’Anthropologie de Paris. BMSAP}, - author = {Labra, Nicole and Leprince, Yann and Rivière, Denis and Santin, Mathieu and Mangin, Jean François and Albessard-Ball, Lou and Beaudet, Amélie and Broadfield, Douglas and Bruner, Emiliano and Carlson, Kristian J. and Cofran, Zachary and Falk, Dean and Gilissen, Emmanuel and Gómez-Robles, Aida and Neubauer, Simon and Pearson, Alannah and Röding, Carolin and Zhang, Yameng and Mounier, Aurélien and Balzeau, Antoine}, - month = jan, - year = {2023}, - note = {Number: (s) -Publisher: Société d'anthropologie de Paris}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FFFQTGEA/Labra et al. - 2023 - Comparative study of manual identification of brai.pdf:application/pdf}, -} - -@article{hopkins_genetic_2023, - title = {Genetic determinants of individual variation in the superior temporal sulcus of chimpanzees ({Pan} troglodytes)}, - volume = {33}, - issn = {1047-3211}, - url = {https://doi.org/10.1093/cercor/bhac183}, - doi = {10.1093/cercor/bhac183}, - abstract = {The superior temporal sulcus (STS) is a conserved fold that divides the middle and superior temporal gyri. In humans, there is considerable variation in the shape, folding pattern, lateralization, and depth of the STS that have been reported to be associated with social cognition and linguistic functions. We examined the role that genetic factors play on individual variation in STS morphology in chimpanzees. The surface area and depth of the STS were quantified in sample of 292 captive chimpanzees comprised of two genetically isolated population of individuals. The chimpanzees had been previously genotyped for AVPR1A and KIAA0319, two genes that play a role in social cognition and communication in humans. Single nucleotide polymorphisms in the KIAA0319 and AVPR1A genes were associated with average depth as well as asymmetries in the STS. By contrast, we found no significant effects of these KIA0319 and AVPR1A polymorphism on surface area and depth measures for the central sulcus. The overall findings indicate that genetic factors account for a small to moderate amount of variation in STS morphology in chimpanzees. These findings are discussed in the context of the role of the STS in social cognition and language in humans and their potential evolutionary origins.}, - number = {5}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Hopkins, William D and Coulon, Oliver and Meguerditchian, Adrien and Staes, Nicky and Sherwood, Chet C and Schapiro, Steven J and Mangin, Jean-Francois and Bradley, Brenda}, - month = mar, - year = {2023}, - pages = {1925--1940}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZP8RT7VH/Hopkins et al. - 2023 - Genetic determinants of individual variation in th.pdf:application/pdf}, -} - -@inproceedings{molina_group-wise_2023, - title = {Group-wise cortical parcellation based on structural connectivity and hierarchical clustering}, - volume = {12567}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670L/Group-wise-cortical-parcellation-based-on-structural-connectivity-and-hierarchical/10.1117/12.2670138.full}, - doi = {10.1117/12.2670138}, - abstract = {This paper presents a new cortical parcellation method based on group-wise connectivity and hierarchical clustering. A preliminary sub-parcellation is performed using intra-subject and inter-subject fiber clustering to obtain representative bundles among subjects with similar shapes and trajectories. The sub-parcellation is obtained by intersecting fiber clusters with cortical meshes. Next, mean connectivity and mean overlap matrices are computed over the sub-parcels to obtain spatial and connectivity information. To hierarchize the information, we propose to weight both matrices, to obtain an affinity graph, and then a dendrogram to merge or divide parcels by their hierarchy. Finally, to obtain homogeneous parcels, the method computes morphological operations. By selecting a different number of clusters over the dendrogram, the method obtains a different number of parcels and a variation in the resulting parcel sizes, depending on the parameters used. We computed the coefficient of variation (CV ) of the parcel size to evaluate the homogeneity of the parcels. Preliminary results suggest that the use of representative clusters and the integration of sub-parcel overlap and connectivity strength provide useful information to generate cortical parcellations at different levels of granularity. Even results are preliminary, this novel method allows researchers to add group-wise connectivity strength and spatial information for the construction of diffusion-based parcellations. Future work will include a detailed analysis of parameters, such as the matrix weights and the number of sub-parcel clusters, and the generation of hierarchical parcellations to improve the insight into the cortex subdivision and hierarchy among parcels.}, - urldate = {2024-03-12}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Molina, Joaquín and Mendoza, Cristóbal and Román, Claudio and Houenou, Josselin and Poupon, Cyril and Mangin, Jean François and El-Deredy, Wael and Hernández, Cecilia and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {172--181}, -} - -@inproceedings{poo_fiber_2023, - title = {Fiber bundles simulator using exponential curves to validate fiber clustering algorithms}, - volume = {12567}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670J/Fiber-bundles-simulator-using-exponential-curves-to-validate-fiber-clustering/10.1117/12.2669811.full}, - doi = {10.1117/12.2669811}, - abstract = {Currently, there are many methods for processing diffusion MRI (dMRI) tractography data, with the aim to identify the main white matter connections. However, methods like fiber clustering lack ground truth, making the evaluation of the effectiveness of different clustering algorithms problematic. An alternative to evaluate the performance and test the efficacy of these algorithms is to use simulated fiber datasets. Nevertheless, the simulation of this data is not trivial due to brain fibers’ irregular and complex shape. Although many fiber bundle simulators exist, they have been developed for other purposes, such as validating tractography algorithms or local diffusion models. In addition, these simulators usually use simple fiber bundle configurations without considering complex bundle shapes. With this in mind, the main goal of this work is to implement a simulator of brain fiber bundles based on exponential curves for validating fiber clustering methods. This representation uses bundle centroids and shape parameters to obtain a more realistic appearance of the fascicles. The simulator was validated using a deep white matter fiber bundle atlas, obtaining a good percentage of intersection between the original and simulated bundles, of up to 82\%. Furthermore, we used groups of simulated bundles for the whole brain to evaluate the performance of a fiber clustering algorithm (QuickBundles) when using different distance thresholds, showing the utility of the proposed simulator.}, - urldate = {2024-03-12}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Poo, Elida and Kublik, Carlos and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {154--163}, -} - -@inproceedings{vindas_geolab_2023, - title = {{GeoLab}: {Geometry}-{Based} {Tractography} {Parcellation} of {Superficial} {White} {Matter}}, - shorttitle = {{GeoLab}}, - url = {https://ieeexplore.ieee.org/abstract/document/10230336}, - doi = {10.1109/ISBI53787.2023.10230336}, - abstract = {Superficial white matter (SWM) has been less studied than long-range connections despite being of interest to clinical research, and few tractography parcellation methods have been adapted to SWM. Here, we propose an efficient geometry-based parcellation method (GeoLab) that allows high-performance segmentation of hundreds of short white matter bundles from a subject. This method has been designed for the SWM atlas of EBRAINS European infrastructure, which is composed of 657 bundles. The atlas projection relies on the precomputed statistics of six bundle-specific geometrical properties of atlas streamlines. In the spirit of RecoBundles, a global and local streamline-based registration (SBR) is used to align the subject to the atlas space. Then, the streamlines are labeled taking into account the six geometrical parameters describing the similarity to the streamlines in the model bundle. Compared to other state-of-the-art methods, GeoLab allows the extraction of more bundles with a higher number of streamlines.}, - urldate = {2024-03-12}, - booktitle = {2023 {IEEE} 20th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Vindas, Nabil and Avila, Nicole Labra and Zhang, Fan and Xue, Tengfei and O’Donnell, Lauren J. and Mangin, Jean-François}, - month = apr, - year = {2023}, - note = {ISSN: 1945-8452}, - keywords = {Brain, Europe, tractography, diffusion MRI, Codes, Computers, Geology, Geometry, Memory management, Streaming media, Superficial White Matter Parcellation, U-Fibers}, - pages = {1--5}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6QEAZXRZ/Vindas et al. - 2023 - GeoLab Geometry-Based Tractography Parcellation o.pdf:application/pdf}, -} - -@article{raffin_cross-sectional_2023, - title = {Cross-sectional associations between cortical thickness and physical activity in older adults with spontaneous memory complaints: {The} {MAPT} {Study}}, - volume = {12}, - issn = {2095-2546}, - shorttitle = {Cross-sectional associations between cortical thickness and physical activity in older adults with spontaneous memory complaints}, - url = {https://www.sciencedirect.com/science/article/pii/S209525462100020X}, - doi = {10.1016/j.jshs.2021.01.011}, - abstract = {Background -Age-related changes in brain structure may constitute the starting point for cerebral function alteration. Physical activity (PA) demonstrated favorable associations with total brain volume, but its relationship with cortical thickness (CT) remains unclear. We investigated the cross-sectional associations between PA level and CT in community-dwelling people aged 70 years and older. -Methods -A total of 403 older adults aged 74.8 ± 4.0 years (mean ± SD) who underwent a baseline magnetic resonance imaging examination and who had data on PA and confounders were included. PA was assessed with a questionnaire. Participants were categorized according to PA levels. Multiple linear regressions were used to compare the brain CT (mm) of the inactive group (no PA at all) with 6 active groups (growing PA levels) in 34 regions of interest. -Results -Compared with inactive persons, people who achieved PA at a level of 1500−1999 metabolic equivalent task-min/week (i.e., about 6−7 h of brisk walking for exercise and those who achieved it at 2000−2999 metabolic equivalent task-min/week (i.e., 8−11 h of brisk walking for exercise) had higher CT in the fusiform gyrus and the temporal pole. Additionally, dose−response associations between PA and CT were found in the fusiform gyrus (B = 0.011, SE = 0.004, adj. p = 0.035), the temporal pole (B = 0.026, SE = 0.009, adj. p = 0.048), and the caudal middle frontal gyrus, the entorhinal, medial orbitofrontal, lateral occipital, and insular cortices. -Conclusion -This study demonstrates a positive association between PA level and CT in temporal areas such as the fusiform gyrus, a brain region often associated to Alzheimer's disease in people aged 70 years and older. Future investigations focusing on PA type may help to fulfil remaining knowledge gaps in this field.}, - number = {3}, - urldate = {2024-03-12}, - journal = {Journal of Sport and Health Science}, - author = {Raffin, Jérémy and Rolland, Yves and Fischer, Clara and Mangin, Jean-François and Gabelle, Audrey and Vellas, Bruno and de Souto Barreto, Philipe}, - month = may, - year = {2023}, - keywords = {Alzheimer's disease, Cortical thickness, Physical activity, Brain aging}, - pages = {324--332}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/G7XK2QTF/Raffin et al. - 2023 - Cross-sectional associations between cortical thic.pdf:application/pdf}, -} - -@article{lespinasse_associations_2023, - title = {Associations among hypertension, dementia biomarkers, and cognition: {The} {MEMENTO} cohort}, - volume = {19}, - copyright = {© 2022 The Authors. Alzheimer's \& Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.}, - issn = {1552-5279}, - shorttitle = {Associations among hypertension, dementia biomarkers, and cognition}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/alz.12866}, - doi = {10.1002/alz.12866}, - abstract = {Introduction Approximately 40\% of dementia cases could be delayed or prevented acting on modifiable risk factors including hypertension. However, the mechanisms underlying the hypertension–dementia association are still poorly understood. Methods We conducted a cross-sectional analysis in 2048 patients from the MEMENTO cohort, a French multicenter clinic-based study of outpatients with either isolated cognitive complaints or mild cognitive impairment. Exposure to hypertension was defined as a combination of high blood pressure (BP) status and antihypertensive treatment intake. Pathway associations were examined through structural equation modeling integrating extensive collection of neuroimaging biomarkers and clinical data. Results Participants treated with high BP had significantly lower cognition compared to the others. This association was mediated by higher neurodegeneration and higher white matter hyperintensities load but not by Alzheimer's disease (AD) biomarkers. Discussion These results highlight the importance of controlling hypertension for prevention of cognitive decline and offer new insights on mechanisms underlying the hypertension–dementia association. Highlights Paths of hypertension–cognition association were assessed by structural equation models. The hypertension–cognition association is not mediated by Alzheimer's disease biomarkers. The hypertension–cognition association is mediated by neurodegeneration and leukoaraiosis. Lower cognition was limited to participants treated with uncontrolled blood pressure. Blood pressure control could contribute to promote healthier brain aging.}, - language = {en}, - number = {6}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia}, - author = {Lespinasse, Jérémie and Chêne, Geneviève and Mangin, Jean-Francois and Dubois, Bruno and Blanc, Frederic and Paquet, Claire and Hanon, Olivier and Planche, Vincent and Gabelle, Audrey and Ceccaldi, Mathieu and Annweiler, Cedric and Krolak-Salmon, Pierre and Godefroy, Olivier and Wallon, David and Sauvée, Mathilde and Bergeret, Sébastien and Chupin, Marie and Proust-Lima, Cécile and Dufouil, Carole and Group, for the MEMENTO study}, - year = {2023}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/alz.12866}, - keywords = {cortical thickness, white matter hyperintensities, cognition, tau, amyloid beta 42, fluorodeoxyglucose positron emission tomography, hippocampal volume, hypertension, mediation, positron emission tomography amyloid, structural equation model}, - pages = {2332--2342}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/24Z59B8X/Lespinasse et al. - 2023 - Associations among hypertension, dementia biomarke.pdf:application/pdf}, -} - -@article{gondova_predicting_2023, - title = {Predicting neurodevelopmental outcomes from neonatal cortical microstructure: {A} conceptual replication study}, - volume = {3}, - issn = {2666-9560}, - shorttitle = {Predicting neurodevelopmental outcomes from neonatal cortical microstructure}, - url = {https://www.sciencedirect.com/science/article/pii/S2666956023000156}, - doi = {10.1016/j.ynirp.2023.100170}, - abstract = {Machine learning combined with large-scale neuroimaging databases has been proposed as a promising tool for improving our understanding of the behavioural emergence and early prediction of the neurodevelopmental outcome. A recent example of this strategy is a study by Ouyang et al. (2020) which suggested that cortical microstructure quantified by diffusion MRI through fractional anisotropy (FA) metric in preterm and full-term neonates can lead to effective prediction of language and cognitive outcomes at 2 years of corrected age as assessed by Bayley Scales of Infant and Toddler Development, Third Edition (BSID-III) composite scores. Given the important need for robust and generalisable tools which can reliably predict the neurodevelopmental outcome of preterm infants, we aimed to replicate the conclusions of this work using a larger independent dataset from the developing Human Connectome Project dataset (dHCP, third release) with early MRI and BSID-III evaluation at 18 months of corrected age. We then aimed to extend the validation of the proposed predictive pipeline through the study of different cohorts (the largest one included 295 neonates, with gestational age between 29 and 42 week and post-menstrual age at MRI between 31 and 45 weeks). This allowed us to evaluate whether some limitations of the original study (mainly small sample size and limited variability in the input and output features used in the predictive models) would influence the prediction results. In contrast to the original study that inspired the current work, our prediction results did not outcompete the random levels. Furthermore, these negative results persisted even when the study settings were expanded. Our findings suggest that the cortical microstructure close to birth described by DTI-FA measures might not be sufficient for a reliable prediction of BSID-III scores during toddlerhood, at least in the current setting, i.e. generally older cohorts and a different processing pipeline. Our inability to conceptually replicate the results of the original study is in line with the previously reported replicability issues within the machine learning field and demonstrates the challenges in defining the good set of practices for the implementation and validation of reliable predictive tools in the neurodevelopmental (and other) fields.}, - number = {2}, - urldate = {2024-03-12}, - journal = {Neuroimage: Reports}, - author = {Gondová, Andrea and Neumane, Sara and Leprince, Yann and Mangin, Jean-François and Arichi, Tomoki and Dubois, Jessica}, - month = jun, - year = {2023}, - keywords = {Prediction, Prematurity, Neonates, Brain development, DTI (Diffusion tensor imaging), Generalisability, ML (machine learning)}, - pages = {100170}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SM2P6FLD/S2666956023000156.html:text/html}, -} - -@misc{foubet_shapes_2023, - title = {On the {Shapes} of the {Precentral} {Gyrus} of {Humans} and {Chimpanzees}}, - url = {https://hal.science/hal-04477128}, - abstract = {The cerebral neocortex, unique to mammals, has the particularity of being folded in many species. This folding is not random but related to the internal structural and functional organization[1,2]. Some patterns can be shared between species, such as the central (CS) and precentral (preCS) sulci in great apes that constitute the boundaries of the precentral gyrus, place of motor cortex (BA 4, and a part of BA6)[3]. -We have developed a method to capture the shape variability of cortical sulci within and between species. Here we examine the interindividual variability of the precentral gyrus (preCG) in humans and chimpanzees. -77 chimps (Pan troglodytes) were scanned in vivo at 3T according to US Department of Health and Human Services guidelines. Using the "Morphologist 2012" pipeline [4], CSs and preCSs were extracted from T2-weighted images, as well as T1-weighted images of sixty human HCP subjects. All sulci were affinely normalized in Talairach space and then with a species-specific homothetic transformation. Right sulci were flipped to allow comparison with left ones. A pairwise shape similarity matrix was computed after rigid alignment [5]. Isomap-based manifold learning was used to capture two axes describing the greatest parts of variance in the space spanned by the sulci. For better visualization, the sulci were rigidly aligned to the sulcus with the minimum distance to the set and local shape averages were performed at regular intervals along the isomap axes. We performed three experiments for intra- and inter-species comparisons. -Our moving averages capture preCG well in both species. The CS highlights the motor knob of the hand, which is larger, deeper, and more ventral in chimps than in humans. The preCS is mainly composed of two parts, far apart in chimps, corresponding to the inferior preCS (IP) and the superior preCS (SP) [7]. Between the IP and SP is a transverse gyrus that merges with the posterior part of the middle frontal gyrus. The width of the preCG is relatively larger in chimps, which is consistent with [6]. -In humans, the CS and preCS are not exactly aligned, with the preCS being more ventral. This may be due to the higher operculation in humans. -The shape variability features expressed on each of the isomap dimensions for the chimp and human experiments are different. No axis exhibits left-right asymmetry. Chimp dimension1 shows a shortening of the ventral portion of the preCG while keeping the transverse gyrus of the preCG aligned with the knob of the hand; as well as a shift of the orientation of SP to the knob. Dimension2 represents the two parts of preCG moving towards the knob. -In humans, dimension1 corresponds to a narrowing of the gyrus dorsally while the hand area develops and a somatosensory knob aligned with the transverse gyrus appears. Dimension2 represents the transverse gyrus reaching the surface simultaneously with the development of a somatosensory knob in the same middle part of the preCG. -The dimension1 that describes the variability of chimps and humans mixed together, shows that they separate along the axis: humans have a dorsal knob and the transverse gyrus connects at the somatosensory knob, while in chimps the gyrus arrives at a more ventral knob.The preCG narrows in this same area.The dimension2 does not separate the species (p=0.10). The hand knob remains in dorsal position while the SP shrinks, no major change ventrally. -Their knob being more dorsal, humans seem to have a longer oro-facial area allowing more complex structures. The transverse gyrus is mainly aligned with the hand knob in chimps while aligned with a more ventral sensory knob in humans. This location may correspond to the midprCG, a region defined by neurosurgical investigations [8] and functionally located between dorsal hand and ventral orofacial cortical representations. Further work may benefit from the addition of fibers tracts and cytoarchitectonic to better understand what these folding variations may reflect.}, - urldate = {2024-03-12}, - author = {Foubet, Ophelie and Sun, Zhong Yi and Hopkins, William and Mangin, Jean-François}, - month = jul, - year = {2023}, - note = {Published: Organization for Human Brain Mapping}, - keywords = {Sulci, central sulcus, chimpanzee, hominids, motor cortex, precentral gyrus}, - annote = {Poster}, - file = {HAL PDF Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TJ8UN7LF/Foubet et al. - 2023 - On the Shapes of the Precentral Gyrus of Humans an.pdf:application/pdf}, -} - -@article{messe_structural_2023, - title = {Structural basis of envelope and phase intrinsic coupling modes in the cerebral cortex}, - volume = {276}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811923003634}, - doi = {10.1016/j.neuroimage.2023.120212}, - abstract = {Intrinsic coupling modes (ICMs) can be observed in ongoing brain activity at multiple spatial and temporal scales. Two families of ICMs can be distinguished: phase and envelope ICMs. The principles that shape these ICMs remain partly elusive, in particular their relation to the underlying brain structure. Here we explored structure-function relationships in the ferret brain between ICMs quantified from ongoing brain activity recorded with chronically implanted micro-ECoG arrays and structural connectivity (SC) obtained from high-resolution diffusion MRI tractography. Large-scale computational models were used to explore the ability to predict both types of ICMs. Importantly, all investigations were conducted with ICM measures that are sensitive or insensitive to volume conduction effects. The results show that both types of ICMs are significantly related to SC, except for phase ICMs when using measures removing zero-lag coupling. The correlation between SC and ICMs increases with increasing frequency which is accompanied by reduced delays. Computational models produced results that were highly dependent on the specific parameter settings. The most consistent predictions were derived from measures solely based on SC. Overall, the results demonstrate that patterns of cortical functional coupling as reflected in both phase and envelope ICMs are both related, albeit to different degrees, to the underlying structural connectivity in the cerebral cortex.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Messé, Arnaud and Hollensteiner, Karl J. and Delettre, Céline and Dell-Brown, Leigh-Anne and Pieper, Florian and Nentwig, Lena J. and Galindo-Leon, Edgar E. and Larrat, Benoît and Mériaux, Sébastien and Mangin, Jean-François and Reillo, Isabel and de Juan Romero, Camino and Borrell, Víctor and Engler, Gerhard and Toro, Roberto and Engel, Andreas K. and Hilgetag, Claus C.}, - month = aug, - year = {2023}, - keywords = {Brain, Humans, Brain Mapping, Cerebral Cortex, Animals, Electrocorticography, Ferret brain, Ferrets, Intrinsic coupling modes, Structure–function relationship, Time delay}, - pages = {120212}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UGFJRIR8/Messé et al. - 2023 - Structural basis of envelope and phase intrinsic c.pdf:application/pdf}, -} - -@techreport{rybina_eosc-life_2023, - title = {{EOSC}-{Life} {Report} on the work of the {Open} {Call} {Projects}}, - url = {https://hal.science/hal-04185373}, - abstract = {This Deliverable 3.3 is a report on the Digital Life Sciences Open Call and two Internal Calls organised by EOSC-Life WP3. The organisation of these Calls followed the successful integration and support of 8 Demonstrator projects which provided the first concrete use cases in the initial phase of EOSC-Life. The three Calls overall supported 11 scientific user projects, selected to facilitate integration of concrete use-cases across Life Sciences domains into the European Open Science Cloud (EOSC) framework. Through the Calls, the practical goal was to facilitate co-creation of an open, digital collaborative space for life science research by developing FAIR tools, workflows, resources, infrastructures, and guidelines together with the EOSC-Life RIs experts and communities. We report in this Deliverable the following achievements: Organisation of the EOSC-Life Open and Internal Calls; Integrating and training the EOSC-Life WP3 Open Call and Internal Call project teams in EOSC-Life; Activities for connecting project teams with EOSC-Life and LS-RI communities and dissemination of projects outcomes to broader communities; Work done in the individual projects, their results, and impact of developed resources; Recommendations from the EOSC-Life WP3 project teams and the EOSC-Life community for future Open Calls.}, - number = {3.3}, - urldate = {2024-03-12}, - institution = {Zenodo}, - author = {Rybina, Arina and Audergon, Pauline and Pfander, Claudia and Batut, Bérénice and Beracochea, Martin and Bischof, Johanna and Bottländer, Michael and Buchhalter, Ivo and Burel, Jean-Marie and Cancio, Ibon and Carazo, Jose- Maria and Castillo-Rutz, Nayari and Chiusano, Maria Luisa and Clark-Casey, Justin and Cointepas, Yann and Comerci, Marco and Coppens, Frederik and Corre, Erwan and Cox, Cymon-J. and Crockett, Sara and David, Romain and De-Moro, Gianluca and Rochefort, Ludovic De and Eguinoa, Ignacio and Exter, Katrina and Ewbank, Jonathan and Finn, Robert and García-Granero, Juan-José and Goble, Carole and Gormanns, Philipp and Grantner, Tobias and Gribbon, Philip and Grüning, Björn and Guevara, Miguel and Gurwitz, Kim and Haley, Natalie and Harmse, Henriette and Hekkelman, Maarten and Henger, Anna and Heriche, Jean-Karim and Holub, Petr and Houde, Martin and Joosten, Robbie P. and Juty, Nick and Karnbach, Geoffrey and Karoune, Emma and Kensche, Philip R. and Keppler, Antje and Kerfant, Celine and Krajiczek, Martin and Lancelotti, Carla and Leitner, Frauke and Leo, Simone and Longo, Dario and Ludwig, Rebecca and Madella, Marco and Madrigal, Pedro and Magliulo, Mario and Mangin, Jean-Francois and Manning, Jonathan and Marquez, Jose-A. and Matser, Vera and Matteoni, Rafaele and Mayrhofer, Michaela and Miksa, Tomasz and Moreno, Pablo and Nasr, Engy and Newhouse, Steven and Ninidakis, Stelios and Pade, Nicolas and Pafilis, Evangelos and Panagiotopoulou, Maria and Papatheodorou, Irene and Parkinson, Helen and Pavloudi, Christina and Perrakis, Anastassis and Perseil, Isabelle and Pireddu, Luca and Popper, Niki and Potirakis, Antonis and Povey, Marcus and Rauber, Andreas and Romano, Paolo and Rosato, Antonio and Ruiz-Pérez, Javier and Schneider-Lunitz, Valentin and Sakharova, Ekaterina and Seyfarth, Ralf and Soiland-Reyes, Stian and Solovyev, Andrey and Spinazzola, Elisabetta and Strubel, Philipp and Swedlow, Jason and Taverner, Ellie and Twardziok, Sven and Velankar, Sameer and Vignaud, Alexandre and Wagener, Harald and Weise, Martin and Wienk, Hans and Winkler, Dietmar and Zafeiropoulos, Haris and Zaliani, Andrea and Zullino, Sara and Schmidt-Tremmel, Friederike and Blomberg, Niklas}, - month = aug, - year = {2023}, - doi = {10.5281/zenodo.8263074}, - note = {Backup Publisher: EMBL-HD ; CSIC}, - keywords = {Cloud, Cross-RI data, Cross-RI Tools, Life science research infrastructures}, - file = {HAL PDF Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EI7JZJ9A/Rybina et al. - 2023 - EOSC-Life Report on the work of the Open Call Proj.pdf:application/pdf}, -} - -@article{mendoza_convex_2023, - title = {{CONVEX} {HULL} {BASED} {FILTERING} {OF} {SUPERFICIAL} {WHITE} {MATTER} {FIBER} {BUNDLES}}, - volume = {15}, - issn = {2667-2421}, - url = {https://www.ibroneuroreports.org/article/S2667-2421(23)01672-X/fulltext}, - doi = {10.1016/j.ibneur.2023.08.1610}, - language = {English}, - urldate = {2024-03-12}, - journal = {IBRO Neuroscience Reports}, - author = {Mendoza, Cristóbal and Román, Claudio and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = oct, - year = {2023}, - note = {Publisher: Elsevier}, - pages = {S782}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/F2ITETVY/Mendoza et al. - 2023 - CONVEX HULL BASED FILTERING OF SUPERFICIAL WHITE M.pdf:application/pdf}, -} - -@article{poo_brain_2023, - title = {{BRAIN} {FIBER} {BUNDLE} {SIMULATOR} {USING} {SPLINE} {CURVES}}, - volume = {15}, - issn = {2667-2421}, - url = {https://www.ibroneuroreports.org/article/S2667-2421(23)01673-1/fulltext}, - doi = {10.1016/j.ibneur.2023.08.1611}, - language = {English}, - urldate = {2024-03-12}, - journal = {IBRO Neuroscience Reports}, - author = {Poo, Elida and Hernández, Cecilia and Mangin, Jean-François and Guevara, Pamela}, - month = oct, - year = {2023}, - note = {Publisher: Elsevier}, - pages = {S783}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/MG63IAIQ/Poo et al. - 2023 - BRAIN FIBER BUNDLE SIMULATOR USING SPLINE CURVES.pdf:application/pdf}, -} - -@inproceedings{guevara_definition_2023, - address = {Paris, France}, - title = {Définition de la normalité du fer intracérébral par {IRM}/{QSM} pour le diagnostic des maladies neurodégénératives}, - url = {https://hal.science/hal-04271807}, - abstract = {Objectifs : L'objectif de l'étude QSM4SENIOR (projet ESOC-Life H2020, www.eosc-life.eu) est de définir les -valeurs normales de la charge en fer du cerveau d'une population âgée de 55 à 80 ans par un -examen IRM et la mesure du biomarqueur innovant d'imagerie basé sur la cartographie -quantitative de la susceptibilité magnétique QSM (de Rochefort et al., MRM, 2010) dans la -matière grise profonde. Un rationnel scientifique fort existe entre accumulation de fer, QSM, -vieillissement cérébral et l’évolution de pathologies neurodégénératives (Ravanfar et al., Front. -Neurosci., 2021). Nous présentons ici les principales méthodes et les résultats du traitement -basé sur l'informatique dématérialisée dans l'infrastructure européenne de recherche de.NBI -cloud (www.denbi.de/cloud) ainsi que le contrôle qualité de ce biomarqueur d'imagerie. -Matériel et méthode : Les examens IRM ont été réalisé à ultra-haut champ (7T, Neurospin, CEA) de la cohorte SENIOR (Haeger et al, Alzheimers Res Ther., 2020) pour lesquels les cartes de QSM et R2* ont été -calculées. Les données relatives aux habitudes de vie telles que la consommation de tabac et -d'alcool, les comorbidités et les analyses sanguines ont été aussi exploitées. Une évaluation -neuropsychologique a été incluse au projet afin d’évaluer les capacités cognitives des patients. - -Résultats : Nous avons montré que dans la population vieillissante de l’étude QSM4SENIOR, nous pouvions -détecter des variations significatives des biomarqueurs QSM et R2* dans différentes régions dans -la substance grise profonde sans que cela soit relié à des modifications de l'état de santé et du -mode de vie des personnes incluses dans la cohorte. En outre, nous avons démontré que les -biomarqueurs QSM et R2* sont complémentaires. Enfin, nous avons pu obtenir les valeurs -normales à 7T de QSM pour les personnes âgées de 55 à 80 ans dans différentes régions de la -substance grise profonde. - -Conclusion : La robustesse de notre méthodologie, incluant un contrôle qualité adapté et via un traitement -automatisé sur une infrastructure « cloud » européenne de recherche a permis de définir les -valeurs normales du biomarqueur de la susceptibilité magnétique QSM sur la cohorte SENIOR. -Cette méthodologie permettra de fiabiliser les études multicentriques sur le sujet. Nous -envisageons l’interfaçage de ces outils avec les principales cohortes neurologiques afin -d'améliorer les études de recherche clinique impliquant des mesures IRM basées sur la -susceptibilité magnétique.}, - urldate = {2024-03-12}, - booktitle = {Journées {Francophones} de {Radiologie} 2023}, - publisher = {Marc ZINS}, - author = {Guevara, Miguel and Roche, Stéphane and Cam, Davy and Badagbon, Jacques and Bottlaender, Michel and Cointepas, Yann and Mangin, Jean-François and Vignaud, Alexandre and Rochefort, Ludovic De}, - month = oct, - year = {2023}, - keywords = {IRM, pathologies neurodégénératives, QSM, susceptibilité magnétique}, -} - -@inproceedings{vidal_comparing_2023, - title = {Comparing {White} {Matter} {Fiber} {Bundle} {Segmentation} {Methods} for {Autism} {Prediction}}, - url = {https://ieeexplore.ieee.org/abstract/document/10373470}, - doi = {10.1109/SIPAIM56729.2023.10373470}, - abstract = {Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that affects social communication and behavior. Early diagnosis is crucial to enhance the patient’s quality of life through treatments and therapies. In this research, two white matter (WM) fiber bundle segmentation methods are analyzed and compared in terms of their performance and impact on the results obtained from the analyzes applied to a database comprising 37 adolescents, 19 subjects with autism and 18 controls. To achieve this, we conducted the segmentation of deep white matter tracts, and computed average diffusion-based indices for each tract, such as Apparent Diffusion Coefficient (ADC), Fractional Anisotropy (FA), and Generalized Fractional Anisotropy (GFA). We applied statistical tests to identify features with significant differences between groups based on the results of two segmentation methods. Significant differences in diffusion-based indices were found in certain cingulate, thalamic, corticospinal, and corpus callosum fascicles. Furthermore, we performed classification between patients and controls using each fascicle feature independently with the Support Vector Machine (SVM) and Decision Trees (DT) algorithms. Finally, we applied the classifiers to the most relevant features for each segmentation method. Overall, even with the limitations of our small database, we demonstrated that the segmentation algorithm has a high impact on WM tract-based analyzes and prediction, with the autocencoder-based algorithm showing better results than a distance-based method.}, - urldate = {2024-03-12}, - booktitle = {2023 19th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis} ({SIPAIM})}, - author = {Vidal, Natalia and Navarrete, Sebastián and Román, Claudio and Houenou, Josselin and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = nov, - year = {2023}, - keywords = {Support vector machines, Databases, Diffusion Magnetic Resonance Imaging, Autism, White Matter, Prediction algorithms, Machine Learning, Machine learning algorithms, Tractography, Anisotropic magnetoresistance, Optical fiber communication}, - pages = {1--5}, -} - -@inproceedings{prieto_multiscale_2023, - title = {Multiscale cortical parcellation based on geodesic distance and hierarchical clustering}, - url = {https://ieeexplore.ieee.org/abstract/document/10373421}, - doi = {10.1109/SIPAIM56729.2023.10373421}, - abstract = {Brain neuronal networks of structural and func-tional connections have a hierarchical organization and a complex relationship between them. To study brain dynamics, it is important to identify the cortical level of parcellation of greater metastability. This paper presents a new multiscale cortical parcellation method based on the geodesic distance between vertices of the cortical surface and agglomerative hierarchical clustering, starting from an anatomical parcellation. First, the centroids of each region are efficiently calculated using the geodesic distance between the region’s vertices. Then, an affinity graph is constructed between the region centroids, based on the geodesic distance, from which a dendrogram is constructed using hierarchical clustering. Finally, an adaptive tree partitioning method is employed to obtain parcellations at various granularity levels, producing a multiscale parcellation. Furthermore, we propose an optimized method for the calculation of structural connectomes for each parcellation level. This framework will be made available and can be applied to different fine-grained parcellations. Additional information, such as structural connectivity information can be easily added to the framework. In future work this multiscale cortical parcellation will allow for simulations of cerebral dynamics at different levels.}, - urldate = {2024-03-12}, - booktitle = {2023 19th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis} ({SIPAIM})}, - author = {Prieto, Yarelis and Molina, Joaquín and Otero, Mónica and Mangin, Jean-François and Hernández, Cecilia and El-Deredy, Wael and Guevara, Pamela}, - month = nov, - year = {2023}, - keywords = {Organizations, hierarchical clustering, Biological neural networks, dendrogram, geodesic distance, Information processing, multiscale cortical parcellation}, - pages = {1--5}, -} - -@article{grasset_physical_2023, - title = {Physical activity, biomarkers of brain pathologies and dementia risk: {Results} from the {Memento} clinical cohort}, - volume = {19}, - issn = {1552-5260, 1552-5279}, - shorttitle = {Physical activity, biomarkers of brain pathologies and dementia risk}, - url = {https://alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.13360}, - doi = {10.1002/alz.13360}, - abstract = {Abstract - - INTRODUCTION - This study aims to examine whether physical activity moderates the association between biomarkers of brain pathologies and dementia risk. - - - METHODS - From the Memento cohort, we analyzed 1044 patients with mild cognitive impairment, aged 60 and older. Self‐reported physical activity was assessed using the International Physical Activity Questionnaire. Biomarkers of brain pathologies comprised medial temporal lobe atrophy (MTA), white matter lesions, and plasma amyloid beta (Aβ)42/40 and phosphorylated tau181. Association between physical activity and risk of developing dementia over 5 years of follow‐up, and interactions with biomarkers of brain pathologies were tested. - - - RESULTS - Physical activity moderated the association between MTA and plasma Aβ42/40 level and increased dementia risk. Compared to participants with low physical activity, associations of both MTA and plasma Aβ42/40 on dementia risk were attenuated in participants with high physical activity. - - - DISCUSSION - Although reverse causality cannot be excluded, this work suggests that physical activity may contribute to cognitive reserve. - - - Highlights - - - - Physical activity is an interesting modifiable target for dementia prevention. - - - Physical activity may moderate the impact of brain pathology on dementia risk. - - - Medial temporal lobe atrophy and plasma amyloid beta 42/40 ratio were associated with increased dementia risk especially in those with low level of physical activity.}, - language = {en}, - number = {12}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia}, - author = {Grasset, Leslie and Planche, Vincent and Bouteloup, Vincent and Azouani, Chabha and Dubois, Bruno and Blanc, Frédéric and Paquet, Claire and David, Renaud and Belin, Catherine and Jonveaux, Thérèse and Julian, Adrien and Pariente, Jérémie and Mangin, Jean‐François and Chêne, Geneviève and Dufouil, Carole and {the Memento Cohort Study Group}}, - month = dec, - year = {2023}, - pages = {5700--5718}, -} - -@article{roman_clustering_2017, - title = {Clustering of {Whole}-{Brain} {White} {Matter} {Short} {Association} {Bundles} {Using} {HARDI} {Data}}, - volume = {11}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2017.00073}, - doi = {10.3389/fninf.2017.00073}, - abstract = {Human brain connectivity is extremely complex and variable across subjects. While long association and projection bundles are stable and have been deeply studied, short association bundles present higher inter-subject variability and few studies have been carried out to adequately describe the structure, shape and reproducibility of these bundles. However, their analysis is crucial in order to understand brain function and better characterize the human connectome. In this work, we propose an automatic method to identify reproducible short association bundles of the superficial white matter, based on inter-subject hierarchical clustering. The method is applied to the whole brain and finds representative clusters of similar fibers belonging to a group of subjects, according to a distance metric between fibers. We experimented with both affine and a non-linear registration and, due to better reproducibility, chose the results obtained from non-linear registration. Once the clusters are calculated, our method performs automatic labeling of the most stable connections based on individual cortical parcellations. We compare results between two independent groups of subjects from a HARDI database in order to generate reproducible connections for the creation of an atlas. To perform a better validation of the results, we used a bagging strategy that uses pairs of groups of 27 subjects from a database of 74 subjects. The result is an atlas with 44 bundles in the left hemisphere and 49 in the right hemisphere, of which 33 bundles are found in both hemispheres. Finally, we use the atlas to automatically segment 78 new subjects from a different HARDI database and analyze stability and lateralization results.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {Román, Claudio and Guevara, Miguel and Valenzuela, Ronald and Figueroa, Miguel and Houenou, Josselin and Duclap, Delphine and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela}, - month = dec, - year = {2017}, - note = {Publisher: Frontiers}, - keywords = {HARDI, hierarchical clustering, dMRI, short association bundles, white matter}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QZWU9WHU/Román et al. - 2017 - Clustering of Whole-Brain White Matter Short Assoc.pdf:application/pdf}, -} - -@article{moon_association_2018, - title = {Association {Between} {Red} {Blood} {Cells} {Omega}-3 {Polyunsaturated} {Fatty} {Acids} and {White} {Matter} {Hyperintensities}: {The} {MAPT} {Study}}, - volume = {22}, - issn = {1279-7707}, - shorttitle = {Association {Between} {Red} {Blood} {Cells} {Omega}-3 {Polyunsaturated} {Fatty} {Acids} and {White} {Matter} {Hyperintensities}}, - url = {https://www.sciencedirect.com/science/article/pii/S1279770723022443}, - doi = {10.1007/s12603-017-0965-5}, - abstract = {Objectives -The association between circulating biomarkers of red blood cells (RBC) omega-3 polyunsaturated fatty acids (PUFAs) and cerebral white matter hyperintensities (WMH) on the brain MRI remains yet unclear. We investigated the cross-sectional and prospective associations of RBC omega-3 PUFAs with WMH in dementia-free older adults with subjective memory complaints. -Design -Participants were 234 older adults with assessments for both PUFA and MRI near to baseline; among them, 79 also had an MRI assessment at 3-year follow-up. The measurement of WMH volume was obtained by an automated segmentation algorithm. We related individual or combinational baseline RBC omega-3 PUFAs levels with baseline WMH volumes and WMH evolution over 3 years. We carried out multiple (cross-sectional) and mixed-effect (prospective analysis, with random effects at participant's level) linear regressions with adjustment for age, sex, time interval between date of blood draw for measurement of fatty acids and date of brain MRI, the status of APOE e4 carrier, body mass index, and vascular risk factors. Associations were considered significant at p ≤ 0.006 to take into account multiplicity (8 comparisons). -Results -None of the eight RBC omega-3 PUFAs tested was significantly associated with WMH at both cross-sectional and prospective analyses. -Conclusions -We did not find any association between omega-3 PUFAs and WMH in non-demented older adults with memory complaints. A longer longitudinal study with data on omega-3 PUFAs and WMH would contribute important information to this field.}, - number = {1}, - urldate = {2024-03-12}, - journal = {The Journal of nutrition, health and aging}, - author = {Moon, So Young and de Souto Barreto, P. and Chupin, M. and Mangin, J. F. and Bouyahia, A. and Fillon, L. and Andrieu, S. and Vellas, B.}, - month = jan, - year = {2018}, - keywords = {longitudinal, white matter hyperintensities, Omega-3 polyunsaturated fatty acids}, - pages = {174--179}, -} - -@article{epelbaum_neural_2018, - title = {Neural correlates of episodic memory in the {Memento} cohort}, - volume = {4}, - issn = {2352-8737}, - url = {https://www.sciencedirect.com/science/article/pii/S2352873718300209}, - doi = {10.1016/j.trci.2018.03.010}, - abstract = {Introduction -The free and cued selective reminding test is used to identify memory deficits in mild cognitive impairment and demented patients. It allows assessing three processes: encoding, storage, and recollection of verbal episodic memory. -Methods -We investigated the neural correlates of these three memory processes in a large cohort study. The Memento cohort enrolled 2323 outpatients presenting either with subjective cognitive decline or mild cognitive impairment who underwent cognitive, structural MRI and, for a subset, fluorodeoxyglucose–positron emission tomography evaluations. -Results -Encoding was associated with a network including parietal and temporal cortices; storage was mainly associated with entorhinal and parahippocampal regions, bilaterally; retrieval was associated with a widespread network encompassing frontal regions. -Discussion -The neural correlates of episodic memory processes can be assessed in large and standardized cohorts of patients at risk for Alzheimer's disease. Their relation to pathophysiological markers of Alzheimer's disease remains to be studied.}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia: Translational Research \& Clinical Interventions}, - author = {Epelbaum, Stephane and Bouteloup, Vincent and Mangin, Jean F. and La Corte, Valentina and Migliaccio, Raffaela and Bertin, Hugo and Habert, Marie O. and Fischer, Clara and Azouani, Chabha and Fillon, Ludovic and Chupin, Marie and Vellas, Bruno and Pasquier, Florence and Dartigues, Jean F. and Blanc, Fréderic and Gabelle, Audrey and Ceccaldi, Mathieu and Krolak-Salmon, Pierre and Hugon, Jacques and Hanon, Olivier and Rouaud, Olivier and David, Renaud and Chêne, Genevieve and Dubois, Bruno and Dufouil, Carole}, - month = jan, - year = {2018}, - keywords = {MRI, Alzheimer's disease, Memory, Fluorodeoxyglucose-PET, Multicenter cohort}, - pages = {224--233}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7944EJWB/Epelbaum et al. - 2018 - Neural correlates of episodic memory in the Mement.pdf:application/pdf}, -} - -@inproceedings{borne_patch-based_2018, - address = {Cham}, - series = {Lecture {Notes} in {Computer} {Science}}, - title = {A {Patch}-{Based} {Segmentation} {Approach} with {High} {Level} {Representation} of the {Data} for {Cortical} {Sulci} {Recognition}}, - isbn = {978-3-030-00500-9}, - doi = {10.1007/978-3-030-00500-9_13}, - abstract = {Because of the strong variability of the cortical sulci, their automatic recognition is still a challenging problem. The last algorithm developed in our laboratory for 125 sulci reaches an average recognition rate around 86\%. It has been applied to thousands of brains for morphometric studies (www.brainvisa.info). A weak point of this approach is the modeling of the training dataset as a single template of sulcus-wise probability maps, losing information about the alternative patterns of each sulcus. To overcome this limit, we propose a different strategy inspired by Multi-Atlas Segmentation (MAS) and more particularly the patch-based approaches. As the standard way of extracting patches does not seem capable of exploiting the sulci geometry and the relations between them, which we believe to be the discriminative features for recognition, we propose a new patch generation strategy based on a high level representation of the sulci. We show that our new approach is slightly, but significantly, better than the reference one, while we still have an avenue of potential refinements that were beyond reach for a single template strategy.}, - language = {en}, - booktitle = {Patch-{Based} {Techniques} in {Medical} {Imaging}}, - publisher = {Springer International Publishing}, - author = {Borne, Léonie and Mangin, Jean-François and Rivière, Denis}, - editor = {Bai, Wenjia and Sanroma, Gerard and Wu, Guorong and Munsell, Brent C. and Zhan, Yiqiang and Coupé, Pierrick}, - year = {2018}, - keywords = {MRI, Cortical sulci labeling, Patch-based segmentation}, - pages = {114--121}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/KPFZGS5W/Borne et al. - 2018 - A Patch-Based Segmentation Approach with High Leve.pdf:application/pdf}, -} - -@article{habert_evaluation_2018, - title = {Evaluation of amyloid status in a cohort of elderly individuals with memory complaints: validation of the method of quantification and determination of positivity thresholds}, - volume = {32}, - issn = {1864-6433}, - shorttitle = {Evaluation of amyloid status in a cohort of elderly individuals with memory complaints}, - url = {https://doi.org/10.1007/s12149-017-1221-0}, - doi = {10.1007/s12149-017-1221-0}, - abstract = {Our aim is to validate the process steps implemented by the French CATI platform to assess amyloid status, obtained from 18F-Florbetapir PET scans, in a cohort of 318 cognitively normal subjects participating in the INSIGHT-preAD study. Our objective was to develop a method with partial volume effect correction (PVEC) on untransformed PET images, using an automated pipeline (“RACHEL”) adapted to large series of patients and including quality checks of results.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Annals of Nuclear Medicine}, - author = {Habert, Marie-Odile and Bertin, Hugo and Labit, Mickael and Diallo, Mamadou and Marie, Sullivan and Martineau, Kelly and Kas, Aurélie and Causse-Lemercier, Valérie and Bakardjian, Hovagim and Epelbaum, Stéphane and Chételat, Gael and Houot, Marion and Hampel, Harald and Dubois, Bruno and Mangin, Jean-François and Audrain, C. and Bakardjian, H. and Benali, H. and Bertin, H. and Boukadida, L. and Cacciamani, F. and Causse-Lemercier, V. and Cavedo, E. and Chiesa, P. and Colliot, O. and Dos Santos, A. and Dubois, B. and Durrleman, S. and Epelbaum, S. and Gagliardi, G. and Genthon, R. and Habert, M.-O. and Hampel, H. and Jungalee, N. and Kas, A. and Lehericy, S. and Lamari, F. and Letondor, C. and Levy, M. and Lista, S. and Mochel, F. and Nyasse, F. and Poisson, C. and Potier, M. C. and Revillon, M. and Rojkova, K. and Roy, P. and Santos-Andrade, K. and Santos, A. and Simon, V. and Sole, M. and Tandetnik, C. and Thiebaud De Schotten, M. and {INSIGHT-AD study group}}, - month = feb, - year = {2018}, - keywords = {Humans, Software, Neuroimaging, Image Processing, Computer-Assisted, Reference Values, Adolescent, Child, Female, Male, Reaction Time, Positron-Emission Tomography, Aged, Cognition, Attention Deficit Disorder with Hyperactivity, Memory, Prefrontal Cortex, Alzheimer’s disease, Amyloid, 18F-Florbetapir, Amyloid burden quantification, Brain PET, Aniline Compounds, Ethylene Glycols, Attention-deficit/hyperactivity disorder, Inattention, Multi-informant, Reaction time variability, Ventromedial prefrontal cortex}, - pages = {75--86}, - annote = {MEDLINE:29633962}, - annote = {MEDLINE:29633962}, - file = {Accepted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/42XN2KUL/Albaugh et al. - 2017 - Inattention and Reaction Time Variability Are Link.pdf:application/pdf}, -} - -@article{ginsburger_improving_2018, - title = {Improving the {Realism} of {White} {Matter} {Numerical} {Phantoms}: {A} {Step} toward a {Better} {Understanding} of the {Influence} of {Structural} {Disorders} in {Diffusion} {MRI}}, - volume = {6}, - issn = {2296-424X}, - shorttitle = {Improving the {Realism} of {White} {Matter} {Numerical} {Phantoms}}, - url = {https://www.frontiersin.org/articles/10.3389/fphy.2018.00012}, - doi = {10.3389/fphy.2018.00012}, - abstract = {White matter is composed of irregularly packed axons leading to a structural disorder in the extra-axonal space. Diffusion MRI experiments using oscillating gradient spin echo sequences have shown that the diffusivity transverse to axons in this extra-axonal space is dependent on the frequency of the employed sequence. In this study, we observe the same frequency-dependence using 3D simulations of the diffusion process in disordered media. We design a novel white matter numerical phantom generation algorithm which constructs biomimicking geometric configurations with few design parameters, and enables to control the level of disorder of the generated phantoms. The influence of various geometrical parameters present in white matter, such as global angular dispersion, tortuosity, presence of Ranvier nodes, beading, on the extra-cellular perpendicular diffusivity frequency dependence was investigated by simulating the diffusion process in numerical phantoms of increasing complexity and fitting the resulting simulated diffusion MR signal attenuation with an adequate analytical model designed for trapezoidal OGSE sequences. This work suggests that angular dispersion and especially beading have non-negligible effects on this extracellular diffusion metrics that may be measured using standard OGSE DW-MRI clinical protocols.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Physics}, - author = {Ginsburger, Kévin and Poupon, Fabrice and Beaujoin, Justine and Estournet, Delphine and Matuschke, Felix and Mangin, Jean-François and Axer, Markus and Poupon, Cyril}, - month = feb, - year = {2018}, - note = {Publisher: Frontiers}, - keywords = {Axonal Diameter, Biomimicking numerical phantoms, diffusion time-dependence, Monte-Carlo Simulations, Trapezoidal OGSE sequences, white matter microstructure}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TWWXMXTJ/Ginsburger et al. - 2018 - Improving the Realism of White Matter Numerical Ph.pdf:application/pdf}, -} - -@article{moon_physical_2018, - title = {Physical {Activity} and {Changes} in {White} {Matter} {Hyperintensities} over {Three} {Years}}, - volume = {22}, - issn = {1279-7707}, - url = {https://www.sciencedirect.com/science/article/pii/S1279770723021619}, - doi = {10.1007/s12603-017-0959-3}, - abstract = {Objectives -Since physical activity (PA) has demonstrated benefits for cardiovascular health, it is possible to hypothesize that higher or increasing PA slows the progression of white matter hyperintensities (WMH). We investigated the association between PA and the progression of WMH in non-demented older adults with memory complaints. -Design -We included 152 participants (mean age 74.7±3.8 years; 63.8\% women) in the analyses, in whom information on self-reported PA and MRI was available at both baseline and 3-year follow-up. From the PA questionnaire, the baseline metabolic equivalent of task (MET-minute/week) and changes in MET-minute/week over three years were separately calculated for overall, leisure-time, and non-leisure time PA. WMH volume at baseline and 3-year follow-up was obtained by using an automated segmentation algorithm. -Results -Mixed-effect linear regression models showed that none of the baseline PA variables was associated with progression of WMH over time. People who had decreased their PA levels over three years tended to show greater progression of WMH compared with those who had maintained PA levels of ≥1200 MET-min/week (roughly equivalent to ≥300 minutes of brisk walking) in the unadjusted model (β±SE=4.85±2.42, p=0.045); however, this association was no longer significant after adjustment for confounders (β±SE =3.63±2.18, p=0.096). -Conclusions -We did not find any significant association between PA and WMH in non-demented older adults with memory complaints. However, decrease over time in PA levels tended to be associated with progression of WMH. A larger longitudinal study with data on PA assessed using objective measures would provide important information in this field.}, - number = {3}, - urldate = {2024-03-12}, - journal = {The Journal of nutrition, health and aging}, - author = {Moon, So Young and de Souto Barreto, P. and Cesari, M. and Chupin, M. and Mangin, J. F. and Bouyahia, A. and Fillon, L. and Andrieu, S. and Vellas, B.}, - month = mar, - year = {2018}, - keywords = {longitudinal, white matter hyperintensities, Physical activity}, - pages = {425--430}, -} - -@article{le_guen_genetic_2018, - title = {Genetic {Influence} on the {Sulcal} {Pits}: {On} the {Origin} of the {First} {Cortical} {Folds}}, - volume = {28}, - issn = {1047-3211}, - shorttitle = {Genetic {Influence} on the {Sulcal} {Pits}}, - url = {https://doi.org/10.1093/cercor/bhx098}, - doi = {10.1093/cercor/bhx098}, - abstract = {The influence of genes on cortical structures has been assessed through various phenotypes. The sulcal pits, which are the putative first cortical folds, have for long been assumed to be under tight genetic control, but this was never quantified. We estimated the pit depth heritability in various brain regions using the high quality and large sample size of the Human Connectome Project pedigree cohort. Analysis of additive genetic variance indicated that their heritability ranges between 0.2 and 0.5 and displays a regional genetic control with an overall symmetric pattern between hemispheres. However, a noticeable asymmetry of heritability estimates is observed in the superior temporal sulcus and could thus be related to language lateralization. The heritability range estimated in this study reinforces the idea that cortical shape is determined primarily by nongenetic factors, which is consistent with the important increase of cortical folding from birth to adult life and thus predominantly constrained by environmental factors. Nevertheless, the genetic cues, implicated with various local levels of heritability in the formation of sulcal pits, play a fundamental role in the normal gyral pattern development. Quantifying their influence and identifying the underlying genetic variants would provide insight into neurodevelopmental disorders.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Le Guen, Yann and Auzias, Guillaume and Leroy, François and Noulhiane, Marion and Dehaene-Lambertz, Ghislaine and Duchesnay, Edouard and Mangin, Jean-François and Coulon, Olivier and Frouin, Vincent}, - month = jun, - year = {2018}, - keywords = {imaging-genetic, sulcal pits, STS, brain asymmetry}, - pages = {1922--1933}, - annote = {MEDLINE:28444225}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati}, - annote = {UnicogPMID: 28444225}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/54XH832D/Le Guen et al. - 2018 - Genetic Influence on the Sulcal Pits On the Origi.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IW6UP4ZS/Genetic-Influence-on-the-Sulcal-Pits-On-the-Origin.html:text/html}, -} - -@article{beaujoin_post-mortem_2018, - title = {Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion {MRI} at 11.7 {T}}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-018-1617-1}, - doi = {10.1007/s00429-018-1617-1}, - abstract = {The human hippocampus plays a key role in memory management and is one of the first structures affected by Alzheimer’s disease. Ultra-high magnetic resonance imaging provides access to its inner structure in vivo. However, gradient limitations on clinical systems hinder access to its inner connectivity and microstructure. A major target of this paper is the demonstration of diffusion MRI potential, using ultra-high field (11.7 T) and strong gradients (750 mT/m), to reveal the extra- and intra-hippocampal connectivity in addition to its microstructure. To this purpose, a multiple-shell diffusion-weighted acquisition protocol was developed to reach an ultra-high spatio-angular resolution with a good signal-to-noise ratio. The MRI data set was analyzed using analytical Q-Ball Imaging, Diffusion Tensor Imaging (DTI), and Neurite Orientation Dispersion and Density Imaging models. High Angular Resolution Diffusion Imaging estimates allowed us to obtain an accurate tractography resolving more complex fiber architecture than DTI models, and subsequently provided a map of the cross-regional connectivity. The neurite density was akin to that found in the histological literature, revealing the three hippocampal layers. Moreover, a gradient of connectivity and neurite density was observed between the anterior and the posterior part of the hippocampus. These results demonstrate that ex vivo ultra-high field/ultra-high gradients diffusion-weighted MRI allows the mapping of the inner connectivity of the human hippocampus, its microstructure, and to accurately reconstruct elements of the polysynaptic intra-hippocampal pathway using fiber tractography techniques at very high spatial/angular resolutions.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Beaujoin, Justine and Palomero-Gallagher, Nicola and Boumezbeur, Fawzi and Axer, Markus and Bernard, Jeremy and Poupon, Fabrice and Schmitz, Daniel and Mangin, Jean-François and Poupon, Cyril}, - month = jun, - year = {2018}, - keywords = {Human hippocampus, Structural connectivity, Microstructure imaging, Neurite density, Diffusion MRI}, - pages = {2157--2179}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/D7RW9LR5/Beaujoin et al. - 2018 - Post-mortem inference of the human hippocampal con.pdf:application/pdf}, -} - -@article{hanon_plasma_2018, - title = {Plasma amyloid levels within the {Alzheimer}'s process and correlations with central biomarkers}, - volume = {14}, - issn = {1552-5260}, - url = {https://www.sciencedirect.com/science/article/pii/S1552526018300219}, - doi = {10.1016/j.jalz.2018.01.004}, - abstract = {Introduction -Diagnostic relevance of plasma amyloid β (Aβ) for Alzheimer's disease (AD) process yields conflicting results. The objective of the study was to assess plasma levels of Aβ42 and Aβ40 in amnestic mild cognitive impairment (MCI), nonamnestic MCI, and AD patients and to investigate relationships between peripheral and central biomarkers. -Methods -One thousand forty participants (417 amnestic MCI, 122 nonamnestic MCI, and 501 AD) from the Biomarker of AmyLoïd pepTide and AlZheimer's diseAse Risk multicenter prospective study with cognition, plasma, cerebrospinal fluid (CSF), and magnetic resonance imaging assessments were included. -Results -Plasma Aβ1–42 and Aβ1–40 were lower in AD (36.9 [11.7] and 263 [80] pg/mL) than in amnestic MCI (38.2 [11.9] and 269 [68] pg/mL) than in nonamnestic MCI (39.7 [10.5] and 272 [52] pg/mL), respectively (P = .01 for overall difference between groups for Aβ1–42 and P = .04 for Aβ1–40). Globally, plasma Aβ1–42 correlated with age, Mini–Mental State Examination, and APOE ε4 allele. Plasma Aβ1–42 correlated with all CSF biomarkers in MCI but only with CSF Aβ42 in AD. -Discussion -Plasma Aβ was associated with cognitive status and CSF biomarkers, suggesting the interest of plasma amyloid biomarkers for diagnosis purpose.}, - number = {7}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia}, - author = {Hanon, Olivier and Vidal, Jean-Sébastien and Lehmann, Sylvain and Bombois, Stéphanie and Allinquant, Bernadette and Tréluyer, Jean-Marc and Gelé, Patrick and Delmaire, Christine and Blanc, Fredéric and Mangin, Jean-François and Buée, Luc and Touchon, Jacques and Hugon, Jacques and Vellas, Bruno and Galbrun, Evelyne and Benetos, Athanase and Berrut, Gilles and Paillaud, Elèna and Wallon, David and Castelnovo, Giovanni and Volpe-Gillot, Lisette and Paccalin, Marc and Robert, Philippe-Henri and Godefroy, Olivier and Dantoine, Thierry and Camus, Vincent and Belmin, Joël and Vandel, Pierre and Novella, Jean-Luc and Duron, Emmanuelle and Rigaud, Anne-Sophie and Schraen-Maschke, Suzanna and Gabelle, Audrey and Hanon, Olivier and Blanc, Frédéric and Boudali, Yasmina and Gabelle, Audrey and Seux, Marie–Laure and Lenoir, Hermine and Bayle, Catherine and Bombois, Stéphanie and Delbeuck, Xavier and Moulin, Florence and Duron, Emmanuelle and Latour, Florence and Plichart, Matthieu and Pichierri, Sophie and Orvoën, Galdric and Galbrun, Evelyne and Castelnovo, Giovanni and Volpe–Gillot, Lisette and Labourée, Florien and Cassagnaud, Pascaline and Paquet, Claire and Lala, Françoise and Dumurgier, Julien and Rigaud, Anne–Sophie and Perret–Guillaume, Christine and Alonso, Eliana and du Boisgueheneuc, Foucaud and Hugonot–Diener, Laurence and Rollin–Sillaire, Adeline and Martinaud, Olivier and Boully, Clémence and Spivac, Yann and Devendeville, Agnès and Belmin, Joël and Robert, Philippe–Henri and Dantoine, Thierry and Caillard, Laure and Wallon, David and Hannequin, Didier and Sastre, Nathalie and Haffen, Sophie and Kearney–Schwartz, Anna and Novella, Jean–Luc and Deramecourt, Vincent and Chauvire, Valérie and Abitbol, Gabiel and Schwald, Nathalie and Hommet, Caroline and Sellal, François and Cariot, Marie–Ange and Abdellaoui, Mohamed and Benisty, Sarah and Gherabli, Salim and Anthony, Pierre and Bloch, Frédéric and Charasz, Nathalie and Chauvelier, Sophie and Gaubert, Jean–Yves and Sacco, Guillaume and Guerin, Olivier and Boddaert, Jacques and Paccalin, Marc and Mackowiak, Marie–Anne and Rabus, Marie–Thérèse and Gissot, Valérie and Benetos, Athanase and Picard, Candice and Guillemaud, Céline and Gervais, Claire and Hugon, Jaques and Michel, Jean–Marc and David, Jean–Philippe and Paulin, Marion and Ousset, Pierre–Jean and Vandel, Pierre and Pariel, Sylvie and Camus, Vincent and Chawakilian, Anne and Joffredo, Léna and Troussiere, Anne–Cécile and Adam, Cécile and Dupuy, Diane and Paillaud, Elèna and Briault, Hélène and Saulnier, Isabelle and Mondon, Karl and Picat, Marie–Agnès and Laurent, Marie and Godefroy, Olivier and Daheb, Rezki and Libercier, Stéphanie and Krabchi, Djamila and Chupin, Marie and Vidal, Jean–Sébastien and Chaussade, Edouard and Lehmann, Sylvain and Schraen-Maschke, Suzanna}, - month = jul, - year = {2018}, - keywords = {Alzheimer's disease, Mild cognitive impairment, Dementia, Amyloid β peptides, Cohort study, CSF biomarkers, Plasma biomarkers}, - pages = {858--868}, -} - -@article{le_guen_chaotic_2018, - title = {The chaotic morphology of the left superior temporal sulcus is genetically constrained}, - volume = {174}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918302568}, - doi = {10.1016/j.neuroimage.2018.03.046}, - abstract = {The asymmetry of the superior temporal sulcus (STS) has been identified as a species-specific feature of the human brain. The so-called superior temporal asymmetrical pit (STAP) area is observed from the last trimester of gestation onwards and is far less pronounced in the chimpanzee brain. This asymmetry is associated with more frequent sulcal interruptions, named plis de passage (PPs), leading to the irregular morphology of the left sulcus. In this paper, we aimed to characterize the variability, asymmetry, and heritability of these interruptions in the STS in comparison with the other main sulci. We developed an automated method to extract PPs across the cortex based on a highly reproducible grid of sulcal pits across individuals, which we applied to a subset of Human Connectome Project (HCP) subjects (N = 820). We report that only a few PPs across the cortex are genetically constrained, namely in the collateral, postcentral and superior temporal sulci and the calcarine fissure. Moreover, some PPs occur more often in one hemisphere than the other, namely in the precentral, postcentral, intraparietal sulci, as well as in both inferior and superior temporal sulci. Most importantly, we found that only the interruptions within the STAP region are both asymmetric and genetically constrained. Because this morphological pattern is located in an area of the left hemisphere related to speech, our results suggest structural constraints on the architecture of the linguistic network.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Le Guen, Yann and Leroy, François and Auzias, Guillaume and Riviere, Denis and Grigis, Antoine and Mangin, Jean-François and Coulon, Olivier and Dehaene-Lambertz, Ghislaine and Frouin, Vincent}, - month = jul, - year = {2018}, - keywords = {Heritability, Cortical folding, Imaging genetics, Pli de passage, Structural MRI, STS asymmetry}, - pages = {297--307}, -} - -@article{bouyeure_three-dimensional_2018, - title = {Three-{Dimensional} {Probabilistic} {Maps} of {Mesial} {Temporal} {Lobe} {Structures} in {Children} and {Adolescents}’ {Brains}}, - volume = {12}, - issn = {1662-5129}, - url = {https://www.frontiersin.org/articles/10.3389/fnana.2018.00098}, - doi = {10.3389/fnana.2018.00098}, - abstract = {The hippocampus and the adjacent perirhinal, entorhinal, temporopolar and parahippocampal cortices are interconnected in a hierarchical MTL system crucial for memory processes. A probabilistic description of the anatomical location and spatial variability of MTL cortices in the child and adolescent brain would help to assess structure-function relationships. The rhinal sulcus (RS) and the collateral sulcus (CS) that border MTL cortices and influence their morphology have never been described in these populations. In this study, we identified the aforementioned structures on magnetic resonance images of 38 healthy subjects aged 7-17 years old. Relative to sulcal morphometry in the MTL, we showed RS-CS conformation is an additional factor of variability in the MTL that is not explained by other variables such as age, sex and brain volume; with an innovative method using permutation testing of the extrema of structures of interest, we showed that RS-SC conformation was not associated with differences of location of MTL sulci. Relative to probabilistic maps, we offered for the first time a systematic mapping of MTL structures in children and adolescent, mapping all the structures of the MTL system while taking sulcal morphology into account. Our results, with the probabilistic maps described here being freely available for download, will help to understand the anatomy of this region and help functional and clinical studies to accurately test structure-function hypotheses in the MTL during development.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroanatomy}, - author = {Bouyeure, Antoine and Germanaud, David and Bekha, Dhaif and Delattre, Victor and Lefèvre, Julien and Pinabiaux, Charlotte and Mangin, Jean-Francois and Rivière, Denis and Fischer, Clara and Chiron, Catherine and Hertz-Pannier, Lucie and Noulhiane, Marion}, - month = nov, - year = {2018}, - note = {Publisher: Frontiers}, - keywords = {Hippocampus, development, medial temporal lobe, hippocampus, parahippocampal gyrus, probabilistic maps, Brain developement, Parahippocampal Gyrus, probabilistic map}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DV9ZQRVB/Bouyeure et al. - 2018 - Three-Dimensional Probabilistic Maps of Mesial Tem.pdf:application/pdf}, -} - -@article{lebenberg_framework_2018, - title = {A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-018-1735-9}, - doi = {10.1007/s00429-018-1735-9}, - abstract = {Robust spatial alignment of post mortem data and in vivo MRI acquisitions from different ages, especially from the early developmental stages, into standard spaces is still a bottleneck hampering easy comparison with the mainstream neuroimaging results. In this paper, we test a landmark-based spatial normalization strategy as a framework for the seamless integration of any macroscopic dataset in the context of the Human Brain Project (HBP). This strategy stems from an approach called DISCO embedding sulcal constraints in a registration framework used to initialize DARTEL, the widely used spatial normalization approach proposed in the SPM software. We show that this strategy is efficient with a heterogeneous dataset including challenging data as preterm newborns, infants, post mortem histological data and a synthetic atlas computed from averaging the ICBM database, as well as more commonly studied data acquired in vivo in adults. We then describe some perspectives for a research program aiming at improving folding pattern matching for atlas inference in the context of the future HBP’s portal.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Lebenberg, J. and Labit, M. and Auzias, G. and Mohlberg, H. and Fischer, C. and Rivière, D. and Duchesnay, E. and Kabdebon, C. and Leroy, F. and Labra, N. and Poupon, F. and Dickscheid, T. and Hertz-Pannier, L. and Poupon, C. and Dehaene-Lambertz, G. and Hüppi, P. and Amunts, K. and Dubois, J. and Mangin, J.-F.}, - month = dec, - year = {2018}, - keywords = {Algorithms, Brain, Humans, Magnetic Resonance Imaging, Software, MRI, Image Processing, Computer-Assisted, Adult, Middle Aged, Databases, Factual, Aged, Aged, 80 and over, Atlases as Topic, Cytoarchitecture, Diffeomorphism, Folding pattern, HBP, Infant, Newborn, Infant, Premature, Spatial normalization}, - pages = {4153--4168}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UTZ99AGC/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8F53LJM9/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QM4UDBZI/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf}, -} - -@article{hou_measurement_2019, - title = {Measurement of {Sylvian} {Fissure} asymmetry and occipital bending in humans and {Pan} troglodytes}, - volume = {184}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918307432}, - doi = {10.1016/j.neuroimage.2018.08.045}, - abstract = {The evolution of human-specific lateralised functions such as language has been linked to the development of structural asymmetries in the brain. Here we applied state of the art image analysis techniques to measure Sylvian Fissure (SF) asymmetry and Occipital Bending (OB) in 3D Magnetic Resonance (MR) images of the brain obtained in-vivo for 30 humans and 30 chimpanzees (Pan troglodytes). SF morphology differed between species, with the human SF terminating more superiorly in right inferior parietal lobe, an asymmetry that was on average absent in chimpanzees (F (1,52) = 5.963, p = 0.018). Irrespective of morphology, Total SF Length was, as previously reported, leftward in humans but not in chimpanzees, although the difference did not reach significance between species. However, when only brains possessing comparable bilateral SF bifurcation morphology were compared, humans showed previously reported “Typical” left-lateralised Anterior-Horizontal (AH-SF) and right-lateralised Vertical (V-SF) SF asymmetries. In contrast, chimpanzees lacked both asymmetries, and this approached being a significant difference between-species in the AH-SF segment (F (1, 34) = 3.680, p = 0.064). On average in humans the left occipital lobe crossed the midline toward the right (Rightward OB) which was significantly different from the chimpanzee cohort that showed no average OB (Independent-Samples Mann-Whitney U Test, p = 0.012). Furthermore, OB was related to SF asymmetry in humans, such that the more rightward V-SF and leftward AH-SF, the more rightward the OB. This “Default” pattern of SF and OB asymmetries was found in 41.7\% of human individuals with bilateral SF bifurcation but none of the chimpanzees. To our knowledge, this is the first study highlighting that a pattern of SF and OB asymmetry distinguishes the human from the chimpanzee brain, and suggests this may be associated with a unique trajectory of brain development and functional abilities in humans.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Hou, Lewis and Xiang, Li and Crow, Timothy J. and Leroy, François and Rivière, Denis and Mangin, Jean-François and Roberts, Neil}, - month = jan, - year = {2019}, - pages = {855--870}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GUNF5VHT/S1053811918307432.html:text/html;Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/KVSKQ2WH/Hou et al. - 2019 - Measurement of Sylvian Fissure asymmetry and occip.pdf:application/pdf}, -} - -@article{dubois_dynamics_2019, - title = {The dynamics of cortical folding waves and prematurity-related deviations revealed by spatial and spectral analysis of gyrification}, - volume = {185}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918301903}, - doi = {10.1016/j.neuroimage.2018.03.005}, - abstract = {In the human brain, the appearance of cortical sulci is a complex process that takes place mostly during the second half of pregnancy, with a relatively stable temporal sequence across individuals. Since deviant gyrification patterns have been observed in many neurodevelopmental disorders, mapping cortical development in vivo from the early stages on is an essential step to uncover new markers for diagnosis or prognosis. Recently this has been made possible by MRI combined with post-processing tools, but the reported results are still fragmented. Here we aimed to characterize the typical folding progression ex utero from the pre- to the post-term period, by considering 58 healthy preterm and full-term newborns and infants imaged between 27 and 62 weeks of post-menstrual age. Using a method of spectral analysis of gyrification (SPANGY), we detailed the spatial-frequency structure of cortical patterns in a quantitative way. The modeling of developmental trajectories revealed three successive waves that might correspond to primary, secondary and tertiary folding. Some deviations were further detected in 10 premature infants without apparent neurological impairment and imaged at term equivalent age, suggesting that our approach is sensitive enough to highlight the subtle impact of preterm birth and extra-uterine life on folding.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Dubois, Jessica and Lefèvre, Julien and Angleys, Hugo and Leroy, François and Fischer, Clara and Lebenberg, Jessica and Dehaene-Lambertz, Ghislaine and Borradori-Tolsa, Cristina and Lazeyras, François and Hertz-Pannier, Lucie and Mangin, Jean-François and Hüppi, Petra S. and Germanaud, David}, - month = jan, - year = {2019}, - keywords = {Magnetic resonance imaging (MRI), Prematurity, Cortex, Development, Sulcation}, - pages = {934--946}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GTNEE79H/Dubois et al. - 2019 - The dynamics of cortical folding waves and prematu.pdf:application/pdf}, -} - -@article{lebenberg_mapping_2019, - title = {Mapping the asynchrony of cortical maturation in the infant brain: {A} {MRI} multi-parametric clustering approach}, - volume = {185}, - issn = {1053-8119}, - shorttitle = {Mapping the asynchrony of cortical maturation in the infant brain}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918306372}, - doi = {10.1016/j.neuroimage.2018.07.022}, - abstract = {While the main neural networks are in place at term birth, intense changes in cortical microstructure occur during early infancy with the development of dendritic arborization, synaptogenesis and fiber myelination. These maturational processes are thought to relate to behavioral acquisitions and the development of cognitive abilities. Nevertheless, in vivo investigations of such relationships are still lacking in healthy infants. To bridge this gap, we aimed to study the cortical maturation using non-invasive Magnetic Resonance Imaging, over a largely unexplored period (1–5 post-natal months). In a first univariate step, we focused on different quantitative parameters: longitudinal relaxation time (T1), transverse relaxation time (T2), and axial diffusivity from diffusion tensor imaging (λ//) These individual maps, acquired with echo-planar imaging to limit the acquisition time, showed spatial distortions that were first corrected to reliably match the thin cortical ribbon identified on high-resolution T2-weighted images. Averaged maps were also computed over the infants group to summarize the parameter characteristics during early infancy. In a second step, we considered a multi-parametric approach that leverages parameters complementarity, avoids reliance on pre-defined regions of interest, and does not require spatial constraints. Our clustering strategy allowed us to group cortical voxels over all infants in 5 clusters with distinct microstructural T1 and λ// properties The cluster maps over individual cortical surfaces and over the group were in sound agreement with benchmark post mortem studies of sub-cortical white matter myelination, showing a progressive maturation of 1) primary sensori-motor areas, 2) adjacent unimodal associative cortices, and 3) higher-order associative regions. This study thus opens a consistent approach to study cortical maturation in vivo.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Lebenberg, J. and Mangin, J. -F. and Thirion, B. and Poupon, C. and Hertz-Pannier, L. and Leroy, F. and Adibpour, P. and Dehaene-Lambertz, G. and Dubois, J.}, - month = jan, - year = {2019}, - keywords = {Clustering, Cortical maturation, Diffusion tensor imaging DTI, Human brain project (HBP), Infancy, Magnetic resonance imaging MRI, Quantitative T1 and T2 mapping}, - pages = {641--653}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8N52EF8U/Lebenberg et al. - 2019 - Mapping the asynchrony of cortical maturation in t.pdf:application/pdf}, -} - -@inproceedings{le_guen_heritability_2019, - title = {Heritability of surface area and cortical thickness: a comparison between the {Human} {Connectome} {Project} and the {UK} {Biobank} dataset}, - shorttitle = {Heritability of surface area and cortical thickness}, - url = {https://ieeexplore.ieee.org/abstract/document/8759539}, - doi = {10.1109/ISBI.2019.8759539}, - abstract = {Heritability of the regional thickness/surface in human cortex is established. Yet the estimates vary substantially depending on cohorts or the information they are derived from: pedigree or genotyping. Here we present three heritability studies of the cortex phenotype in two cohorts showing: i) both pedigree and genotyping or ii) genotyping only. We obtained clearly correlated heritability values between studies with a shift appearing between cohorts. Spatial pattern of heritability remains highly consistent across cohorts.}, - urldate = {2024-03-12}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Le Guen, Yann and Karkar, Slim and Grigis, Antoine and Philippe, Cathy and Mangin, Jean-François and Frouin, Vincent}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {Sociology, Statistics, Magnetic resonance imaging, heritability, imaging-genetic, cortical thickness, Genomics, Bioinformatics, surface area}, - pages = {1887--1890}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FC8YYEQ4/Le Guen et al. - 2019 - Heritability of surface area and cortical thicknes.pdf:application/pdf}, -} - -@inproceedings{avila_inference_2019, - address = {Cham}, - series = {Mathematics and {Visualization}}, - title = {Inference of an {Extended} {Short} {Fiber} {Bundle} {Atlas} {Using} {Sulcus}-{Based} {Constraints} for a {Diffeomorphic} {Inter}-subject {Alignment}}, - isbn = {978-3-030-05831-9}, - doi = {10.1007/978-3-030-05831-9_25}, - abstract = {We present a new framework for the creation of an extended atlas of short fiber bundlesShort fiber bundles between 20 and 80 mm length. This method uses a Diffeomorphic inter-subject alignmentDiffeomorphic inter-subject alignment procedure including information of cortical foldings and forces the accurate match of the sulci that have to be circumvented by the U-bundlesU-bundle. Then, a clustering is performed to extract the most reproducible bundles across subjects. First results show an increased number of U-bundlesU-bundle consistently mapped in the general population compared with previous atlases created from the same database. Future analysis over this new extended Brain atlasBrain atlas may improve our understanding of the relationship between the folding pattern and the U-bundleU-bundle variability. The ultimate aim will be the possibility to detect abnormal configurations induced by developmental issues.}, - language = {en}, - booktitle = {Computational {Diffusion} {MRI}}, - publisher = {Springer International Publishing}, - author = {Avila, Nicole Labra and Lebenberg, Jessica and Rivière, Denis and Auzias, Guillaume and Fischer, Clara and Poupon, Fabrice and Guevara, Pamela and Poupon, Cyril and Mangin, Jean-François}, - editor = {Bonet-Carne, Elisenda and Grussu, Francesco and Ning, Lipeng and Sepehrband, Farshid and Tax, Chantal M. W.}, - year = {2019}, - keywords = {Sulci, Cortical folding pattern, Bundle atlas, dMRI, Diffusion MRI, White matter, Brain atlas, Diffeomorphic alignment, Short fiber bundles, Sulcus base alignment, U-bundles, U-fiber}, - pages = {323--333}, -} - -@article{ginsburger_medusa_2019, - title = {{MEDUSA}: {A} {GPU}-based tool to create realistic phantoms of the brain microstructure using tiny spheres}, - volume = {193}, - issn = {1053-8119}, - shorttitle = {{MEDUSA}}, - url = {https://www.sciencedirect.com/science/article/pii/S105381191930151X}, - doi = {10.1016/j.neuroimage.2019.02.055}, - abstract = {A GPU-based tool to generate realistic phantoms of the brain microstructure is presented. Using a spherical meshing technique which decomposes each microstructural item into a set of overlapping spheres, the phantom construction is made very fast while reliably avoiding the collisions between items in the scene. This novel method is applied to the construction of human brain white matter microstructural components, namely axonal fibers, oligodendrocytes and astrocytes. The algorithm reaches high values of packing density and angular dispersion for the axonal fibers, even in the case of multiple white matter fiber populations and enables the construction of complex biomimicking geometries including myelinated axons, beaded axons, and glial cells. The method can be readily adapted to model gray matter microstructure.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Ginsburger, Kévin and Matuschke, Felix and Poupon, Fabrice and Mangin, Jean-François and Axer, Markus and Poupon, Cyril}, - month = jun, - year = {2019}, - keywords = {Diffusion MRI, White matter, GPU, Phantom generation}, - pages = {10--24}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FLUUQRUL/Ginsburger et al. - 2019 - MEDUSA A GPU-based tool to create realistic phant.pdf:application/pdf}, -} - -@article{de_guio_alteration_2019, - title = {Alteration of the {Cortex} {Shape} as a {Proxy} of {White} {Matter} {Swelling} in {Severe} {Cerebral} {Small} {Vessel} {Disease}}, - volume = {10}, - issn = {1664-2295}, - url = {https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2019.00753/full}, - doi = {10.3389/fneur.2019.00753}, - abstract = {{\textless}p{\textgreater}CADASIL is a monogenic small vessel disease characterized by the accumulation of brain tissue lesions of microvascular origin leading to strokes and cognitive deficits. Both cortical and parenchymal alterations have been described using various MRI markers. However, relationships between cortical and subcortical alterations remain largely unexplored. While brain atrophy is a preponderant feature in cerebral small vessel disease, recent results in CADASIL suggest slightly larger brain volumes and increased white matter water content at early stages of the disease by comparison to controls. We hypothesized in this study that increased water content in gyral white matter balances expected brain atrophy. Direct white matter volume computation is challenging in these patients given widespread subcortical alterations. Instead, our approach was that a gyral white matter swelling would translate into a modification of the shape of cortical gyri. Our goal was then to assess the relationship between subcortical lesions and possible alteration of the cortex shape. More specifically, aims of this work were to assess 1) morphometric differences of the cortex shape between CADASIL patients and controls 2) the relationship between the cortex shape and the volume of white matter hyperintensities (WMH), a reflect of white matter alterations. Twenty-one patients at the early stage of the disease and 28 age- and sex-matched controls were included. Cortical surfaces were reconstructed from 3D-T1-weighted images. Folding power assessed from spectral analysis of gyrification and cortical morphometry using curvedness and shape index were computed as proxies of the cortex shape. Influence of segmentation errors were evaluated through the simulation of WMH in controls. As a result, patients had larger folding power and curvedness compared to controls. They also presented lower shape indices both related to sulci and gyri. In patients, the volume of WMH was associated with decreased gyral shape index. These results suggest that the cortex shape of CADASIL patients is different compared to controls and that the enlargement of gyri is related to the extent of white matter alterations. The study of the cortex shape might be another way to evaluate subcortical swelling or atrophy in various neurological disorders.{\textless}/p{\textgreater}}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neurology}, - author = {De Guio, François and Germanaud, David and Lefèvre, Julien and Fischer, Clara and Mangin, Jean-François and Chabriat, Hugues and Jouvent, Eric}, - month = jul, - year = {2019}, - note = {Publisher: Frontiers}, - keywords = {CADASIL, Cortex, Morphometry -, small vessel disease (SVD), White matter hyper intensities}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GH9LU7AK/De Guio et al. - 2019 - Alteration of the Cortex Shape as a Proxy of White.pdf:application/pdf}, -} - -@article{delettre_comparison_2019, - title = {Comparison between diffusion {MRI} tractography and histological tract-tracing of cortico-cortical structural connectivity in the ferret brain}, - volume = {3}, - issn = {2472-1751}, - url = {https://doi.org/10.1162/netn_a_00098}, - doi = {10.1162/netn_a_00098}, - abstract = {The anatomical wiring of the brain is a central focus in network neuroscience. -Diffusion MRI tractography offers the unique opportunity to investigate the -brain fiber architecture in vivo and noninvasively. However, -its reliability is still highly debated. Here, we explored the ability of -diffusion MRI tractography to match invasive anatomical tract-tracing -connectivity data of the ferret brain. We also investigated the influence of -several state-of-the-art tractography algorithms on this match to ground truth -connectivity data. Tract-tracing connectivity data were obtained from retrograde -tracer injections into the occipital, parietal, and temporal cortices of adult -ferrets. We found that the relative densities of projections identified from the -anatomical experiments were highly correlated with the estimates from all the -studied diffusion tractography algorithms (Spearman’s rho ranging from -0.67 to 0.91), while only small, nonsignificant variations appeared across the -tractography algorithms. These results are comparable to findings reported in -mouse and monkey, increasing the confidence in diffusion MRI tractography -results. Moreover, our results provide insights into the variations of -sensitivity and specificity of the tractography algorithms, and hence into the -influence of choosing one algorithm over another.In this article we used tract-tracing data as a gold standard to validate the use -of diffusion MRI tractography for inferring structural connectivity in the -ferret brain as well as for assessing the influence of several state-of-the-art -tractography algorithms on the inferred connections. We found high -correspondence between diffusion MRI tractography and tract-tracing with little -differences between the explored algorithms. We conclude that diffusion MRI -tractography provides a worthwhile whole-brain estimate of structural -connectivity that can be employed in further anatomical, developmental, and -computational studies of the ferret brain.}, - number = {4}, - urldate = {2024-03-12}, - journal = {Network Neuroscience}, - author = {Delettre, Céline and Messé, Arnaud and Dell, Leigh-Anne and Foubet, Ophélie and Heuer, Katja and Larrat, Benoit and Meriaux, Sebastien and Mangin, Jean-Francois and Reillo, Isabel and de Juan Romero, Camino and Borrell, Victor and Toro, Roberto and Hilgetag, Claus C.}, - month = sep, - year = {2019}, - pages = {1038--1050}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/4FUY3XEH/Delettre et al. - 2019 - Comparison between diffusion MRI tractography and .pdf:application/pdf}, -} - -@article{ji_increased_2019, - title = {Increased and {Decreased} {Superficial} {White} {Matter} {Structural} {Connectivity} in {Schizophrenia} and {Bipolar} {Disorder}}, - volume = {45}, - issn = {0586-7614}, - url = {https://doi.org/10.1093/schbul/sbz015}, - doi = {10.1093/schbul/sbz015}, - abstract = {Schizophrenia (SZ) and bipolar disorder (BD) are often conceptualized as “disconnection syndromes,” with substantial evidence of abnormalities in deep white matter tracts, forming the substrates of long-range connectivity, seen in both disorders. However, the study of superficial white matter (SWM) U-shaped short-range tracts remained challenging until recently, although findings from postmortem studies suggest they are likely integral components of SZ and BD neuropathology. This diffusion weighted imaging (DWI) study aimed to investigate SWM microstructure in vivo in both SZ and BD for the first time. We performed whole brain tractography in 31 people with SZ, 32 people with BD and 54 controls using BrainVISA and Connectomist 2.0. Segmentation and labeling of SWM tracts were performed using a novel, comprehensive U-fiber atlas. Analysis of covariances yielded significant generalized fractional anisotropy (gFA) differences for 17 SWM bundles in frontal, parietal, and temporal cortices. Post hoc analyses showed gFA reductions in both patient groups as compared with controls in bundles connecting regions involved in language processing, mood regulation, working memory, and motor function (pars opercularis, insula, anterior cingulate, precentral gyrus). We also found increased gFA in SZ patients in areas overlapping the default mode network (inferior parietal, middle temporal, precuneus), supporting functional hyperconnectivity of this network evidenced in SZ. We thus illustrate that short U-fibers are vulnerable to the pathological processes in major psychiatric illnesses, encouraging improved understanding of their anatomy and function.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Schizophrenia Bulletin}, - author = {Ji, Ellen and Guevara, Pamela and Guevara, Miguel and Grigis, Antoine and Labra, Nicole and Sarrazin, Samuel and Hamdani, Nora and Bellivier, Frank and Delavest, Marine and Leboyer, Marion and Tamouza, Ryad and Poupon, Cyril and Mangin, Jean-François and Houenou, Josselin}, - month = oct, - year = {2019}, - pages = {1367--1378}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Y7YQ6NHY/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A6NRGXW3/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf}, -} - -@article{gilson_network_2019, - title = {Network analysis of whole-brain {fMRI} dynamics: {A} new framework based on dynamic communicability}, - volume = {201}, - issn = {1053-8119}, - shorttitle = {Network analysis of whole-brain {fMRI} dynamics}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811919305889}, - doi = {10.1016/j.neuroimage.2019.116007}, - abstract = {Neuroimaging techniques such as MRI have been widely used to explore the associations between brain areas. Structural connectivity (SC) captures the anatomical pathways across the brain and functional connectivity (FC) measures the correlation between the activity of brain regions. These connectivity measures have been much studied using network theory in order to uncover the distributed organization of brain structures, in particular FC for task-specific brain communication. However, the application of network theory to study FC matrices is often “static” despite the dynamic nature of time series obtained from fMRI. The present study aims to overcome this limitation by introducing a network-oriented analysis applied to whole-brain effective connectivity (EC) useful to interpret the brain dynamics. Technically, we tune a multivariate Ornstein-Uhlenbeck (MOU) process to reproduce the statistics of the whole-brain resting-state fMRI signals, which provides estimates for MOU-EC as well as input properties (similar to local excitabilities). The network analysis is then based on the Green function (or network impulse response) that describes the interactions between nodes across time for the estimated dynamics. This model-based approach provides time-dependent graph-like descriptor, named communicability, that characterize the roles that either nodes or connections play in the propagation of activity within the network. They can be used at both global and local levels, and also enables the comparison of estimates from real data with surrogates (e.g. random network or ring lattice). In contrast to classical graph approaches to study SC or FC, our framework stresses the importance of taking the temporal aspect of fMRI signals into account. Our results show a merging of functional communities over time, moving from segregated to global integration of the network activity. Our formalism sets a solid ground for the analysis and interpretation of fMRI data, including task-evoked activity.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Gilson, Matthieu and Kouvaris, Nikos E. and Deco, Gustavo and Mangin, Jean-François and Poupon, Cyril and Lefranc, Sandrine and Rivière, Denis and Zamora-López, Gorka}, - month = nov, - year = {2019}, - pages = {116007}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/D8EJIZX8/S1053811919305889.html:text/html;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3AR2H57H/Gilson et al. - 2019 - Network analysis of whole-brain fMRI dynamics A n.pdf:application/pdf}, -} - -@article{mangin_plis_2019, - title = {“{Plis} de passage” {Deserve} a {Role} in {Models} of the {Cortical} {Folding} {Process}}, - volume = {32}, - issn = {1573-6792}, - url = {https://doi.org/10.1007/s10548-019-00734-8}, - doi = {10.1007/s10548-019-00734-8}, - abstract = {Cortical folding is a hallmark of brain topography whose variability across individuals remains a puzzle. In this paper, we call for an effort to improve our understanding of the pli de passage phenomenon, namely annectant gyri buried in the depth of the main sulci. We suggest that plis de passage could become an interesting benchmark for models of the cortical folding process. As an illustration, we speculate on the link between modern biological models of cortical folding and the development of the Pli de Passage Frontal Moyen (PPFM) in the middle of the central sulcus. For this purpose, we have detected nine interrupted central sulci in the Human Connectome Project dataset, which are used to explore the organization of the hand sensorimotor areas in this rare configuration of the PPFM.}, - language = {en}, - number = {6}, - urldate = {2024-03-12}, - journal = {Brain Topography}, - author = {Mangin, Jean-François and Le Guen, Yann and Labra, Nicole and Grigis, Antoine and Frouin, Vincent and Guevara, Miguel and Fischer, Clara and Rivière, Denis and Hopkins, William D. and Régis, Jean and Sun, Zhong Yi}, - month = nov, - year = {2019}, - keywords = {Cortical folding, Central sulcus, Pli de passage, Sulcal pits, Sulcal roots}, - pages = {1035--1048}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6DSRSA4Q/Mangin et al. - 2019 - “Plis de passage” Deserve a Role in Models of the .pdf:application/pdf}, -} - -@article{tamura_integrated_2019, - title = {Integrated datasets of normalized brain with functional localization using intra-operative electrical stimulation}, - volume = {14}, - issn = {1861-6429}, - url = {https://doi.org/10.1007/s11548-019-01957-7}, - doi = {10.1007/s11548-019-01957-7}, - abstract = {The purpose of this study was to transform brain mapping data into a digitized intra-operative MRI and integrated brain function dataset for predictive glioma surgery considering tumor resection volume, as well as the intra-operative and postoperative complication rates.}, - language = {en}, - number = {12}, - urldate = {2024-03-12}, - journal = {International Journal of Computer Assisted Radiology and Surgery}, - author = {Tamura, Manabu and Sato, Ikuma and Maruyama, Takashi and Ohshima, Kazuma and Mangin, Jean-François and Nitta, Masayuki and Saito, Taiichi and Yamada, Hiroyuki and Minami, Shinji and Masamune, Ken and Kawamata, Takakazu and Iseki, Hiroshi and Muragaki, Yoshihiro}, - month = dec, - year = {2019}, - keywords = {Normalization, Brain mapping, Digitization, Predictive glioma surgery, Transformation}, - pages = {2109--2122}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/88FURG8H/Tamura et al. - 2019 - Integrated datasets of normalized brain with funct.pdf:application/pdf}, -} - -@article{bertoux_sulcal_2019, - title = {Sulcal morphology in {Alzheimer}'s disease: an effective marker of diagnosis and cognition}, - volume = {84}, - issn = {0197-4580}, - shorttitle = {Sulcal morphology in {Alzheimer}'s disease}, - url = {https://www.sciencedirect.com/science/article/pii/S0197458019302192}, - doi = {10.1016/j.neurobiolaging.2019.07.015}, - abstract = {Measuring the morphology of brain sulci has been recently proposed as a novel imaging approach in Alzheimer's disease (AD). We aimed to investigate the relevance of such an approach in AD, by exploring its (1) clinical relevance in comparison with traditional imaging methods, (2) relationship with amyloid deposition, (3) association with cognitive functions. Here, 51 patients (n = 32 mild cognitive impairment/mild dementia-AD, n = 19 moderate/severe dementia-AD) diagnosed according to clinical-biological criteria (CSF biomarkers and amyloid-PET) and 29 controls (with negative amyloid-PET) underwent neuropsychological and 3T-MRI examinations. Mean sulcal width (SW) and mean cortical thickness around the sulcus (CT-S) were automatically measured. We found higher SW and lower CT-S in patients with AD than in controls. These differences were more pronounced at later stages of the disease and provided the best diagnostic accuracies among the imaging markers. Correlations were not found between CT-S or SW and amyloid deposition but between specific cognitive functions and regional CT-S/SW in key associated regions. Sulcal morphology is a good supporting diagnosis tool that reflects the main cognitive impairments in AD. It could be considered as a good surrogate marker to evaluate the efficacy of new drugs.}, - urldate = {2024-03-12}, - journal = {Neurobiology of Aging}, - author = {Bertoux, Maxime and Lagarde, Julien and Corlier, Fabian and Hamelin, Lorraine and Mangin, Jean-François and Colliot, Olivier and Chupin, Marie and Braskie, Meredith N. and Thompson, Paul M. and Bottlaender, Michel and Sarazin, Marie}, - month = dec, - year = {2019}, - keywords = {Alzheimer's disease, Cortical thickness, Sulcal width, Sulcal morphology, Data-driven science}, - pages = {41--49}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7WV9G7G4/Bertoux et al. - 2019 - Sulcal morphology in Alzheimer's disease an effec.pdf:application/pdf}, -} - -@article{mangin_neocortical_2020, - title = {Neocortical morphometry in {Huntington}'s disease: {Indication} of the coexistence of abnormal neurodevelopmental and neurodegenerative processes}, - volume = {26}, - issn = {2213-1582}, - shorttitle = {Neocortical morphometry in {Huntington}'s disease}, - url = {https://www.sciencedirect.com/science/article/pii/S2213158220300486}, - doi = {10.1016/j.nicl.2020.102211}, - abstract = {Huntington's disease (HD) is an inherited, autosomal dominant disorder that is characteristically thought of as a degenerative disorder. Despite cellular and molecular grounds suggesting HD could also impact normal development, there has been scarce systems-level data obtained from in vivo human studies supporting this hypothesis. Sulcus-specific morphometry analysis may help disentangle the contribution of coexisting neurodegenerative and neurodevelopmental processes, but such an approach has never been used in HD. Here, we investigated cortical sulcal depth, related to degenerative process, as well as cortical sulcal length, related to developmental process, in early-stage HD and age-matched healthy controls. This morphometric analysis revealed significant differences in the HD participants compared with the healthy controls bilaterally in the central and intra-parietal sulcus, but also in the left intermediate frontal sulcus and calcarine fissure. As the primary visual cortex is not connected to the striatum, the latter result adds to the increasing in vivo evidence for primary cortical degeneration in HD. Those sulcal measures that differed between HD and healthy populations were mainly atrophy-related, showing shallower sulci in HD. Conversely, the sulcal morphometry also revealed a crucial difference in the imprint of the Sylvian fissure that could not be related to loss of grey matter volume: an absence of asymmetry in the length of this fissure in HD. Strong asymmetry in that cortical region is typically observed in healthy development. As the formation of the Sylvian fissure appears early in utero, and marked asymmetry is specifically found in this area of the neocortex in newborns, this novel finding likely indicates the foetal timing of a disease-specific, genetic interplay with neurodevelopment.}, - urldate = {2024-03-12}, - journal = {NeuroImage: Clinical}, - author = {Mangin, Jean-Francois and Rivière, Denis and Duchesnay, Edouard and Cointepas, Yann and Gaura, Véronique and Verny, Christophe and Damier, Philippe and Krystkowiak, Pierre and Bachoud-Lévi, Anne-Catherine and Hantraye, Philippe and Remy, Philippe and Douaud, Gwenaëlle}, - month = jan, - year = {2020}, - keywords = {MRI, Asymmetry, Cortical morphometry, Huntington's disease, Neurodevelopment, Sylvian fissure}, - pages = {102211}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B9Z93VA9/S2213158220300486.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B5Y6HREA/Mangin et al. - 2020 - Neocortical morphometry in Huntington's disease I.pdf:application/pdf}, -} - -@article{dauphinot_subjective_2020, - title = {Subjective cognitive and non-cognitive complaints and brain {MRI} biomarkers in the {MEMENTO} cohort}, - volume = {12}, - copyright = {© 2020 The Authors. Alzheimer's \& Dementia: Diagnosis, Assessment \& Disease Monitoring published by Wiley Periodicals, Inc. on behalf of Alzheimer's Association}, - issn = {2352-8729}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/dad2.12051}, - doi = {10.1002/dad2.12051}, - abstract = {Introduction Subjective cognitive complaints may be a signature of preclinical stage Alzheimer's disease. However, the link between subjective cognitive and non-cognitive complaints and brain alterations remains unclear. Methods The relationship between cognitive and non-cognitive complaints and brain biomarkers, measured by structural magnetic resonance imaging, was investigated in 2056 participants of the MEMENTO cohort of outpatients, who were dementia-free at baseline. We assessed whether the cognitive status at inclusion or the presence of the apolipoprotein E gene variant (APOE) ε4 could modulate the association between the intensity of complaints and brain lesions. Results Smaller hippocampal volume was associated with higher memory complaints and discomfort in daily life. In APOE ε4 carriers, smaller whole-brain white matter and gray matter volumes and gyrification indices in several regions of interest of the parietal and temporal lobes, in the entorhinal and the para-hippocampal gyrus, were associated with higher memory complaint score. Conclusions The intensity of subjective complaints in not only memory but discomfort in daily life was associated with brain degeneration markers. The presence of APOE ε4 modulated the relationships between subjective memory complaints and brain alterations.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia: Diagnosis, Assessment \& Disease Monitoring}, - author = {Dauphinot, Virginie and Bouteloup, Vincent and Mangin, Jean-François and Vellas, Bruno and Pasquier, Florence and Blanc, Frédéric and Hanon, Olivier and Gabelle, Audrey and Annweiler, Cédric and David, Renaud and Planche, Vincent and Godefroy, Olivier and Rivasseau-Jonveaux, Thérèse and Chupin, Marie and Fischer, Clara and Chêne, Geneviève and Dufouil, Carole and Krolak-Salmon, Pierre}, - year = {2020}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/dad2.12051}, - keywords = {magnetic resonance imaging, multi-center cohort, preclinical AD, subjective health complaints}, - pages = {e12051}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BXEVBKA3/Dauphinot et al. - 2020 - Subjective cognitive and non-cognitive complaints .pdf:application/pdf}, -} - -@article{vonk_semantic_2020, - title = {Semantic loss marks early {Alzheimer}'s disease-related neurodegeneration in older adults without dementia}, - volume = {12}, - copyright = {© 2020 The Authors. Alzheimer's \& Dementia: Diagnosis, Assessment \& Disease Monitoring published by Wiley Periodicals LLC on behalf of Alzheimer's Association}, - issn = {2352-8729}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/dad2.12066}, - doi = {10.1002/dad2.12066}, - abstract = {Objective To assess progression of semantic loss in early stages of cognitive decline using semantic and letter fluency performance, and its relation with Alzheimer's disease (AD)-specific neurodegeneration using longitudinal multimodal neuroimaging measures. Methods Change in verbal fluency was analyzed among 2261 non-demented individuals with a follow-up diagnosis of no mild cognitive impairment (MCI), amnestic MCI (aMCI), non-amnestic MCI (naMCI), or incident dementia, using linear mixed models across 4 years of follow-up, and relations with magnetic resonance imaging (MRI; n = 1536) and 18F-fluorodeoxyglucose brain positron emission tomography (18F-FDG-PET) imaging (n = 756) using linear regression models across 2 years of follow-up. Results Semantic fluency declined—fastest in those at higher risk for AD (apolipoprotein E [APOE] e4 carriers, Clinical Dementia Rating score of .5, aMCI, or incident dementia)—while letter fluency did not except for those with incident dementia. Lower baseline semantic fluency was associated with an increase in white matter hyperintensities and total mean cortical thinning over time, and regionally with less hippocampal volume as well as more cortical thinning and reduced 18F-FDG-PET uptake in the inferior parietal lobule, entorhinal cortex, isthmus cingulate, and precuneus–posterior cingulate area. In contrast, baseline letter fluency was not associated with change in total nor regional neurodegeneration. Whole-brain neurodegeneration over time was associated with faster decline in both fluencies, while AD-specific regions were associated with a faster rate of decline in semantic but not letter fluency. Interpretation This study provides strong evidence of distinctive degeneration of semantic abilities early on in relation to both cognitive decline and AD-specific neurodegeneration.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia: Diagnosis, Assessment \& Disease Monitoring}, - author = {Vonk, Jet M. J. and Bouteloup, Vincent and Mangin, Jean-François and Dubois, Bruno and Blanc, Frédéric and Gabelle, Audrey and Ceccaldi, Mathieu and Annweiler, Cédric and Krolak-Salmon, Pierre and Belin, Catherine and Rivasseau-Jonveaux, Thérèse and Julian, Adrien and Sellal, François and Magnin, Eloi and Chupin, Marie and Habert, Marie-Odile and Chêne, Geneviève and Dufouil, Carole and Group, {and} on behalf of the MEMENTO cohort Study}, - year = {2020}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/dad2.12066}, - keywords = {Alzheimer's disease, neuroimaging, MCI, cohort studies, biomarkers, amnestic, category fluency, cognitive aging, letter fluency, semantic fluency, verbal fluency}, - pages = {e12066}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RJQAU9IN/Vonk et al. - 2020 - Semantic loss marks early Alzheimer's disease-rela.pdf:application/pdf}, -} - -@book{charidimou_cerebral_2020, - title = {Cerebral {Small} {Vessel} {Diseases}: {From} {Vessel} {Alterations} to {Cortical} {Parenchymal} {Injury}}, - isbn = {978-2-88963-587-0}, - shorttitle = {Cerebral {Small} {Vessel} {Diseases}}, - language = {en}, - publisher = {Frontiers Media SA}, - author = {Charidimou, Andreas and Jouvent, Eric and Veluw, Susanne J. Van}, - month = mar, - year = {2020}, - note = {Google-Books-ID: TBrWDwAAQBAJ}, -} - -@article{maltais_prospective_2020, - title = {Prospective {Associations} {Between} {Diffusion} {Tensor} {Imaging} {Parameters} and {Frailty} in {Older} {Adults}}, - volume = {68}, - copyright = {© 2020 The American Geriatrics Society}, - issn = {1532-5415}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16343}, - doi = {10.1111/jgs.16343}, - abstract = {BACKGROUND Cross-sectional associations have been found between frail individuals and worse white matter (WM) integrity. However, the prospective association between WM integrity and frailty is still unclear. Our objectives were to measure associations between WM integrity using diffusion tensor imaging (DTI) and the 5-year worsening of frailty in community-dwelling older adults. DESIGN Secondary analysis of the randomized controlled Multidomain Alzheimer Preventive Trial (MAPT). SETTING Thirteen memory centers in France and Monaco between 2008 and 2011. PARTICIPANTS Participants (mean age = 74.7 ± 3.9 years) with no dementia at baseline who had functional magnetic resonance imaging performed as part of the MAPT study (n = 227). MEASUREMENTS Fractional anisotropy and mean diffusivity (MD), axial diffusivity (AxD), and radial diffusivity (RD) were acquired for 10 different brain regions. Frailty was assessed by the Fried frailty phenotype (score from 0 to 5, higher is worse) at up to seven time points for 5 years. Mixed effect ordinal logistic regression model was used to assess the prospective association between DTI parameters (independent variables) and frailty (dependent variable). All the analyses were adjusted for age, sex, baseline total intracranial volume, and the presence of one of the following cardiovascular risk factors (hypertension, diabetes, and/or hypercholesterolemia). RESULTS A statistically significant association was found between the RD, AxD, and MD for different brain regions (anterior limb of internal capsule, external capsule, posterior corona radiata, posterior thalamic radiation, superior corona radiata, superior frontal occipital fasciculus, and superior longitudinal fasciculus) and worsening of frailty over 5 years after adjusting for multiple comparisons. CONCLUSIONS This is the first study to show that WM integrity is associated with frailty in older adults. The mechanisms related to these results require further investigation. J Am Geriatr Soc 68:1050–1055, 2020}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Journal of the American Geriatrics Society}, - author = {Maltais, Mathieu and de Souto Barreto, Philipe and Perus, Lisa and Mangin, Jean-François and Grigis, Antoine and Chupin, Marie and Bouyahia, Ali and Gabelle, Audrey and Delrieux, Julien and Rolland, Yves and Vellas, Bruno and Group, for the Multidomain Alzheimer Preventive Trial/Data Sharing Alzheimer (MAPT/DSA) Study}, - year = {2020}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jgs.16343}, - keywords = {brain health, diffusion magnetic resonance imagingfrailty, physical capacity}, - pages = {1050--1055}, -} - -@article{guevara_superficial_2020, - title = {Superficial white matter: {A} review on the {dMRI} analysis methods and applications}, - volume = {212}, - issn = {1053-8119}, - shorttitle = {Superficial white matter}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811920301609}, - doi = {10.1016/j.neuroimage.2020.116673}, - abstract = {The mapping of human brain connections is still an on going task. Unlike deep white matter (DWM), which has been extensively studied and well documented, superficial white matter (SWM) has been often left aside. Improving our understanding of the SWM is an important goal for a better understanding of the brain network and its relation to several pathologies. The shape and localization of these short bundles present a high variability across subjects. Furthermore, the small diameter of most superficial bundles and partial volume effects induced by their proximity to the cortex leads to complex tratography issues. Therefore, the mapping of SWM bundles and the use of the resulting atlases for clinical studies requiere dedicated methodologies that are reviewed in this paper.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Guevara, Pamela and Román, Claudio and Mangin, Jean-François}, - month = may, - year = {2020}, - keywords = {Tractography, Short association fibers, Diffusion-weighted imaging, Superficial white matter, U-fibers, White matter bundle}, - pages = {116673}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6N93BWK3/Guevara et al. - 2020 - Superficial white matter A review on the dMRI ana.pdf:application/pdf}, -} - -@inproceedings{lopez-lopez_geosp_2020, - address = {Montreal, QC, Canada}, - title = {{GeoSP}: {A} parallel method for a cortical surface parcellation based on geodesic distance}, - isbn = {978-1-72811-990-8}, - shorttitle = {{GeoSP}}, - url = {https://ieeexplore.ieee.org/document/9175779/}, - doi = {10.1109/EMBC44109.2020.9175779}, - urldate = {2024-03-12}, - booktitle = {2020 42nd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - publisher = {IEEE}, - author = {Lopez-Lopez, Narciso and Vazquez, Andrea and Poupon, Cyril and Mangin, Jean-Francois and Ladra, Susana and Guevara, Pamela}, - month = jul, - year = {2020}, - pages = {1696--1700}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EZEUZVBT/Lopez-Lopez et al. - 2020 - GeoSP A parallel method for a cortical surface pa.pdf:application/pdf}, -} - -@inproceedings{huerta_inter-subject_2020, - title = {Inter-{Subject} {Clustering} of {Brain} {Fibers} from {Whole}-{Brain} {Tractography}}, - url = {https://ieeexplore.ieee.org/abstract/document/9175342}, - doi = {10.1109/EMBC44109.2020.9175342}, - abstract = {This work presents an effective multiple subject clustering method using whole-brain tractography datasets. The method is able to obtain fiber clusters that are representative of the population. The proposed approach first applies a fast intra-subject clustering algorithm on each subject obtaining the cluster centroids for all subjects. Second, it compresses the collection of centroids to a latent space through the encoder of a trained autoencoder. Finally, it uses a modified HDBSCAN with adjusted parameters on the encoded centroids of all subjects to obtain the final inter-subject clusters. The results shows that the proposed method outperforms other clustering strategies, and it is able to retrieve known fascicles in a reasonable execution time, achieving a precision over 87\% and F1 score above 86\% on a collection of 20 simulated subjects.}, - urldate = {2024-03-12}, - booktitle = {2020 42nd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Huerta, Isaías and Vázquez, Andrea and López-López, Narciso and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela and Hernández, Cecilia}, - month = jul, - year = {2020}, - note = {ISSN: 2694-0604}, - keywords = {Sociology, Statistics, Clustering algorithms, Measurement, Image reconstruction, White matter, Optical fiber networks}, - pages = {1687--1691}, -} - -@article{lopez-lopez_coarse_2020, - title = {From {Coarse} to {Fine}-{Grained} {Parcellation} of the {Cortical} {Surface} {Using} a {Fiber}-{Bundle} {Atlas}}, - volume = {14}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2020.00032}, - doi = {10.3389/fninf.2020.00032}, - abstract = {We present a hybrid method to create fine-grained parcellations of the cortical surface, from a coarse-grained parcellation according to an anatomical atlas, based on cortico-cortical connectivity. The connectivity information is obtained from segmented superficial and deep white matter bundles, according to bundle atlases, instead of the whole tractography. Thus, a direct matching between the fiber bundles and the cortical regions is obtained, avoiding the problem of finding the correspondence of the cortical parcels among subjects. Generating parcels from segmented fiber bundles can give a good representation of the human brain connectome since they are based on bundle atlases that contain the most reproducible short and long connections found on a population of subjects. The method first processes the tractography of each subject and extracts the bundles of the atlas, based on a segmentation algorithm. Next, the intersection between the fiber bundles and the cortical mesh is calculated, to define the initial and final intersection points of each fiber. A fiber filtering is then applied to eliminate misclassified fibers, based on the anatomical definition of each bundle and the labels of Desikan-Killiany anatomical parcellation. Then, a parcellation algorithm is performed to create a subdivision of the anatomical regions of the cortex, reproducible across subjects. This step resolves the overlapping of the fiber bundle extremities over the cortical mesh within each anatomical region. For the analysis, it considers the density of the connections and the degree of overlapping, represented with a graph. One of our parcellations, an atlas composed of 160 parcels, achieves a reproducibility across subjects of ≈ 0.74, based on the average Dice's coefficient between subject's connectivity matrices, rather than ≈ 0.73 obtained for a macro anatomical parcellation of 150 parcels. Moreover, we compared two of our parcellations with state-of-the-art atlases, finding a degree of similarity with dMRI, functional, anatomical, and multi-modal atlases. The higher similarity was found for our parcellation composed of 185 sub-parcels with another parcellation based on dMRI data from the same database, but created with a different approach, leading to 130 parcels in common based on a Dice's coefficient ≥ 0.5.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {López-López, Narciso and Vázquez, Andrea and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Ladra, Susana and Guevara, Pamela}, - month = sep, - year = {2020}, - note = {Publisher: Frontiers}, - keywords = {tractography, parcellation, connectivity, Cortex, white matter, fiber bundle}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7YR7NN5G/López-López et al. - 2020 - From Coarse to Fine-Grained Parcellation of the Co.pdf:application/pdf}, -} - -@article{pizzagalli_reliability_2020, - title = {The reliability and heritability of cortical folds and their genetic correlations across hemispheres}, - volume = {3}, - copyright = {2020 The Author(s)}, - issn = {2399-3642}, - url = {https://www.nature.com/articles/s42003-020-01163-1}, - doi = {10.1038/s42003-020-01163-1}, - abstract = {Cortical folds help drive the parcellation of the human cortex into functionally specific regions. Variations in the length, depth, width, and surface area of these sulcal landmarks have been associated with disease, and may be genetically mediated. Before estimating the heritability of sulcal variation, the extent to which these metrics can be reliably extracted from in-vivo MRI must be established. Using four independent test-retest datasets, we found high reliability across the brain (intraclass correlation interquartile range: 0.65–0.85). Heritability estimates were derived for three family-based cohorts using variance components analysis and pooled (total N {\textgreater} 3000); the overall sulcal heritability pattern was correlated to that derived for a large population cohort (N {\textgreater} 9000) calculated using genomic complex trait analysis. Overall, sulcal width was the most heritable metric, and earlier forming sulci showed higher heritability. The inter-hemispheric genetic correlations were high, yet select sulci showed incomplete pleiotropy, suggesting hemisphere-specific genetic influences.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Communications Biology}, - author = {Pizzagalli, Fabrizio and Auzias, Guillaume and Yang, Qifan and Mathias, Samuel R. and Faskowitz, Joshua and Boyd, Joshua D. and Amini, Armand and Rivière, Denis and McMahon, Katie L. and de Zubicaray, Greig I. and Martin, Nicholas G. and Mangin, Jean-François and Glahn, David C. and Blangero, John and Wright, Margaret J. and Thompson, Paul M. and Kochunov, Peter and Jahanshad, Neda}, - month = sep, - year = {2020}, - note = {Publisher: Nature Publishing Group}, - keywords = {Neuroscience, Heritable quantitative trait}, - pages = {1--12}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5LA2TUQR/Pizzagalli et al. - 2020 - The reliability and heritability of cortical folds.pdf:application/pdf}, -} - -@article{lu_cross-sectional_2020, - title = {Cross-sectional and prospective associations between cerebral cortical thickness and frailty in older adults}, - volume = {139}, - issn = {0531-5565}, - url = {https://www.sciencedirect.com/science/article/pii/S0531556520303661}, - doi = {10.1016/j.exger.2020.111018}, - abstract = {Background -Several neurodegenerative markers measured by magnetic resonance imaging (MRI) have shown to be related with frailty. While most studies have focused on surrogates of cerebral vascular damage such as increased white matter lesions, the associations between cortical atrophy and frailty were less often investigated. -Objectives -To investigate the cross-sectional and prospective associations between cortical thickness and frailty evolution in older adults. -Methods -We enrolled 484 community-dwelling adults aged ≥70 years, participants from the Multidomain Alzheimer Preventive Trial (MAPT), with data on cerebral cortical thickness and frailty. Cortical thickness was acquired by MRI for whole-brain and regional cortices. Two function-specific regions of interest, i.e., mobility-related regions and Alzheimer's disease (AD) signature, were selected on the basis of previous studies. Frailty status was assessed by the Fried frailty phenotype (i.e., weakness, slowness, involuntary weight loss, fatigue and low physical activity level) at baseline, after 6 months and every year until the end of the 5-year follow-up. -Results -Older adults with higher global cortical thickness were less likely to be pre-frail and frail at baseline (adjusted OR: 0.13, 95\% CI: 0.03–0.65, p = 0.013). In addition, higher cortical thickness in mobility-related and AD-signature regions were associated with lower likelihood of being pre-frail and frail. Similar associations were observed for having weakness and slowness. However, neither global nor region-specific cortical thickness showed prospective associations with future frailty onset. -Conclusions -The global and regional cortical thickness cross-sectionally associated with frailty in older adults, but no prospective associations with incident frailty were found. The longitudinal relationship between cortical thickness and frailty evolution requires further investigation.}, - urldate = {2024-03-12}, - journal = {Experimental Gerontology}, - author = {Lu, Wan-Hsuan and de Souto Barreto, Philipe and Rolland, Yves and Rodríguez-Mañas, Leocadio and Bouyahia, Ali and Fischer, Clara and Mangin, Jean-François and Giudici, Kelly Virecoulon and Vellas, Bruno}, - month = oct, - year = {2020}, - keywords = {Alzheimer's disease, Cortical thickness, Brain aging, Older adults, Frailty}, - pages = {111018}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/I7GG8UHG/Lu et al. - 2020 - Cross-sectional and prospective associations betwe.pdf:application/pdf}, -} - -@article{vazquez_ffclust_2020, - title = {{FFClust}: {Fast} fiber clustering for large tractography datasets for a detailed study of brain connectivity}, - volume = {220}, - issn = {1053-8119}, - shorttitle = {{FFClust}}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811920305565}, - doi = {10.1016/j.neuroimage.2020.117070}, - abstract = {Automated methods that can identify white matter bundles from large tractography datasets have several applications in neuroscience research. In these applications, clustering algorithms have shown to play an important role in the analysis and visualization of white matter structure, generating useful data which can be the basis for further studies. This work proposes FFClust, an efficient fiber clustering method for large tractography datasets containing millions of fibers. Resulting clusters describe the whole set of main white matter fascicles present on an individual brain. The method aims to identify compact and homogeneous clusters, which enables several applications. In individuals, the clusters can be used to study the local connectivity in pathological brains, while at population level, the processing and analysis of reproducible bundles, and other post-processing algorithms can be carried out to study the brain connectivity and create new white matter bundle atlases. The proposed method was evaluated in terms of quality and execution time performance versus the state-of-the-art clustering techniques used in the area. Results show that FFClust is effective in the creation of compact clusters, with a low intra-cluster distance, while keeping a good quality Davies–Bouldin index, which is a metric that quantifies the quality of clustering approaches. Furthermore, it is about 8.6 times faster than the most efficient state-of-the-art method for one million fibers dataset. In addition, we show that FFClust is able to correctly identify atlas bundles connecting different brain regions, as an example of application and the utility of compact clusters.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Vázquez, Andrea and López-López, Narciso and Sánchez, Alexis and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = oct, - year = {2020}, - keywords = {Tractography, Fiber clustering, White matter bundle}, - pages = {117070}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BQ4YZUH6/Vázquez et al. - 2020 - FFClust Fast fiber clustering for large tractogra.pdf:application/pdf}, -} - -@article{sarrazin_neuroimaging_2020, - title = {Neuroimaging {Evidence} for {Increased} {Neurite} {Density} in {Patients} {Taking} {Lithium}: {A} {Replication} {Study}}, - volume = {90}, - issn = {0033-3190}, - shorttitle = {Neuroimaging {Evidence} for {Increased} {Neurite} {Density} in {Patients} {Taking} {Lithium}}, - url = {https://doi.org/10.1159/000507556}, - doi = {10.1159/000507556}, - abstract = {Dear Editor,The biological mechanisms underlying the efficacy of lithium therapy remain largely unknown. In Psychotherapy and Psychosomatics [1], we have recently published the first study showing increased neurite density in patients taking lithium with Neurite Orientation Dispersion and Density Imaging (NODDI), an advanced model of MRI diffusion [2]. Albeit confirming previous results associating lithium with changes of grey matter volume [3], replication remains a priority in the field of neuroscience [4].Here, we report a replication of our previous results – higher neurite density within the left frontal cortex – in patients under lithium therapy compared with patients without lithium therapy, in a completely independent sample. Data were collected in Calgary (AB, Canada) from 23 controls and 26 patients with bipolar disorder upon which only 7 (26.9\%) were prescribed with lithium at the time of scan. MRI data were acquired with a General Electric MR750 3T device and included T1 structural MRI (MPRAGE, voxel size: 1 × 1 × 1 mm), and multi-shell, high angular resolution diffusion MRI (EPI, 96 × 96 × 60, voxel size: 2.5 × 2.5 × 2.5 mm), 98 gradient directions, 3 b-shells: b = 300, 700, and 2,000 mm2/s (8, 30, and 60 directions, respectively) and 10 b = 0 mm2/s images (1, 3, and 6 per shell, respectively). Both the MRI manufacturer and the diffusion weighted acquisition (number of directions, b values) were different from the original publication [1]. The sole measure of interest was the mean intracellular fraction within the left frontal cortex as defined by the Desikan-Killiany atlas [1].}, - number = {1}, - urldate = {2024-03-12}, - journal = {Psychotherapy and Psychosomatics}, - author = {Sarrazin, Samuel and Poupon, Cyril and Uszynski, Ivy and Teillac, Achille and Mangin, Jean-François and Polosan, Mircea and Favre, Pauline and Laidi, Charles and D'Albis, Marc-Antoine and Leboyer, Marion and Lledo, Pierre-Marie and Henry, Chantal and Emsell, Louise and Shakeel, Mohammed K. and Goghari, Vina M. and Houenou, Josselin}, - month = may, - year = {2020}, - pages = {71--72}, -} - -@article{berkovitch_disruption_2021, - title = {Disruption of {Conscious} {Access} in {Psychosis} {Is} {Associated} with {Altered} {Structural} {Brain} {Connectivity}}, - volume = {41}, - copyright = {Copyright © 2021 the authors. SfN exclusive license.}, - issn = {0270-6474, 1529-2401}, - url = {https://www.jneurosci.org/content/41/3/513}, - doi = {10.1523/JNEUROSCI.0945-20.2020}, - abstract = {According to global neuronal workspace (GNW) theory, conscious access relies on long-distance cerebral connectivity to allow a global neuronal ignition coding for conscious content. In patients with schizophrenia and bipolar disorder, both alterations in cerebral connectivity and an increased threshold for conscious perception have been reported. The implications of abnormal structural connectivity for disrupted conscious access and the relationship between these two deficits and psychopathology remain unclear. The aim of this study was to determine the extent to which structural connectivity is correlated with consciousness threshold, particularly in psychosis. We used a visual masking paradigm to measure consciousness threshold, and diffusion MRI tractography to assess structural connectivity in 97 humans of either sex with varying degrees of psychosis: healthy control subjects (n = 46), schizophrenia patients (n = 25), and bipolar disorder patients with (n = 17) and without (n = 9) a history of psychosis. Patients with psychosis (schizophrenia and bipolar disorder with psychotic features) had an elevated masking threshold compared with control subjects and bipolar disorder patients without psychotic features. Masking threshold correlated negatively with the mean general fractional anisotropy of white matter tracts exclusively within the GNW network (inferior frontal-occipital fasciculus, cingulum, and corpus callosum). Mediation analysis demonstrated that alterations in long-distance connectivity were associated with an increased masking threshold, which in turn was linked to psychotic symptoms. Our findings support the hypothesis that long-distance structural connectivity within the GNW plays a crucial role in conscious access, and that conscious access may mediate the association between impaired structural connectivity and psychosis.}, - language = {en}, - number = {3}, - urldate = {2024-03-12}, - journal = {Journal of Neuroscience}, - author = {Berkovitch, Lucie and Charles, Lucie and Cul, Antoine Del and Hamdani, Nora and Delavest, Marine and Sarrazin, Samuel and Mangin, Jean-François and Guevara, Pamela and Ji, Ellen and d'Albis, Marc-Antoine and Gaillard, Raphaël and Bellivier, Frank and Poupon, Cyril and Leboyer, Marion and Tamouza, Ryad and Dehaene, Stanislas and Houenou, Josselin}, - month = jan, - year = {2021}, - pmid = {33229501}, - note = {Publisher: Society for Neuroscience -Section: Research Articles}, - keywords = {schizophrenia, tractography, bipolar disorder, cerebral connectivity, consciousness, global neuronal workspace}, - pages = {513--523}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AK2V75RR/Berkovitch et al. - 2021 - Disruption of Conscious Access in Psychosis Is Ass.pdf:application/pdf}, -} - -@article{guerville_kidney_2021, - title = {Kidney {Function} and {Cognitive} {Decline} in {Older} {Adults}: {Examining} the {Role} of {Neurodegeneration}}, - volume = {69}, - copyright = {© 2021 The American Geriatrics Society}, - issn = {1532-5415}, - shorttitle = {Kidney {Function} and {Cognitive} {Decline} in {Older} {Adults}}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16954}, - doi = {10.1111/jgs.16954}, - abstract = {BACKGROUND/OBJECTIVES Cognitive decline associated with impaired kidney function might involve neurodegeneration. Our objectives were to evaluate the longitudinal association between kidney function and cognitive decline in older adults and to assess the involvement of cortical beta-amyloid and hippocampal atrophy (features of Alzheimer's disease (AD)) in this association. DESIGN Secondary analysis of the randomized controlled Multidomain Alzheimer Preventive Trial (MAPT). SETTINGS Thirteen memory centers (France and Monaco, 2008–2016). PARTICIPANTS A total of 1,334 community-dwellers {\textgreater}70 years old without dementia at baseline. MEASUREMENTS We estimated glomerular filtration rate (eGFR) from serum creatinine using CKD-Epi equation. Cognition was assessed at baseline, 6, 12, 24, 36, 48, and 60 months using a composite Z-score designed for MAPT. The Clinical Dementia Rating (CDR) score was used to assess cognition and functional independence. We examined the association between eGFR and (1) evolution of the composite cognitive Z-score using mixed-effect models and (2) progression on CDR using Cox models and mixed-effect models. Adjustments were made for age, sex, education, ApoE genotype, cardiovascular risk factors and disease, hippocampal volume (measured with magnetic resonance), and cortical beta-amyloid (measured with positron emission tomography). RESULTS Median (IQR) eGFR was 73(60–84) mL/min/1.73 m2. Two hundred sixty-nine participants experienced progression on CDR score during follow-up. eGFR{\textless}60 was significantly associated with progression on CDR score (adjusted hazard ratio (aHR) = 1.35, 95\% CI 1.01–1.80) and with both the cognitive and functional independence components of CDR, but not with the evolution of the composite cognitive Z-score (adjusted β-coefficient −0.004, 95\% CI −0.014; 0.006). Associations were not modified after further adjustment for beta-amyloid (subsample: n = 252) and hippocampal volume (subsample: n = 270). CONCLUSIONS We did not find a mild to moderate renal insufficiency to be associated with brain imaging features of AD, and our results do not support the involvement of AD mechanisms in the incidence of cognitive impairment and functional decline associated with chronic kidney disease.}, - language = {en}, - number = {3}, - urldate = {2024-03-12}, - journal = {Journal of the American Geriatrics Society}, - author = {Guerville, Florent and De Souto Barreto, Philipe and Coley, Nicola and Andrieu, Sandrine and Mangin, Jean-François and Chupin, Marie and Payoux, Pierre and Ousset, Pierre-Jean and Rolland, Yves and Vellas, Bruno and Group, the MAPT/DSA}, - year = {2021}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jgs.16954}, - keywords = {cognition, hippocampal volume, beta-amyloid, glomerular filtration rate, older persons}, - pages = {651--659}, -} - -@article{he_fiveyear_2021, - title = {Five‐{Year} {Lower} {Extremity} {Function} is {Associated} with {White} {Matter} {Abnormality} in {Older} {Adults}}, - volume = {69}, - issn = {0002-8614, 1532-5415}, - url = {https://agsjournals.onlinelibrary.wiley.com/doi/10.1111/jgs.16989}, - doi = {10.1111/jgs.16989}, - abstract = {Objective - To explore associations between changes of lower extremity function (LEF) parameters over a 5‐year period and diffusion tensor imaging (DTI) parameters of white matter tracts among community‐dwelling older adults. - - - Design - A secondary analysis on image and physical function data collected from the Multidomain Alzheimer's Preventive Trial (MAPT). - - - Participants - 208 older adults (aged 75 ± 4 years, with spontaneous memory complaint or limited instrumental daily living activity or slow gait speed, 60\% female) of the MAPT‐magnetic resonance imaging (MRI) ancillary study. The time interval between a participant's enrolment and MRI scan was on average 110 ± 97 days. - - - Measurements - Forty‐eight white matter tracts (WMTs) were measured. LEF parameters (measured after the MRI scan) were assessed as the short physical performance battery (SPPB) score, gait speed, and chair stands time over a 5‐year period. Mixed‐effects models were performed to explore the associations between baseline DTI values and the progression of LEF parameters. Bonferroni correction was applied for multiple comparison correction. - - - Results - The progression of LEF was associated with 35 baseline DTI parameters from 24 WMTs. Higher baseline DTI parameter values were related to more decreases in SPPB score and gait speed, and greater increases in chair stands time. Bilateral uncinate fasciculus was associated with all LEF parameters. Other WMTs in cingulum, cerebral and cerebellar peduncle, internal capsule, and corpus callosum also showed close connections with LEF changes. - - - Conclusions - Our findings show that DTI parameters of some WMTs are associated with the 5‐year decline in LEF, suggesting that alterations in WMT integrity (evaluated by DTI parameters) might be used to explore potential causes of impaired mobility in older adults when no clear explanations can be found.}, - language = {en}, - number = {4}, - urldate = {2024-03-12}, - journal = {Journal of the American Geriatrics Society}, - author = {He, Lingxiao and De Souto Barreto, Philipe and Giudici, Kelly Virecoulon and Gabelle, Audrey and Perus, Lisa and Mangin, Jean‐François and Rolland, Yves and Vellas, Bruno and {Other Individuals in the MAPT/DSA Group}}, - month = apr, - year = {2021}, - pages = {995--1002}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/2ZZ8D3F2/He et al. - 2021 - Five‐Year Lower Extremity Function is Associated w.pdf:application/pdf}, -} - -@inproceedings{roman_study_2021, - title = {Study {Of} {Precentral}-{Postcentral} {Connections} {On} {Hcp} {Data} {Using} {Probabilistic} {Tractography} {And} {Fiber} {Clustering}}, - url = {https://ieeexplore.ieee.org/abstract/document/9434093}, - doi = {10.1109/ISBI48211.2021.9434093}, - abstract = {The study of the superficial white matter and its description is essential for the understanding of human brain function and the study of pathogenesis. However, the study of these fibers is still an incomplete task due to the high inter-subject variability and the size of this kind of fibers. In this work, a superficial white matter bundle identification based on fiber clustering was performed using probabilistic tractography on 100 subjects from the The Human Connectome Project (HCP) data, aligned with a non-linear registration. The method starts with an intra-subject clustering, followed by a segmentation of fibers connecting the precentral (PrC) and postcentral (PoC) regions, based on a ROI atlas. Due to the high amount of fibers, they were randomly separated into groups. An inter-subject clustering was applied on the fibers of each group, and then two clustering levels were applied to select the most reproducible bundles. Seven bundles per hemisphere were obtained, connecting the PrC and PoC regions. These were compared with bundles from previous atlases, showing in general more coverage and some bundles not found in previous atlases.}, - urldate = {2024-03-12}, - booktitle = {2021 {IEEE} 18th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Román, C. and López-López, N. and Houenou, J. and Poupon, C. and Mangin, J.-F. and Hernández, C. and Guevara, P.}, - month = apr, - year = {2021}, - note = {ISSN: 1945-8452}, - keywords = {Probabilistic logic, Tractography, Short association fibers, Diffusion-weighted imaging, Task analysis, Biomedical imaging, White matter, Superficial white matter, White matter bundle}, - pages = {55--59}, -} - -@article{hozer_lithium_2021, - title = {Lithium prevents grey matter atrophy in patients with bipolar disorder: an international multicenter study}, - volume = {51}, - issn = {0033-2917, 1469-8978}, - shorttitle = {Lithium prevents grey matter atrophy in patients with bipolar disorder}, - url = {https://www.cambridge.org/core/journals/psychological-medicine/article/abs/lithium-prevents-grey-matter-atrophy-in-patients-with-bipolar-disorder-an-international-multicenter-study/6267A7E11F17EFDF5857F06E4C233D4F}, - doi = {10.1017/S0033291719004112}, - abstract = {BackgroundLithium (Li) is the gold standard treatment for bipolar disorder (BD). However, its mechanisms of action remain unknown but include neurotrophic effects. We here investigated the influence of Li on cortical and local grey matter (GM) volumes in a large international sample of patients with BD and healthy controls (HC).MethodsWe analyzed high-resolution T1-weighted structural magnetic resonance imaging scans of 271 patients with BD type I (120 undergoing Li) and 316 HC. Cortical and local GM volumes were compared using voxel-wise approaches with voxel-based morphometry and SIENAX using FSL. We used multiple linear regression models to test the influence of Li on cortical and local GM volumes, taking into account potential confounding factors such as a history of alcohol misuse.ResultsPatients taking Li had greater cortical GM volume than patients without. Patients undergoing Li had greater regional GM volumes in the right middle frontal gyrus, the right anterior cingulate gyrus, and the left fusiform gyrus in comparison with patients not taking Li.ConclusionsOur results in a large multicentric sample support the hypothesis that Li could exert neurotrophic and neuroprotective effects limiting pathological GM atrophy in key brain regions associated with BD.}, - language = {en}, - number = {7}, - urldate = {2024-03-12}, - journal = {Psychological Medicine}, - author = {Hozer, Franz and Sarrazin, Samuel and Laidi, Charles and Favre, Pauline and Pauling, Melissa and Cannon, Dara and McDonald, Colm and Emsell, Louise and Mangin, Jean-François and Duchesnay, Edouard and Bellani, Marcella and Brambilla, Paolo and Wessa, Michele and Linke, Julia and Polosan, Mircea and Versace, Amelia and Phillips, Mary L. and Delavest, Marine and Bellivier, Frank and Hamdani, Nora and d'Albis, Marc-Antoine and Leboyer, Marion and Houenou, Josselin}, - month = may, - year = {2021}, - keywords = {MRI, lithium, Bipolar disorder, grey matter volume}, - pages = {1201--1210}, -} - -@article{harvey_increased_2021, - title = {Increased representation of the non-dominant hand in pianists demonstrated by measurement of {3D} morphology of the central sulcus}, - volume = {1}, - issn = {2634-4416}, - url = {https://doi.org/10.1093/psyrad/kkab004}, - doi = {10.1093/psyrad/kkab004}, - abstract = {Post-mortem and magnetic resonance imaging (MRI) studies of the central sulcus, as an indicator of motor cortex, have shown that in the general population there is greater representation of the dominant compared to the non-dominant hand. Studies of musicians, who are highly skilled in performing complex finger movements, have suggested this dominance is affected by musical training, but methods and findings have been mixed.In the present study, an automated image analysis pipeline using a 3D mesh approach was applied to measure central sulcus (CS) asymmetry on MR images obtained for a cohort of right-handed pianists and matched controls.The depth, length, and surface area (SA) of the CS and thickness of the cortical mantle adjacent to the CS were measured in each cerebral hemisphere by applying the BrainVISA Morphologist 2012 software pipeline to 3D T1-weighted MR images of the brain obtained for 15 right-handed pianists and 14 controls, matched with respect to age, sex, and handedness. Asymmetry indices (AIs) were calculated for each parameter and multivariate analysis of covariance (MANCOVA), and post hoc tests were performed to compare differences between the pianist and control groups.A one-way MANCOVA across the four AIs, controlling for age and sex, revealed a significant main effect of group (P = 0.04), and post hoc analysis revealed that while SA was significantly greater in the left than the right cerebral hemisphere in controls (P \< 0.001), there was no significant difference between left and right SA in the pianists (P = 0.634). Independent samples t-tests revealed that the SA of right CS was significantly larger in pianists compared to controls (P = 0.015), with no between-group differences in left CS.Application of an image analysis pipeline to 3D MR images has provided robust evidence of significantly increased representation of the non-dominant hand in the brain of pianists compared to age-, sex-, and handedness-matched controls. This finding supports prior research showing structural differences in the central sulcus in musicians and is interpreted to reflect the long-term motor training and high skill level of right-handed pianists in using their left hand.}, - number = {2}, - urldate = {2024-03-12}, - journal = {Psychoradiology}, - author = {Harvey, Adam and Hou, Lewis and Davidson-Kelly, Kirsteen and Schaefer, Rebecca S and Hong, Sujin and Mangin, Jean-François and Overy, Katie and Roberts, Neil}, - month = jun, - year = {2021}, - pages = {66--72}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BY486IK4/Harvey et al. - 2021 - Increased representation of the non-dominant hand .pdf:application/pdf}, -} - -@article{borne_automatic_2021, - title = {Automatic recognition of specific local cortical folding patterns}, - volume = {238}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921004857}, - doi = {10.1016/j.neuroimage.2021.118208}, - abstract = {The study of local cortical folding patterns showed links with psychiatric illnesses as well as cognitive functions. Despite the tools now available to visualize cortical folds in 3D, manually classifying local sulcal patterns is a time-consuming and tedious task. In fact, 3D visualization of folds helps experts to identify different sulcal patterns but fold variability is so high that the distinction between these patterns sometimes requires the definition of complex criteria, making manual classification difficult and not reliable. However, the assessment of the impact of these patterns on the functional organization of the cortex could benefit from the study of large databases, especially when studying rare patterns. In this paper, several algorithms for the automatic classification of fold patterns are proposed to allow morphological studies to be extended and confirmed on such large databases. Three methods are proposed, the first based on a Support Vector Machine (SVM) classifier, the second on the Scoring by Non-local Image Patch Estimator (SNIPE) approach and the third based on a 3D Convolution Neural Network (CNN). These methods are generic enough to be applicable to a wide range of folding patterns. They are tested on two types of patterns for which there is currently no method to automatically identify them: the Anterior Cingulate Cortex (ACC) patterns and the Power Button Sign (PBS). The two ACC patterns are almost equally present whereas PBS is a particularly rare pattern in the general population. The three models proposed achieve balanced accuracies of approximately 80\% for ACC patterns classification and 60\% for PBS classification. The CNN-based model is more interesting for the classification of ACC patterns thanks to its rapid execution. However, SVM and SNIPE-based models are more effective in managing unbalanced problems such as PBS recognition.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Borne, Léonie and Rivière, Denis and Cachia, Arnaud and Roca, Pauline and Mellerio, Charles and Oppenheim, Catherine and Mangin, Jean-François}, - month = sep, - year = {2021}, - keywords = {Machine learning, Classification, Pattern recognition, Supervised learning, Convolution neural network, Cortical sulci}, - pages = {118208}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DXI82JMS/S1053811921004857.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YTEV3PN7/Borne et al. - 2021 - Automatic recognition of specific local cortical f.pdf:application/pdf}, -} - -@article{goicovich_fiber_2021, - title = {Fiber {Clustering} {Acceleration} {With} a {Modified} {Kmeans}++ {Algorithm} {Using} {Data} {Parallelism}}, - volume = {15}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2021.727859}, - doi = {10.3389/fninf.2021.727859}, - abstract = {Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets. These methods enable exploratory bundle inspection using visualization and other methods that require identifying brain white matter structures in individuals or a population. Some applications, such as real-time visualization and inter-subject clustering, need fast and high-quality intra-subject clustering algorithms. This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm. The proposed GPGPU implementation exploits data parallelism using both multicore and GPU fine-grained parallelism present in commodity architectures, including current laptops and desktop computers. Our approach implements all FFClust steps in parallel, improving execution times in all of them. In addition, our parallel approach includes a parallel Kmeans++ algorithm implementation and defines a new variant of Kmeans++ to reduce the impact of choosing outliers as initial centroids. The results show that our approach provides clustering quality results very similar to FFClust, and it requires an execution time of 3.5 seconds for processing about a million fibers, achieving a speedup of 11.5 times compared to FFClust.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {Goicovich, Isaac and Olivares, Paulo and Román, Claudio and Vázquez, Andrea and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela and Hernández, Cecilia}, - month = sep, - year = {2021}, - note = {Publisher: Frontiers}, - keywords = {Fiber clustering, White matter bundle, Data parallelism, GPGPU - CUDA, Parallel Computing}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5NEWXUYM/Goicovich et al. - 2021 - Fiber Clustering Acceleration With a Modified Kmea.pdf:application/pdf}, -} - -@article{cachia_towards_2021, - title = {Towards {Deciphering} the {Fetal} {Foundation} of {Normal} {Cognition} and {Cognitive} {Symptoms} {From} {Sulcation} of the {Cortex}}, - volume = {15}, - issn = {1662-5129}, - url = {https://www.frontiersin.org/articles/10.3389/fnana.2021.712862}, - doi = {10.3389/fnana.2021.712862}, - abstract = {Growing evidence supports that prenatal processes play an important role for cognitive ability in normal and clinical conditions. In this context, several neuroimaging studies searched for features in postnatal life that could serve as a proxy for earlier developmental events. A very interesting candidate is the sulcal, or sulco-gyral, patterns, macroscopic features of the cortex anatomy related to the fold topology - e.g. continuous vs interrupted/broken fold, present vs absent fold - or their spatial organization. Indeed, as opposed to quantitative features of the cortical sheet (e.g. thickness, surface area or curvature) taking decades to reach the levels measured in adult, the qualitative sulcal patterns are mainly determined before birth and stable across the lifespan. The sulcal patterns therefore offer a window on the fetal constraints on specific brain areas on cognitive abilities and clinical symptoms that manifest later in life. After a global review of the cerebral cortex sulcation, its mechanisms, its ontogenesis along with methodological issues on how to measure the sulcal patterns, we present a selection of studies illustrating that analysis of the sulcal patterns can provide information on prenatal dispositions to cognition (with a focus on cognitive control and academic abilities) and cognitive symptoms (with a focus on schizophrenia and bipolar disorders). Finally, perspectives of sulcal studies are discussed.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroanatomy}, - author = {Cachia, Arnaud and Borst, Grégoire and Jardri, Renaud and Raznahan, Armin and Murray, Graham K. and Mangin, Jean-François and Plaze, Marion}, - month = sep, - year = {2021}, - note = {Publisher: Frontiers}, - keywords = {MRI, neurodevelopment, Psychiatry, Sulcation, gyrification, Psychology}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AW29GM28/Cachia et al. - 2021 - Towards Deciphering the Fetal Foundation of Normal.pdf:application/pdf}, -} - -@article{raffin_cross-sectional_2021, - title = {Cross-sectional and longitudinal interaction effects of physical activity and \textit{{APOE}}-\textit{ε4} on white matter integrity in older adults: {The} {MAPT} study}, - volume = {152}, - issn = {0378-5122}, - shorttitle = {Cross-sectional and longitudinal interaction effects of physical activity and \textit{{APOE}}-\textit{ε4} on white matter integrity in older adults}, - url = {https://www.sciencedirect.com/science/article/pii/S0378512221001158}, - doi = {10.1016/j.maturitas.2021.06.010}, - abstract = {ABSTRACT11ApoE-ɛ4: Apolipoprotein-E epsilon 4; ROI: Region of Interest; WM: White matter; CG: Cingulum (cingulate gyrus), CH: Cingulum-hippocampal projection, SLF: Superior longitudinal fasciculus, Fx: Fornix Stria terminalis, SS: Sagittal stratum; ALIC: Anterior Limb of the Internal Capsule, ACR: Anterior corona radiata; PCR: Posterior Corona radiata; SCR: Superior Corona Radiata; UF: Uncinate Fasciculus; CSp: Corticospinal tract; InfCP: Inferior Cerebellar Peduncle; MidCP: Middle Cerebellar Peduncle; SupCP: Superior Cerebellar Peduncle; PonCro: Pontine crossing tract; BDC: Body of corpus callosum; GCC: Genu of corpus callosum; SCC: Splenium of corpus callosum; CP: Cerebral Peduncle; PLIC: Posterior limb of internal capsule; RIC: Retrolenticular part of internal capsule L: left; R; Right; PA: Physical activity; MET: Metabolic equivalent task. -Background -Physical activity (PA) has been shown to modulate the detrimental effect of carrying the apolipoprotein-E epsilon 4 (APOE-ɛ4) allele on brain structure. However, the current literature mainly provides cross-sectional data, and longitudinal studies investigating the interaction between genotype and PA on white matter (WM) integrity are lacking. -Objectives -We investigated both the cross-sectional and the longitudinal interactive effects of APOE-ɛ4 and PA on WM integrity in older adults. -Methods -Fractional anisotropy, as well as axial, radial, and mean diffusivity, extracted from brain diffusion tensor imaging (DTI) were used to assess WM integrity in non-demented older adults. They were categorized according to their APOE-ɛ4 status (carriers vs. non-carriers), and their level of total (TPA), moderate to vigorous (MVPA) and light (LPA) PA were assessed using a questionnaire. Mixed model regressions were performed to test the interactive effects of APOE-ɛ4 status and PA on WM integrity at baseline and over a 3-year follow-up. -Results -190 subjects with a mean age 74.5 years (SD = 3.9) were examined. Despite a lack of cross-sectional associations, sensitivity analyses revealed that, in the carrier group only, higher levels of LPA, but not MVPA, were mainly associated with higher axial and mean diffusivity values over time. -Conclusions -This study partially confirms the previously reported interactive associations between PA, APOE-ɛ4 genotype and WM integrity, supporting the hypothesis that PA may protect against fiber loss in WM tracts containing crossing fibers. Future studies assessing sedentary behaviors in addition to PA could bring relevant contributions to the field. -Clinical trial registration number from ClinicalTrials.gov -NCT00672685}, - urldate = {2024-03-12}, - journal = {Maturitas}, - author = {Raffin, Jérémy and Rolland, Yves and He, Lingxiao and Perus, Lisa and Mangin, Jean-François and Gabelle, Audrey and Virecoulon Giudici, Kelly and Vellas, Bruno and de Souto Barreto, Philipe}, - month = oct, - year = {2021}, - keywords = {Genotype, Brain structure, Physical exercise}, - pages = {10--19}, -} - -@article{balzeau_what_2021, - title = {What {Are} the {Synergies} between {Paleoanthropology} and {Brain} {Imaging}?}, - volume = {13}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - issn = {2073-8994}, - url = {https://www.mdpi.com/2073-8994/13/10/1974}, - doi = {10.3390/sym13101974}, - abstract = {We are interested here in the central organ of our thoughts: the brain. Advances in neuroscience have made it possible to obtain increasing information on the anatomy of this organ, at ever-higher resolutions, with different imaging techniques, on ever-larger samples. At the same time, paleoanthropology has to deal with partial reflections on the shape of the brain, on fragmentary specimens and small samples in an attempt to approach the morphology of the brain of past human species. It undeniably emerges from the perspective we propose here that paleoanthropology has much to gain from interacting more with the field of neuroimaging. Improving our understanding of the morphology of the endocast necessarily involves studying the external surface of the brain and the link it maintains with the internal surface of the skull. The contribution of neuroimaging will allow us to better define the relationship between brain and endocast. Models of intra- and inter-species variability in brain morphology inferred from large neuroimaging databases will help make the most of the rare endocasts of extinct species. We also conclude that exchanges between these two disciplines will also be beneficial to our knowledge of the Homo sapiens brain. Documenting the anatomy among other human species and including the variation over time within our own species are approaches that offer us a new perspective through which to appreciate what really characterizes the brain of humanity today.}, - language = {en}, - number = {10}, - urldate = {2024-03-12}, - journal = {Symmetry}, - author = {Balzeau, Antoine and Mangin, Jean-François}, - month = oct, - year = {2021}, - note = {Number: 10 -Publisher: Multidisciplinary Digital Publishing Institute}, - keywords = {artificial intelligence, brain-endocast correspondence, interdisciplinarity, paleontology}, - pages = {1974}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/PY879J3E/Balzeau et Mangin - 2021 - What Are the Synergies between Paleoanthropology a.pdf:application/pdf}, -} - -@article{schilling_tractography_2021, - title = {Tractography dissection variability: {What} happens when 42 groups dissect 14 white matter bundles on the same dataset?}, - volume = {243}, - issn = {1053-8119}, - shorttitle = {Tractography dissection variability}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921007758}, - doi = {10.1016/j.neuroimage.2021.118502}, - abstract = {White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Schilling, Kurt G. and Rheault, François and Petit, Laurent and Hansen, Colin B. and Nath, Vishwesh and Yeh, Fang-Cheng and Girard, Gabriel and Barakovic, Muhamed and Rafael-Patino, Jonathan and Yu, Thomas and Fischi-Gomez, Elda and Pizzolato, Marco and Ocampo-Pineda, Mario and Schiavi, Simona and Canales-Rodríguez, Erick J. and Daducci, Alessandro and Granziera, Cristina and Innocenti, Giorgio and Thiran, Jean-Philippe and Mancini, Laura and Wastling, Stephen and Cocozza, Sirio and Petracca, Maria and Pontillo, Giuseppe and Mancini, Matteo and Vos, Sjoerd B. and Vakharia, Vejay N. and Duncan, John S. and Melero, Helena and Manzanedo, Lidia and Sanz-Morales, Emilio and Peña-Melián, Ángel and Calamante, Fernando and Attyé, Arnaud and Cabeen, Ryan P. and Korobova, Laura and Toga, Arthur W. and Vijayakumari, Anupa Ambili and Parker, Drew and Verma, Ragini and Radwan, Ahmed and Sunaert, Stefan and Emsell, Louise and De Luca, Alberto and Leemans, Alexander and Bajada, Claude J. and Haroon, Hamied and Azadbakht, Hojjatollah and Chamberland, Maxime and Genc, Sila and Tax, Chantal M. W. and Yeh, Ping-Hong and Srikanchana, Rujirutana and Mcknight, Colin D. and Yang, Joseph Yuan-Mou and Chen, Jian and Kelly, Claire E. and Yeh, Chun-Hung and Cochereau, Jerome and Maller, Jerome J. and Welton, Thomas and Almairac, Fabien and Seunarine, Kiran K and Clark, Chris A. and Zhang, Fan and Makris, Nikos and Golby, Alexandra and Rathi, Yogesh and O'Donnell, Lauren J. and Xia, Yihao and Aydogan, Dogu Baran and Shi, Yonggang and Fernandes, Francisco Guerreiro and Raemaekers, Mathijs and Warrington, Shaun and Michielse, Stijn and Ramírez-Manzanares, Alonso and Concha, Luis and Aranda, Ramón and Meraz, Mariano Rivera and Lerma-Usabiaga, Garikoitz and Roitman, Lucas and Fekonja, Lucius S. and Calarco, Navona and Joseph, Michael and Nakua, Hajer and Voineskos, Aristotle N. and Karan, Philippe and Grenier, Gabrielle and Legarreta, Jon Haitz and Adluru, Nagesh and Nair, Veena A. and Prabhakaran, Vivek and Alexander, Andrew L. and Kamagata, Koji and Saito, Yuya and Uchida, Wataru and Andica, Christina and Abe, Masahiro and Bayrak, Roza G. and Wheeler-Kingshott, Claudia A. M. Gandini and D'Angelo, Egidio and Palesi, Fulvia and Savini, Giovanni and Rolandi, Nicolò and Guevara, Pamela and Houenou, Josselin and López-López, Narciso and Mangin, Jean-François and Poupon, Cyril and Román, Claudio and Vázquez, Andrea and Maffei, Chiara and Arantes, Mavilde and Andrade, José Paulo and Silva, Susana Maria and Calhoun, Vince D. and Caverzasi, Eduardo and Sacco, Simone and Lauricella, Michael and Pestilli, Franco and Bullock, Daniel and Zhan, Yang and Brignoni-Perez, Edith and Lebel, Catherine and Reynolds, Jess E and Nestrasil, Igor and Labounek, René and Lenglet, Christophe and Paulson, Amy and Aulicka, Stefania and Heilbronner, Sarah R. and Heuer, Katja and Chandio, Bramsh Qamar and Guaje, Javier and Tang, Wei and Garyfallidis, Eleftherios and Raja, Rajikha and Anderson, Adam W. and Landman, Bennett A. and Descoteaux, Maxime}, - month = nov, - year = {2021}, - keywords = {Tractography, White matter, Bundle segmentation, Dissection, Fiber pathways}, - pages = {118502}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BW5AD93V/Schilling et al. - 2021 - Tractography dissection variability What happens .pdf:application/pdf}, -} - -@article{lu_biological_2021, - title = {Biological and {Neuroimaging} {Markers} as {Predictors} of 5-{Year} {Incident} {Frailty} in {Older} {Adults}: {A} {Secondary} {Analysis} of the {MAPT} {Study}}, - volume = {76}, - issn = {1079-5006}, - shorttitle = {Biological and {Neuroimaging} {Markers} as {Predictors} of 5-{Year} {Incident} {Frailty} in {Older} {Adults}}, - url = {https://doi.org/10.1093/gerona/glaa296}, - doi = {10.1093/gerona/glaa296}, - abstract = {This study aims to investigate the predictive value of biological and neuroimaging markers to determine incident frailty among older people for a period of 5 years.We included 1394 adults aged 70 years and older from the Multidomain Alzheimer Preventive Trial, who were not frail at baseline (according to Fried’s criteria) and who had at least 1 post-baseline measurement of frailty. Participants who progressed to frailty during the 5-year follow-up were categorized as “incident frailty” and those who remained non-frail were categorized as “without frailty.” The differences of baseline biochemical factors (25-hydroxyvitamin D, homocysteine, omega-3 index, C-reactive protein), other biological markers (Apolipoprotein E genotypes, amyloid-β deposits), and neuroimaging data (gray matter volume, hippocampal volume, white matter hyperintensities) were compared between groups. Cox proportional hazard model was used to evaluate the associations between biomarkers and incident frailty.A total of 195 participants (14.0\%) became frail over 5 years. Although 25-hydroxyvitamin D deficiency, homocysteine levels, low-grade inflammation (persistently increased C-reactive protein 3–10 mg/L), gray matter, and hippocampal volume were significantly associated with incident frailty in unadjusted models, these associations disappeared after adjustment for age, sex, and other confounders. Omega-3 index was the sole marker that presented a trend of association with incident frailty (hazard ratio: 0.92; 95\% confidence interval: 0.83–1.01; p = .082).This study failed to identify biomarkers able to predict frailty incidence in community-dwelling older adults for a period of 5 years. Further longitudinal research with multiple measurements of biomarkers and frailty is needed to evaluate the long-term relationships between changes in biomarkers levels and frailty evolution.}, - number = {11}, - urldate = {2024-03-12}, - journal = {The Journals of Gerontology: Series A}, - author = {Lu, Wan-Hsuan and de Souto Barreto, Philipe and Rolland, Yves and Bouyahia, Ali and Fischer, Clara and Mangin, Jean-François and Giudici, Kelly V and Vellas, Bruno and {MAPT/DSA Group}}, - month = nov, - year = {2021}, - pages = {e361--e369}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZJTABB5D/Lu et al. - 2021 - Biological and Neuroimaging Markers as Predictors .pdf:application/pdf}, -} - -@inproceedings{vergara_group-wise_2021, - title = {Group-{Wise} {Cortical} {Surface} {Parcellation} {Based} on {Inter}-{Subject} {Fiber} {Clustering}}, - url = {https://ieeexplore.ieee.org/abstract/document/9631099}, - doi = {10.1109/EMBC46164.2021.9631099}, - abstract = {We present an automatic algorithm for the group-wise parcellation of the cortical surface. The method is based on the structural connectivity obtained from representative brain fiber clusters, calculated via an inter-subject clustering scheme. Preliminary regions were defined from cluster-cortical mesh intersection points. The final parcellation was obtained using parcel probability maps to model and integrate the connectivity information of all subjects, and graphs to represent the overlap between parcels. Two inter-subject clustering schemes were tested, generating a total of 171 and 109 parcels, respectively. The resulting parcels were quantitatively compared with three state-of-the-art atlases. The best parcellation returned 69 parcels with a Dice similarity coefficient greater than 0.5. To the best of our knowledge, this is the first diffusion-based cortex parcellation method based on whole-brain inter-subject fiber clustering.}, - urldate = {2024-03-12}, - booktitle = {2021 43rd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Vergara, Christopher and Silva, Felipe and Huerta, Isaías and López-López, Narciso and Vázquez, Andrea and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = nov, - year = {2021}, - note = {ISSN: 2694-0604}, - keywords = {Brain modeling, Clustering algorithms, Biology, Optical fiber testing}, - pages = {2655--2659}, -} - -@inproceedings{mendoza_enhanced_2021, - title = {Enhanced {Automatic} {Segmentation} for {Superficial} {White} {Matter} {Fiber} {Bundles} for {Probabilistic} {Tractography} {Datasets}}, - url = {https://ieeexplore.ieee.org/abstract/document/9630529}, - doi = {10.1109/EMBC46164.2021.9630529}, - abstract = {This paper presents an enhanced algorithm for automatic segmentation of superficial white matter (SWM) bundles from probabilistic dMRI tractography datasets, based on a multi-subject bundle atlas. Previous segmentation methods use the maximum Euclidean distance between corresponding points of the subject fibers and the atlas centroids. However, this scheme might include noisy fibers. Here, we propose a three step approach to discard noisy fibers improving the identification of fibers. The first step applies a fiber clustering and the segmentation is performed between the centroids of the clusters and the atlas centroids. This step removes outliers and enables a better identification of fibers with similar shapes. The second step applies a fiber filter based on two different fiber similarities. One is the Symmetrized Segment-Path Distance (SSPD) over 2D ISOMAP and the other is an adapted version of SSPD for 3D space. The last step eliminates noisy fibers by removing those that connect regions that are far from the main atlas bundle connections. We perform an experimental evaluation using ten subjects of the Human Connectome (HCP) database. The evaluation only considers the bundles connecting precentral and postcentral gyri, with a total of seven bundles per hemisphere. For comparison, the bundles of the ten subjects were manually segmented. Bundles segmented with our method were evaluated in terms of similarity to manually segmented bundles and the final number of fibers. The results show that our approach obtains bundles with a higher similarity score than the state-of-the-art method and maintains a similar number of fibers.Clinical relevance—Many brain pathologies or disorders can occur in specific regions of the SWM automatic segmentation of reliable SWM bundles would help applications to clinical research.}, - urldate = {2024-03-12}, - booktitle = {2021 43rd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Mendoza, C. and Román, C. and Vázquez, A. and Poupon, C. and Mangin, J.-F. and Hernández, C. and Guevara, P.}, - month = nov, - year = {2021}, - note = {ISSN: 2694-0604}, - keywords = {Sociology, Probabilistic logic, Reliability, Shape, Three-dimensional displays, Trajectory, Noise measurement}, - pages = {3654--3658}, -} - -@inproceedings{leprince_morphological_2020, - title = {The morphological evolution of the primate brain revealed by alignment of the cortical sulci}, - url = {https://cea.hal.science/cea-02868500/document}, - urldate = {2024-03-12}, - author = {Leprince, Yann and Stochino, Alexia and Foubet, Ophélie and Hopkins, William D. and Mangin, Jean-François}, - year = {2020}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/C9GB2JIX/Leprince et al. - 2020 - The morphological evolution of the primate brain r.pdf:application/pdf}, -} - -@article{laidi_cerebellar_2019, - title = {Cerebellar parcellation in schizophrenia and bipolar disorder}, - volume = {140}, - copyright = {© 2019 John Wiley \& Sons A/S. Published by John Wiley \& Sons Ltd}, - issn = {1600-0447}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acps.13087}, - doi = {10.1111/acps.13087}, - abstract = {Objective The cerebellum is involved in cognitive processing and emotion control. Cerebellar alterations could explain symptoms of schizophrenia spectrum disorder (SZ) and bipolar disorder (BD). In addition, literature suggests that lithium might influence cerebellar anatomy. Our aim was to study cerebellar anatomy in SZ and BD, and investigate the effect of lithium. Methods Participants from 7 centers worldwide underwent a 3T MRI. We included 182 patients with SZ, 144 patients with BD, and 322 controls. We automatically segmented the cerebellum using the CERES pipeline. All outputs were visually inspected. Results Patients with SZ showed a smaller global cerebellar gray matter volume compared to controls, with most of the changes located to the cognitive part of the cerebellum (Crus II and lobule VIIb). This decrease was present in the subgroup of patients with recent-onset SZ. We did not find any alterations in the cerebellum in patients with BD. However, patients medicated with lithium had a larger size of the anterior cerebellum, compared to patients not treated with lithium. Conclusion Our multicenter study supports a distinct pattern of cerebellar alterations in SZ and BD.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Laidi, C. and Hajek, T. and Spaniel, F. and Kolenic, M. and d'Albis, M.-A. and Sarrazin, S. and Mangin, J.-F. and Duchesnay, E. and Brambilla, P. and Wessa, M. and Linke, J. and Polosan, M. and Favre, P. and Versace, A. L. and Phillips, M. L. and Manjon, J. V. and Romero, J. E. and Hozer, F. and Leboyer, M. and Coupe, P. and Houenou, J.}, - year = {2019}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acps.13087}, - keywords = {cerebellum, lithium, parcellation, segmentation}, - pages = {468--476}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8ZYKANPT/Laidi et al. - 2019 - Cerebellar parcellation in schizophrenia and bipol.pdf:application/pdf}, -} - -@article{planche_clinical_2021, - title = {Clinical relevance of brain atrophy subtypes categorization in memory clinics}, - volume = {17}, - copyright = {© 2021 the Alzheimer's Association}, - issn = {1552-5279}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/alz.12231}, - doi = {10.1002/alz.12231}, - abstract = {Introduction The clinical relevance of brain atrophy subtypes categorization in non-demented persons without a priori knowledge regarding their amyloid status or clinical presentation is unknown. Methods A total of 2083 outpatients with either subjective cognitive complaint or mild cognitive impairment at study entry were followed during 4 years (MEMENTO cohort). Atrophy subtypes were defined using baseline magnetic resonance imaging (MRI) and previously described algorithms. Results Typical/diffuse atrophy was associated with faster cognitive decline and the highest risk of developing dementia and Alzheimer's disease (AD) over time, both in the whole analytic sample and in amyloid-positive participants. Hippocampal-sparing and limbic-predominant atrophy were also associated with incident dementia, with faster cognitive decline in the limbic predominant atrophy group. Lewy body dementia was more frequent in the hippocampal-sparing and minimal/no atrophy groups. Discussion Atrophy subtypes categorization predicted different subsequent patterns of cognitive decline and rates of conversion to distinct etiologies of dementia in persons attending memory clinics.}, - language = {en}, - number = {4}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia}, - author = {Planche, Vincent and Bouteloup, Vincent and Mangin, Jean-François and Dubois, Bruno and Delrieu, Julien and Pasquier, Florence and Blanc, Frédéric and Paquet, Claire and Hanon, Olivier and Gabelle, Audrey and Ceccaldi, Matthieu and Annweiler, Cédric and Krolak-Salmon, Pierre and Habert, Marie-Odile and Fischer, Clara and Chupin, Marie and Béjot, Yannick and Godefroy, Olivier and Wallon, David and Sauvée, Mathilde and Bourdel-Marchasson, Isabelle and Jalenques, Isabelle and Tison, François and Chêne, Geneviève and Dufouil, Carole and Group, {and} the MEMENTO Study}, - year = {2021}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/alz.12231}, - keywords = {MRI, Alzheimer disease, dementia, hippocampus, brain atrophy subtypes}, - pages = {641--652}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZYK3VD5L/alz.html:text/html}, -} - -@article{dubois_cognitive_2018, - title = {Cognitive and neuroimaging features and brain β-amyloidosis in individuals at risk of {Alzheimer}'s disease ({INSIGHT}-{preAD}): a longitudinal observational study}, - volume = {17}, - issn = {1474-4422, 1474-4465}, - shorttitle = {Cognitive and neuroimaging features and brain β-amyloidosis in individuals at risk of {Alzheimer}'s disease ({INSIGHT}-{preAD})}, - url = {https://www.thelancet.com/journals/laneur/article/PIIS1474-4422(18)30029-2/abstract}, - doi = {10.1016/S1474-4422(18)30029-2}, - language = {English}, - number = {4}, - urldate = {2024-03-12}, - journal = {The Lancet Neurology}, - author = {Dubois, Bruno and Epelbaum, Stephane and Nyasse, Francis and Bakardjian, Hovagim and Gagliardi, Geoffroy and Uspenskaya, Olga and Houot, Marion and Lista, Simone and Cacciamani, Federica and Potier, Marie-Claude and Bertrand, Anne and Lamari, Foudil and Benali, Habib and Mangin, Jean-François and Colliot, Olivier and Genthon, Remy and Habert, Marie-Odile and Hampel, Harald and Audrain, Christelle and Auffret, Alexandra and Baldacci, Filippo and Benakki, Ismahane and Bertin, Hugo and Boukadida, Laurie and Cavedo, Enrica and Chiesa, Patrizia and Dauphinot, Luce and Santos, Antonio Dos and Dubois, Marion and Durrleman, Stanley and Fontaine, Gaëlle and Genin, Alexis and Glasman, Pauline and Jungalee, Navichka and Kas, Aurélie and Kilani, Maya and Corte, Valentina La and Lehericy, Stephane and Letondor, Claire and Levy, Marcel and Lowrey, Mark and Ly, Juliette and Makiese, Ornella and Metzinger, Christiane and Michon, Agnès and Mochel, Fanny and Poisson, Catherine and Ratovohery, Stephie and Revillon, Marie and Rojkova, Katrine and Roy, Perrine and Santos-Andrade, Katia and Schindler, Rachel and Seux, Laure and Simon, Valérie and Sole, Marine and Tandetnik, Caroline and Teichmann, Marc and Shotten, Michel Thiebaut de and Younsi, Nadjia}, - month = apr, - year = {2018}, - pmid = {29500152}, - note = {Publisher: Elsevier}, - keywords = {Magnetic resonance imaging (MRI), Prematurity, Cortex, Development, Sulcation}, - pages = {335--346}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WWI8Q8CP/Dubois et al. - 2018 - Cognitive and neuroimaging features and brain β-am.pdf:application/pdf}, -} - -@article{frison_diabetes_2021, - title = {Diabetes {Mellitus} and {Cognition}}, - volume = {97}, - url = {https://www.neurology.org/doi/full/10.1212/WNL.0000000000012440}, - doi = {10.1212/WNL.0000000000012440}, - abstract = {Objective -To assess the role of biomarkers of Alzheimer disease (AD), neurodegeneration, and small vessel disease (SVD) as mediators in the association between diabetes mellitus and cognition. -Methods -The study sample was derived from MEMENTO, a cohort of French adults recruited in memory clinics and screened for either isolated subjective cognitive complaints or mild cognitive impairment. Diabetes was defined based on blood glucose assessment, use of antidiabetic agent, or self-report. We used structural equation modeling to assess whether latent variables of AD pathology (PET mean amyloid uptake, Aβ42/Aβ40 ratio, and CSF phosphorylated tau), SVD (white matter hyperintensities volume and visual grading), and neurodegeneration (mean cortical thickness, brain parenchymal fraction, hippocampal volume, and mean fluorodeoxyglucose uptake) mediate the association between diabetes and a latent variable of cognition (5 neuropsychological tests), adjusting for potential confounders. -Results -There were 254 (11.1\%) participants with diabetes among 2,288 participants (median age 71.6 years; 61.8\% women). The association between diabetes and lower cognition was significantly mediated by higher neurodegeneration (standardized indirect effect: −0.061, 95\% confidence interval: −0.089, −0.032), but not mediated by SVD and AD markers. Results were similar when considering latent variables of memory or executive functioning. -Conclusion -In a large clinical cohort in the elderly, diabetes is associated with lower cognition through neurodegeneration, independently of SVD and AD biomarkers.}, - number = {8}, - urldate = {2024-03-12}, - journal = {Neurology}, - author = {Frison, Eric and Proust-Lima, Cecile and Mangin, Jean-Francois and Habert, Marie-Odile and Bombois, Stephanie and Ousset, Pierre-Jean and Pasquier, Florence and Hanon, Olivier and Paquet, Claire and Gabelle, Audrey and Ceccaldi, Mathieu and Annweiler, Cédric and Krolak-Salmon, Pierre and Béjot, Yannick and Belin, Catherine and Wallon, David and Sauvee, Mathilde and Beaufils, Emilie and Bourdel-Marchasson, Isabelle and Jalenques, Isabelle and Chupin, Marie and Chêne, Geneviève and Dufouil, Carole and {on behalf of the MEMENTO Cohort Study Group}}, - month = aug, - year = {2021}, - note = {Publisher: Wolters Kluwer}, - pages = {e836--e848}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8N33R9I6/Frison et al. - 2021 - Diabetes Mellitus and Cognition.pdf:application/pdf}, -} - -@article{karkar_genome-wide_2021, - title = {Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 {UK} {Biobank} subjects}, - volume = {29}, - copyright = {2021 The Author(s)}, - issn = {1476-5438}, - url = {https://www.nature.com/articles/s41431-021-00827-8}, - doi = {10.1038/s41431-021-00827-8}, - abstract = {Neuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome-wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a single block, while the last approach considers each haplotype independently. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {European Journal of Human Genetics}, - author = {Karkar, Slim and Dandine-Roulland, Claire and Mangin, Jean-François and Le Guen, Yann and Philippe, Cathy and Deleuze, Jean-François and Pierre-Jean, Morgane and Le Floch, Edith and Frouin, Vincent}, - month = sep, - year = {2021}, - note = {Publisher: Nature Publishing Group}, - keywords = {Magnetic resonance imaging, Predictive markers, Genetics of the nervous system, Genome-wide association studies, Haplotypes}, - pages = {1424--1437}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RD2URD5E/Karkar et al. - 2021 - Genome-wide haplotype association study in imaging.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/2RCWDAQX/Karkar et al. - 2021 - Genome-wide haplotype association study in imaging.pdf:application/pdf}, -} - -@article{sarrazin_higher_2019, - title = {Higher in vivo {Cortical} {Intracellular} {Volume} {Fraction} {Associated} with {Lithium} {Therapy} in {Bipolar} {Disorder}: {A} {Multicenter} {NODDI} {Study}}, - volume = {88}, - issn = {0033-3190}, - shorttitle = {Higher in vivo {Cortical} {Intracellular} {Volume} {Fraction} {Associated} with {Lithium} {Therapy} in {Bipolar} {Disorder}}, - url = {https://doi.org/10.1159/000498854}, - doi = {10.1159/000498854}, - abstract = {Background: MRI studies in patients with bipolar disorder have suggested that lithium is associated with grey matter increases that may underlie its therapeutic effects. However, the relationship between grey matter volume and cellular microstructural changes is not straightforward, as modifications of different cellular compartments of grey matter may be involved. Objectives: Our aim was to test the hypothesis that dendritic density is higher in patients undergoing lithium therapy than in patients without lithium, using advanced modelling of water diffusion investigated with MRI. Method: We included 41 patients and 40 controls matched for age and gender from two sites. All subjects underwent 3T MRI with 3 shells of diffusion. We used neurite orientation dispersion and density imaging to compare the grey matter neurite density between patients undergoing lithium therapy or not and control subjects. Results: We found a significant group effect in the left prefrontal region (p = 0.001, Bonferroni corrected): patients without lithium had a lower frontal neurite density than controls (p = 0.009), while those on lithium had a higher mean neurite density than those without (p \< 0.001). Patients on lithium were not different from controls (p = 0.08). Conclusions: This is the first study to report in vivo evidence of preserved neurite density of the prefrontal cortex in humans associated with lithium intake. Changes of intracellular volume fraction are thought to reflect changes of grey matter microstructural organization. This reinforces the hypothesis of lithium having a positive effect on the neuronal compartment in humans.}, - number = {3}, - urldate = {2024-03-12}, - journal = {Psychotherapy and Psychosomatics}, - author = {Sarrazin, Samuel and Poupon, Cyril and Teillac, Achille and Mangin, Jean-François and Polosan, Mircea and Favre, Pauline and Laidi, Charles and D'Albis, Marc-Antoine and Leboyer, Marion and Lledo, Pierre-Marie and Henry, Chantal and Houenou, Josselin}, - month = apr, - year = {2019}, - pages = {171--176}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5BWMSZNZ/Higher-in-vivo-Cortical-Intracellular-Volume.html:text/html}, -} - -@article{maltais_prospective_2020-1, - title = {Prospective associations between physical activity levels and white matter integrity in older adults: results from the {MAPT} study}, - volume = {137}, - issn = {0378-5122}, - shorttitle = {Prospective associations between physical activity levels and white matter integrity in older adults}, - url = {https://www.sciencedirect.com/science/article/pii/S0378512220302425}, - doi = {10.1016/j.maturitas.2020.04.012}, - abstract = {Background -Higher levels of physical activity (PA) are known to be associated with better white matter integrity measured by diffusion tensor imaging (DTI) in older adults in cross-sectional studies. However, no studies have investigated the association between PA levels and the evolution of DTI parameters (fractional anisotropy and mean diffusivity). -Objectives -To examine the cross-sectional associations between PA levels and DTI parameters, then to investigate the association between baseline PA levels and the evolution of DTI parameters in older adults. -Methods -Data on magnetic resonance imaging with DTI method from the Multidomain Alzheimer’s Preventive Trial (MAPT) study were used; 228 participants had data on DTI measured at three time-points over five years. Fractional anisotropy and mean diffusivity were acquired for six different brain regions. -Results -No significant associations were found in the cross-sectional analyses. Only one association was found: compared with active individuals, a faster worsening in the mean diffusivity of the uncinate fasciculus region was found in inactive individuals (-5.0 × 10-6 (-9.5 × 10-5, 4.9 × 10-6)). -Conclusions -In this study, we found that the condition of the uncinate fasciculus region may be susceptible to changes in PA levels in older adults. Longitudinal studies that assess fitness and PA using objective measurements (e.g. cardiorespiratory fitness and accelerometry) could shed some new light on this topic.}, - urldate = {2024-03-12}, - journal = {Maturitas}, - author = {Maltais, Mathieu and Rolland, Yves and Boisvert-Vigneault, Katherine and Perus, Lisa and Mangin, Jean-François and Grigis, Antoine and Chupin, Marie and Bouyahia, Ali and Gabelle, Audrey and Delrieux, Julien and Vellas, Bruno and de Souto Barreto, Philipe}, - month = jul, - year = {2020}, - keywords = {magnetic resonance imaging, brain imaging, physical activity}, - pages = {24--29}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3SZNLLDX/S0378512220302425.html:text/html}, -} - -@article{planche_validity_2023, - title = {Validity and {Performance} of {Blood} {Biomarkers} for {Alzheimer} {Disease} to {Predict} {Dementia} {Risk} in a {Large} {Clinic}-{Based} {Cohort}}, - volume = {100}, - url = {https://www.neurology.org/doi/full/10.1212/WNL.0000000000201479}, - doi = {10.1212/WNL.0000000000201479}, - abstract = {Background and Objective -Blood biomarkers for Alzheimer disease (AD) have consistently proven to be associated with CSF or PET biomarkers and effectively discriminate AD from other neurodegenerative diseases. Our aim was to test their utility in clinical practice, from a multicentric unselected prospective cohort where patients presented with a large spectrum of cognitive deficits or complaints. -Methods -The MEMENTO cohort enrolled 2,323 outpatients with subjective cognitive complaint (SCC) or mild cognitive impairment (MCI) consulting in 26 French memory clinics. Participants had neuropsychological assessments, MRI, and blood sampling at baseline. CSF sampling and amyloid PET were optional. Baseline blood Aβ42/40 ratio, total tau, p181-tau, and neurofilament light chain (NfL) were measured using a Simoa HD-X analyzer. An expert committee validated incident dementia cases during a 5-year follow-up period. -Results -Overall, 2,277 individuals had at least 1 baseline blood biomarker available (n = 357 for CSF subsample, n = 649 for PET subsample), among whom 257 were diagnosed with clinical AD/mixed dementia during follow-up. All blood biomarkers but total tau were mildly correlated with their equivalence in the CSF (r = 0.33 to 0.46, p {\textless} 0.0001) and were associated with amyloid-PET status (p {\textless} 0.0001). Blood p181-tau was the best blood biomarker to identify amyloid-PET positivity (area under the curve = 0.74 [95\% CI = 0.69; 0.79]). Higher blood and CSF p181-tau and NfL concentrations were associated with accelerated time to AD dementia onset with similar incidence rates, whereas blood Aβ42/40 was less efficient than CSF Aβ42/40. Blood p181-tau alone was the best blood predictor of 5-year AD/mixed dementia risk (c-index = 0.73 [95\% CI = 0.69; 0.77]); its accuracy was higher in patients with clinical dementia rating (CDR) = 0 (c-index = 0.83 [95\% CI = 0.69; 0.97]) than in patients with CDR = 0.5 (c-index = 0.70 [95\% CI = 0.66; 0.74]). A “clinical” reference model (combining demographics and neuropsychological assessment) predicted AD/mixed dementia risk with a c-index = 0.88 [95\% CI = 0.86–0.91] and performance increased to 0.90 [95\% CI = 0.88; 0.92] when adding blood p181-tau + Aβ42/40. A “research” reference model (clinical model + apolipoprotein E genotype and AD signature on MRI) had a c-index = 0.91 [95\% CI = 0.89–0.93] increasing to 0.92 [95\% CI = 0.90; 0.93] when adding blood p181-tau + Aβ42/40. Chronic kidney disease and vascular comorbidities did not affect predictive performances. -Discussion -In a clinic-based cohort of patients with SCC or MCI, blood biomarkers may be good hallmarks of underlying pathology but add little to 5-year dementia risk prediction models including traditional predictors.}, - number = {5}, - urldate = {2024-03-12}, - journal = {Neurology}, - author = {Planche, Vincent and Bouteloup, Vincent and Pellegrin, Isabelle and Mangin, Jean-Francois and Dubois, Bruno and Ousset, Pierre-Jean and Pasquier, Florence and Blanc, Frederic and Paquet, Claire and Hanon, Olivier and Bennys, Karim and Ceccaldi, Mathieu and Annweiler, Cédric and Krolak-Salmon, Pierre and Godefroy, Olivier and Wallon, David and Sauvee, Mathilde and Boutoleau-Bretonnière, Claire and Bourdel-Marchasson, Isabelle and Jalenques, Isabelle and Chene, Genevieve and Dufouil, Carole and {and the MEMENTO Study Group}}, - month = jan, - year = {2023}, - note = {Publisher: Wolters Kluwer}, - pages = {e473--e484}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JTUYEX8L/Planche et al. - 2023 - Validity and Performance of Blood Biomarkers for A.pdf:application/pdf}, -} - -@article{hanon_plasma_2022, - title = {Plasma amyloid beta predicts conversion to dementia in subjects with mild cognitive impairment: {The} {BALTAZAR} study}, - volume = {18}, - copyright = {© 2022 the Alzheimer's Association}, - issn = {1552-5279}, - shorttitle = {Plasma amyloid beta predicts conversion to dementia in subjects with mild cognitive impairment}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/alz.12613}, - doi = {10.1002/alz.12613}, - abstract = {Introduction Blood-based biomarkers are the next challenge for Alzheimer's disease (AD) diagnosis and prognosis. Methods Mild cognitive impairment (MCI) participants (N = 485) of the BALTAZAR study, a large-scale longitudinal multicenter cohort, were followed-up for 3 years. A total of 165 of them converted to dementia (95\% AD). Associations of conversion and plasma amyloid beta (Aβ)1-42, Aβ1-40, Aβ1-42/Aβ1-40 ratio were analyzed with logistic and Cox models. Results Converters to dementia had lower level of plasma Aβ1-42 (37.1 pg/mL [12.5] vs. 39.2 [11.1] , P value = .03) and lower Aβ1-42/Aβ1-40 ratio than non-converters (0.148 [0.125] vs. 0.154 [0.076], P value = .02). MCI participants in the highest quartile of Aβ1-42/Aβ1-40 ratio ({\textgreater}0.169) had a significant lower risk of conversion (hazard ratio adjusted for age, sex, education, apolipoprotein E ε4, hippocampus atrophy = 0.52 (95\% confidence interval [0.31–0.86], P value = .01). Discussion In this large cohort of MCI subjects we identified a threshold for plasma Aβ1-42/Aβ1-40 ratio that may detect patients with a low risk of conversion to dementia within 3 years.}, - language = {en}, - number = {12}, - urldate = {2024-03-12}, - journal = {Alzheimer's \& Dementia}, - author = {Hanon, Olivier and Vidal, Jean-Sébastien and Lehmann, Sylvain and Bombois, Stéphanie and Allinquant, Bernadette and Baret-Rose, Christiane and Tréluyer, Jean-Marc and Abdoul, Hendy and Gelé, Patrick and Delmaire, Christine and Blanc, Fredéric and Mangin, Jean-François and Buée, Luc and Touchon, Jacques and Hugon, Jacques and Vellas, Bruno and Galbrun, Evelyne and Benetos, Athanase and Berrut, Gilles and Paillaud, Elena and Wallon, David and Castelnovo, Giovanni and Volpe-Gillot, Lisette and Paccalin, Marc and Robert, Philippe and Godefroy, Olivier and Camus, Vincent and Belmin, Joël and Vandel, Pierre and Novella, Jean-Luc and Duron, Emmanuelle and Rigaud, Anne-Sophie and Schraen-Maschke, Susanna and Gabelle, Audrey and Group, the BALTAZAR study}, - year = {2022}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/alz.12613}, - keywords = {Alzheimer's disease, prognosis, mild cognitive impairment, amyloid beta protein, cerebrospinal fluid, major neurocognitive disorder, minor neurocognitive disorder, plasma biomarkers}, - pages = {2537--2550}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/F4B79VSX/alz.html:text/html;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FSIGYURA/Hanon et al. - 2022 - Plasma amyloid beta predicts conversion to dementi.pdf:application/pdf}, -} - -@article{cachia_how_2018, - title = {How interindividual differences in brain anatomy shape reading accuracy}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-017-1516-x}, - doi = {10.1007/s00429-017-1516-x}, - abstract = {The capacity to read develops throughout intensive academic learning and training. Several studies have investigated the impact of reading on the brain, and particularly how the anatomy of the brain changes with reading acquisition. In the present study, we investigated the converse issue, namely whether and how reading acquisition is constrained by the anatomy of the brain. Using multimodal MRI, we found that (a) the pattern (continuous or interrupted sulcus) of the posterior part of the left lateral occipito-temporal sulcus (OTS) hosting the visual word form area (VWFA) predicts reading skills in adults; that (b) this effect is modulated by the age of reading acquisition; and that (c) the length of the OTS sulcal interruption is associated with reading skills. Because the sulcal pattern is determined in utero, our findings suggest that individual difference in reading skills can be traced back to early stages of brain development in addition to the well-established socioeconomic and educational factors.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Cachia, Arnaud and Roell, Margot and Mangin, Jean-François and Sun, Zhong Yi and Jobert, Antoinette and Braga, Lucia and Houde, Olivier and Dehaene, Stanislas and Borst, Grégoire}, - month = mar, - year = {2018}, - keywords = {MRI, Neurodevelopment, VWFA, SES, Reading}, - pages = {701--712}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TRSDQQ4S/Cachia et al. - 2018 - How interindividual differences in brain anatomy s.pdf:application/pdf}, -} - -@article{lemaitre_genetic_2023, - title = {Genetic variations within human gained enhancer elements affect human brain sulcal morphology}, - volume = {265}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922008941}, - doi = {10.1016/j.neuroimage.2022.119773}, - abstract = {The expansion of the cerebral cortex is one of the most distinctive changes in the evolution of the human brain. Cortical expansion and related increases in cortical folding may have contributed to emergence of our capacities for high-order cognitive abilities. Molecular analysis of humans, archaic hominins, and non-human primates has allowed identification of chromosomal regions showing evolutionary changes at different points of our phylogenetic history. In this study, we assessed the contributions of genomic annotations spanning 30 million years to human sulcal morphology measured via MRI in more than 18,000 participants from the UK Biobank. We found that variation within brain-expressed human gained enhancers, regulatory genetic elements that emerged since our last common ancestor with Old World monkeys, explained more trait heritability than expected for the left and right calloso-marginal posterior fissures and the right central sulcus. Intriguingly, these are sulci that have been previously linked to the evolution of locomotion in primates and later on bipedalism in our hominin ancestors.}, - language = {en}, - urldate = {2023-02-06}, - journal = {NeuroImage}, - author = {Lemaitre, Herve and Le Guen, Yann and Tilot, Amanda K. and Stein, Jason L. and Philippe, Cathy and Mangin, Jean-François and Fisher, Simon E. and Frouin, Vincent}, - month = jan, - year = {2023}, - keywords = {Neuroimaging, Evolution, Genome-wide association, Human gained enhancers, Sulcal morphology}, - pages = {119773}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Q5CPE88S/Lemaitre et al. - 2023 - Genetic variations within human gained enhancer el.pdf:application/pdf}, -} - -@article{le_guen_enhancer_2020, - title = {Enhancer {Locus} in ch14q23.1 {Modulates} {Brain} {Asymmetric} {Temporal} {Regions} {Involved} in {Language} {Processing}}, - volume = {30}, - issn = {1047-3211}, - url = {https://doi.org/10.1093/cercor/bhaa112}, - doi = {10.1093/cercor/bhaa112}, - abstract = {Identifying the genes that contribute to the variability in brain regions involved in language processing may shed light on the evolution of brain structures essential to the emergence of language in Homo sapiens. The superior temporal asymmetrical pit (STAP), which is not observed in chimpanzees, represents an ideal phenotype to investigate the genetic variations that support human communication. The left STAP depth was significantly associated with a predicted enhancer annotation located in the 14q23.1 locus, between DACT1 and KIAA0586, in the UK Biobank British discovery sample (N = 16 515). This association was replicated in the IMAGEN cohort (N = 1726) and the UK Biobank non-British validation sample (N = 2161). This genomic region was also associated to a lesser extent with the right STAP depth and the formation of sulcal interruptions, “plis de passage,” in the bilateral STAP but not with other structural brain MRI phenotypes, highlighting its notable association with the superior temporal regions. Diffusion MRI emphasized an association with the fractional anisotropy of the left auditory fibers of the corpus callosum and with networks involved in linguistic processing in resting-state functional MRI. Overall, this evidence demonstrates a specific relationship between this locus and the establishment of the superior temporal regions that support human communication.}, - number = {10}, - urldate = {2023-02-06}, - journal = {Cerebral Cortex}, - author = {Le Guen, Yann and Leroy, François and Philippe, Cathy and {IMAGEN Consortium} and Mangin, Jean-François and Dehaene-Lambertz, Ghislaine and Frouin, Vincent}, - month = sep, - year = {2020}, - pages = {5322--5332}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SCDV84MH/Le Guen et al. - 2020 - Enhancer Locus in ch14q23.1 Modulates Brain Asymme.pdf:application/pdf}, -} - -@article{le_guen_eqtl_2019, - title = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening: evidence from 15,597 {UK} {Biobank} participants with neuroimaging data}, - volume = {224}, - issn = {1863-2661}, - shorttitle = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening}, - url = {https://doi.org/10.1007/s00429-018-1808-9}, - doi = {10.1007/s00429-018-1808-9}, - abstract = {The grey and white matter volumes are known to reduce with age. This cortical shrinkage is visible on magnetic resonance images and is conveniently identified by the increased volume of cerebrospinal fluid in the sulci between two gyri. Here, we replicated this finding using the UK Biobank dataset and studied the genetic influence on these cortical features of aging. We divided all individuals genetically confirmed of British ancestry into two sub-cohorts (12,162 and 3435 subjects for discovery and replication samples, respectively). We found that the heritability of the sulcal opening ranges from 15 to 45\% (SE = 4.8\%). We identified 4 new loci that contribute to this opening, including one that also affects the sulci grey matter thickness. We identified the most significant variant (rs864736) on this locus as being an expression quantitative trait locus (eQTL) for the KCNK2 gene. This gene regulates the immune-cell into the central nervous system (CNS) and controls the CNS inflammation, which is implicated in cortical atrophy and cognitive decline. These results expand our knowledge of the genetic contribution to cortical shrinking and promote further investigation into these variants and genes in pathological context such as Alzheimer’s disease in which brain shrinkage is a key biomarker.}, - language = {en}, - number = {2}, - urldate = {2023-02-06}, - journal = {Brain Structure and Function}, - author = {Le Guen, Yann and Philippe, Cathy and Riviere, Denis and Lemaitre, Hervé and Grigis, Antoine and Fischer, Clara and Dehaene-Lambertz, Ghislaine and Mangin, Jean-François and Frouin, Vincent}, - month = mar, - year = {2019}, - keywords = {Brain ageing, Imaging genetics, CSF, GM thickness, GWAS, Sulci widening}, - pages = {847--857}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VJK7LZXH/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DBSB6Y6V/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf}, -} - -@article{wang_framework_2024, - title = {A framework to improve the alignment of individual cytoarchitectonic maps of the {Julich}-{Brain} atlas using cortical folding landmarks}, - volume = {34}, - url = {https://academic.oup.com/cercor/article-abstract/34/2/bhad538/7571378}, - number = {2}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Wang, Xiaoyu and Leprince, Yann and Lebenberg, Jessica and Langlet, Clement and Mohlberg, Hartmut and Rivière, Denis and Auzias, Guillaume and Dickscheid, Timo and Amunts, Katrin and Mangin, Jean-François}, - year = {2024}, - note = {Publisher: Oxford University Press}, - pages = {bhad538}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7HZ2KYSL/7571378.html:text/html}, -} - -@article{chauvel_vivo_2023, - title = {In vivo mapping of the deep and superficial white matter connectivity in the chimpanzee brain}, - volume = {282}, - issn = {10538119}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S105381192300513X}, - doi = {10.1016/j.neuroimage.2023.120362}, - language = {en}, - urldate = {2024-03-18}, - journal = {NeuroImage}, - author = {Chauvel, Maëlig and Uszynski, Ivy and Herlin, Bastien and Popov, Alexandros and Leprince, Yann and Mangin, Jean-François and Hopkins, William D. and Poupon, Cyril}, - month = nov, - year = {2023}, - keywords = {Diffusion MRI, Chimpanzee brain connectivity, Deep white matter atlas, Superficial white matter atlas}, - pages = {120362}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HW259AB3/Chauvel et al. - 2023 - In vivo mapping of the deep and superficial white .pdf:application/pdf;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RJ7ZUGRJ/Chauvel et al. - 2023 - In vivo mapping of the deep and superficial.pdf:application/pdf}, -} diff --git a/bibutils/data/brainomics_v-20240621.bib b/bibutils/data/brainomics_v-20240621.bib deleted file mode 100644 index 8ebed44..0000000 --- a/bibutils/data/brainomics_v-20240621.bib +++ /dev/null @@ -1,1053 +0,0 @@ - -@article{ibrahim_modeling_2017, - title = {Modeling a linkage between blood transcriptional expression and activity in brain regions to infer the phenotype of schizophrenia patients}, - volume = {3}, - issn = {2334-265X}, - doi = {10.1038/s41537-017-0027-3}, - abstract = {Hundreds of genetic loci participate to schizophrenia liability. It is also known that impaired cerebral connectivity is directly related to the cognitive and affective disturbances in schizophrenia. How genetic susceptibility and brain neural networks interact to specify a pathological phenotype in schizophrenia remains elusive. Imaging genetics, highlighting brain variations, has proven effective to establish links between vulnerability loci and associated clinical traits. As previous imaging genetics works in schizophrenia have essentially focused on structural DNA variants, these findings could be blurred by epigenetic mechanisms taking place during gene expression. We explored the meaningful links between genetic data from peripheral blood tissues on one hand, and regional brain reactivity to emotion task assayed by blood oxygen level-dependent functional magnetic resonance imaging on the other hand, in schizophrenia patients and matched healthy volunteers. We applied Sparse Generalized Canonical Correlation Analysis to identify joint signals between two blocks of variables: (i) the transcriptional expression of 33 candidate genes, and (ii) the blood oxygen level-dependent activity in 16 region of interest. Results suggested that peripheral transcriptional expression is related to brain imaging variations through a sequential pathway, ending with the schizophrenia phenotype. Generalization of such an approach to larger data sets should thus help in outlining the pathways involved in psychiatric illnesses such as schizophrenia. -IMAGING: SEARCHING FOR LINKS TO AID DIAGNOSIS: Researchers explore links between the expression of genes associated with schizophrenia in blood cells and variations in brain activity during emotion processing. El Chérif Ibrahim and Eric Fakra at Aix-Marseille Université, France, and colleagues have developed a method to relate the expression levels of 33 schizophrenia susceptibility genes in blood cells and functional magnetic resonance imaging (fMRI) data obtained as individuals carry out a task that triggers emotional responses. Although they found no significant differences in the expression of genes between the 26 patients with schizophrenia and 26 healthy controls they examined, variations in activity in the superior temporal gyrus were strongly linked to schizophrenia-associated gene expression and presence of disease. Similar analyses of larger data sets will shed further light on the relationship between peripheral molecular changes and disease-related behaviors and ultimately, aid the diagnosis of neuropsychiatric disease.}, - language = {eng}, - number = {1}, - journal = {NPJ schizophrenia}, - author = {Ibrahim, El Chérif and Guillemot, Vincent and Comte, Magali and Tenenhaus, Arthur and Zendjidjian, Xavier Yves and Cancel, Aida and Belzeaux, Raoul and Sauvanaud, Florence and Blin, Olivier and Frouin, Vincent and Fakra, Eric}, - month = sep, - year = {2017}, - pmid = {28883405}, - pmcid = {PMC5589880}, - pages = {25}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZBBQZUMG/Ibrahim et al. - 2017 - Modeling a linkage between blood transcriptional e.pdf:application/pdf}, -} - -@misc{lofstedt_simulated_2014, - title = {Simulated {Data} for {Linear} {Regression} with {Structured} and {Sparse} {Penalties}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - url = {https://hal-cea.archives-ouvertes.fr/cea-00914960/document}, - abstract = {A very active field of research in Bioinformatics is to integrate structure in Machine Learning methods. Methods recently developed claim that they allow simultaneously to link the computed model to the graphical structure of the data set and to select a handful of important features in the analysis. However, there is still no way to simulate data for which we can separate the three properties that such method claim to achieve. These properties are: (i) the sparsity of the solution, i.e., the fact the the model is based on a few features of the data; (ii) the structure of the model; (iii) the relation between the structure of the model and the graphical model behind the generation of the data.}, - language = {en}, - urldate = {2015-12-15}, - author = {Lofstedt, Tommy and Guillemot, Vincent and Frouin, Vincent and Duchesnay, Édouard and Hadj-Selem, Fouad}, - month = jan, - year = {2014}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CHKA93Q4/Lofstedt et al. - 2014 - Simulated Data for Linear Regression with Structur.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EUQ9D63L/cea-00914960v3.html:text/html}, -} - -@article{cury_incomplete_2015, - title = {Incomplete {Hippocampal} {Inversion}: {A} {Comprehensive} {MRI} {Study} of {Over} 2000 {Subjects}}, - volume = {9}, - copyright = {All rights reserved}, - issn = {1662-5129}, - doi = {10.3389/fnana.2015.00160}, - abstract = {The incomplete-hippocampal-inversion (IHI), also known as malrotation, is an atypical anatomical pattern of the hippocampus, which has been reported in healthy subjects in different studies. However, extensive characterization of IHI in a large sample has not yet been performed. Furthermore, it is unclear whether IHI are restricted to the medial-temporal lobe or are associated with more extensive anatomical changes. Here, we studied the characteristics of IHI in a community based sample of 2008 subjects of the IMAGEN database and their association with extra-hippocampal anatomical variations. The presence of IHI was assessed on Ti-weighted anatomical magnetic resonance imaging (MRI) using visual criteria. We assessed the association of IHI with other anatomical changes throughout the brain using automatic morphometry of cortical sulci. We found that IHI were much more frequent in the left hippocampus (left: 17\%, right: 6\%, chi(2) - test, p {\textless} 10(-28)). Compared to subjects without IHI, subjects with IHI displayed morphological changes in several sulci located mainly in the limbic lobe. Our results demonstrate that IHI are a common left-sided phenomenon in normal subjects and that they are associated with morphological changes outside the medial temporal lobe.}, - journal = {FRONTIERS IN NEUROANATOMY}, - author = {Cury, Claire and Toro, Roberto and Cohen, Fanny and Fischer, Clara and Mhaya, Amel and Samper-Gonzalez, Jorge and Hasboun, Dominique and Mangin, Jean-Francois and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Buechel, Christian and Cattrell, Anna and Conrod, Patricia and Flor, Herta and Gallinat, Juergen and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Lemaitre, Herve and Martinot, Jean-Luc and Nees, Frauke and Martinot, Marie-Laure Paillere and Orfanos, Dimitri P. and Paus, Tomas and Poustka, Luise and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Frouin, Vincent and Schumann, Gunter and Glaunes, Joan A. and Colliot, Olivier}, - month = dec, - year = {2015}, - keywords = {MRI, cortical sulci, anatomical variability, IMAGEN database, Large database, malrotation, Human hippocampus}, - pages = {160}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UnatiPMID: 26733822}, -} - -@article{spechler_cannabis_2015, - title = {Cannabis use in early adolescence: {Evidence} of amygdala hypersensitivity to signals of threat}, - volume = {16}, - copyright = {All rights reserved}, - issn = {1878-9293}, - doi = {10.1016/j.dcn.2015.08.007}, - abstract = {Cannabis use in adolescence may be characterized by differences in the neural basis of affective processing. In this study, we used an fMRI affective face processing task to compare a large group (n = 70) of 14-year olds with a history of cannabis use to a group (n = 70) of never-using controls matched on numerous characteristics including IQ, SES, alcohol and cigarette use. The task contained short movies displaying angry and neutral faces. Results indicated that cannabis users had greater reactivity in the bilateral amygdalae to angry faces than neutral faces, an effect that was not observed in their abstinent peers. In contrast, activity levels in the cannabis users in cortical areas including the right temporal-parietal junction and bilateral dorsolateral prefrontal cortex did not discriminate between the two face conditions, but did differ in controls. Results did not change after excluding subjects with any psychiatric symptomology. Given the high density of cannabinoid receptors in the amygdala, our findings suggest cannabis use in early adolescence is associated with hypersensitivity to signals of threat. Hypersensitivity to negative affect in adolescence may place the subject at-risk for mood disorders in adulthood. (C) 2015 Published by Elsevier Ltd.}, - journal = {DEVELOPMENTAL COGNITIVE NEUROSCIENCE}, - author = {Spechler, Philip A. and Orr, Catherine A. and Chaarani, Bader and Kan, Kees-Jan and Mackey, Scott and Morton, Aaron and Snowe, Mitchell P. and Hudson, Kelsey E. and Althoff, Robert R. and Higgins, Stephen T. and Cattrell, Anna and Flor, Herta and Nees, Frauke and Banaschewski, Tobias and Bokde, Arun L. W. and Whelan, Robert and Buechel, Christian and Bromberg, Uli and Conrod, Patricia and Frouin, Vincent and Papadopoulos, Dimitri and Gallinat, Jurgen and Heinz, Andreas and Walter, Henrik and Ittermann, Bernd and Gowland, Penny and Paus, Tomas and Poustka, Luise and Martinot, Jean-Luc and Artiges, Eric and Smolka, Michael N. and Schumann, Gunter and Garavan, Hugh}, - month = dec, - year = {2015}, - keywords = {fMRI, Amygdala, Adolescence, Cannabis, Face processing, Faces}, - pages = {63--70}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UnatiPMID: 26347227}, -} - -@article{papadopoulos_orfanos_brainomics/localizer_2015, - title = {The {Brainomics}/{Localizer} database.}, - volume = {15}, - copyright = {All rights reserved}, - abstract = {The Brainomics/Localizer database exposes part of the data collected by the in-house Localizer project, which planned to acquire four types of data from volunteer research subjects: anatomical MRI scans, functional MRI data, behavioral and demographic data, and DNA sampling. Over the years, this local project has been collecting such data from hundreds of subjects. We had selected 94 of these subjects for their complete datasets, including all four types of data, as the basis for a prior publication; the Brainomics/Localizer database publishes the data associated with these 94 subjects. Since regulatory rules prevent us from making genetic data available for download, the database serves only anatomical MRI scans, functional MRI data, behavioral and demographic data. To publish this set of heterogeneous data, we use dedicated software based on the open-source CubicWeb semantic web framework. Through genericity in the data model and flexibility in the display of data (web pages, CSV, JSON, XML), CubicWeb helps us expose these complex datasets in original and efficient ways.}, - journal = {Neuroimage}, - author = {Papadopoulos Orfanos, D. and Michel, V. and Schwartz, Y. and Pinel, P. and Moreno, A. and Le Bihan, D. and Frouin, V.}, - month = oct, - year = {2015}, - keywords = {Imaging genetics, Semantic web}, - pages = {00874--5}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati - ParietalPMID: 26455807}, -} - -@inproceedings{lofstedt_analysis_2014, - address = {Paris}, - title = {Analysis, {Structured} variable selection for generalized canonical correlation}, - copyright = {All rights reserved}, - booktitle = {International {Conference} on {Partial} {Least} {Squares} and {Related} {Methods}}, - author = {Lofstedt, Tommy and Hadj-Selem, Foaud and Guillemot, Vincent and Philippe, Cathy and Duchesnay, Edouard and Tenenhaus, Arthur and Frouin, Vincent}, - year = {2014}, - pages = {127}, -} - -@article{dauguet_three-dimensional_2007, - title = {Three-dimensional reconstruction of stained histological slices and {3D} non-linear registration with in-vivo {MRI} for whole baboon brain}, - volume = {164}, - copyright = {All rights reserved}, - journal = {J Neurosci Methods}, - author = {Dauguet, J. and Delzescaux, T. and Condé, F. and Mangin, J. F. and Ayache, N. and Hantraye, P. and Frouin, V.}, - year = {2007}, - keywords = {Registration,brainvisa}, - pages = {191--204}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Dauguet-JNM07.pdf}, -} - -@article{ragis_sulcal_2005, - title = {"{Sulcal} root" generic model: a hypothesis to overcome the variability of the human cortex folding patterns}, - volume = {45}, - copyright = {All rights reserved}, - journal = {Neurol Med Chir (Tokyo)}, - author = {Régis, J. and Mangin, J. F. and Ochiai, T. and Frouin, V. and Rivière, D. and Cachia, A. and Tamura, M. and Samson, Y.}, - year = {2005}, - pages = {1--17}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - http://brainvisa.info/pdf/regis-NMChir05.pdfarticle}, -} - -@article{pappata_vivo_2002, - title = {In {Vivo} {Detection} of {Striatal} {Dopamine} {Release} during {Reward}: {A} {PET} {Study} with [(11){C}]{Raclopride} and a {Single} {Dynamic} {Scan} {Approach}}, - volume = {16}, - copyright = {All rights reserved}, - abstract = {Anew simple method is proposed to detect, using PET and [(11)C]raclopride, changes in striatal extracellular dopamine concentration during a rewarded effortful task. This approach aimed to increase the sensitivity in detection of these effects. It requires a single-dynamic PET study and combines the classic kinetic compartmental model with the general linear model of SPM to provide statistical inference on changes in [(11)C]raclopride time-activity curve due to endogenous dopamine release during two short periods of activation. Kinetic simulations predicted that 100\% dopamine increase during two 5- min periods starting at 30 and 60 min after the injection can be detected. Moreover the effects of dopamine release on the [(11)C]raclopride time-activity-curve are different from those induced by CBF increase. These simulated curves were used to construct the statistical linear model and to test voxel-by-voxel in healthy subjects the hypothesis that dopamine is released in the ventral striatum during periods of unexpected monetary gains, but not during periods of unexpected monetary loss. The experimental results are in line with the expected results although the amplitude of the effects due to dopamine release is moderate. The advantages and the limits of this method as well as the relevance of the results for dopamine involvement in reward processing are discussed.}, - journal = {Neuroimage}, - author = {Pappata, S. and Dehaene, S. and Poline, J. and Gregoire, M. and Jobert, A. and Delforge, J. and Frouin, V. and Bottlaender, M. and Dolle, F. and Di Giamberardino, L. and Syrota, A.}, - year = {2002}, - pages = {1015.}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACL}, -} - -@article{dalberto_individual_2018, - title = {Individual differences in stop-related activity are inflated by the adaptive algorithm in the stop signal task.}, - copyright = {All rights reserved}, - doi = {10.1002/hbm.2407}, - journal = {Hum Brain Mapp.}, - author = {D'Alberto, N. and Chaarani, B. and Orr, C. A. and Spechler, P. A. and Albaugh, M. D. and Allgaier, N. and Wonnell, A. and Banaschewski, T. and Bokde, A. L. W. and Bromberg, U. and Büchel, C. and Quinlan, E. B. and Conrod, P. J. and Desrivières, S. and Flor, H. and Fröhner, J. H. and Frouin, V. and Gowland, P. and Heinz, A. and Itterman B, Martinot JL}, - month = apr, - year = {2018}, - annote = {The following values have no corresponding Zotero field:section: PMID:}, -} - -@article{ortuno-sierra_new_2015, - title = {New evidence of factor structure and measurement invariance of the {SDQ} across five {European} nations}, - volume = {24}, - copyright = {All rights reserved}, - issn = {1018-8827}, - doi = {10.1007/s00787-015-0729-x}, - abstract = {The main purpose of the present study was to analyse the internal structure and to test the measurement invariance of the Strengths and Difficulties Questionnaire (SDQ), self-reported version, in five European countries. The sample consisted of 3012 adolescents aged between 12 and 17 years (M = 14.20; SD = 0.83). The five-factor model (with correlated errors added), and the five-factor model (with correlated errors added) with the reverse-worded items allowed to cross-load on the Prosocial subscale, displayed adequate goodness of-fit indices. Multi-group confirmatory factor analysis showed that the five-factor model (with correlated errors added) had partial strong measurement invariance by countries. A total of 11 of the 25 items were non-invariant across samples. The level of internal consistency of the Total difficulties score was 0.84, ranging between 0.69 and 0.78 for the SDQ subscales. The findings indicate that the SDQ's subscales need to be modified in various ways for screening emotional and behavioural problems in the five European countries that were analysed.}, - number = {12}, - journal = {EUROPEAN CHILD \& ADOLESCENT PSYCHIATRY}, - author = {Ortuno-Sierra, Javier and Fonseca-Pedrero, Eduardo and Aritio-Solana, Rebeca and Moreno Velasco, Alvaro and Chocarro de Luis, Edurne and Schumann, Gunter and Cattrell, Anna and Flor, Herta and Nees, Frauke and Banaschewski, Tobias and Bokde, Arun and Whelan, Rob and Buechel, Christian and Bromberg, Uli and Conrod, Patricia and Frouin, Vincent and Papadopoulos, Dimitri and Gallinat, Juergen and Garavan, Hugh and Heinz, Andreas and Walter, Henrik and Struve, Maren and Gowland, Penny and Paus, Tomas and Poustka, Luise and Martinot, Jean-Luc and Paillere-Martinot, Marie-Laure and Vetter, Nora C. and Smolka, Michael N. and Lawrence, Claire}, - month = dec, - year = {2015}, - keywords = {Behavioural problems, Factorial structure, Measurement invariance, SDQ, Self-report}, - pages = {1523--1534}, - annote = {The following values have no corresponding Zotero field:number: 12label: ACL}, - annote = {UnatiPMID: 26036862}, -} - -@article{duchesnay_methodes_2015, - title = {Méthodes de prédiction multivariées basées sur la neuroimagerie : application aux maladies psychiatriques}, - copyright = {All rights reserved}, - shorttitle = {Méthodes de prédiction multivariées basées sur la neuroimagerie}, - journal = {Annales Médico-psychologiques, revue psychiatrique}, - author = {Duchesnay, Edouard and Bourgin, Julie and Hadj-Selem, Fouad and Frouin, Vincent}, - year = {2015}, -} - -@phdthesis{frouin_hdr_2009, - type = {Habilitation à diriger des recherches}, - title = {{HDR} = {Applications} de méthodes d'intégration d'informations en imagerie bio-médicale et génomique fonctionnelle}, - copyright = {All rights reserved}, - school = {Paris XI}, - author = {Frouin, V.}, - year = {2009}, - annote = {The following values have no corresponding Zotero field:label: HDR}, - annote = {Unati}, -} - -@article{stringaris_brains_2015, - title = {The {Brain}'s {Response} to {Reward} {Anticipation} and {Depression} in {Adolescence}: {Dimensionality}, {Specificity}, and {Longitudinal} {Predictions} in a {Community}-{Based} {Sample}}, - volume = {172}, - copyright = {All rights reserved}, - issn = {0002-953X}, - doi = {10.1176/appi.ajp.2015.14101298}, - abstract = {Objective: The authors examined whether alterations in the brain's reward network operate as a mechanism across the spectrum of risk for depression. They then tested whether these alterations are specific to anhedonia as compared with low mood and whether they are predictive of depressive outcomes. Method: Functional MRI was used to collect blood-oxygen-level-dependent (BOLD) responses to anticipation of reward in the monetary incentive task in 1,576 adolescents in a community-based sample. Adolescents with current subthreshold depression and clinical depression were compared with matched healthy subjects. In addition, BOLD responses were compared across adolescents with anhedonia, low mood, or both symptoms, cross-sectionally and longitudinally. Results: Activity in the ventral striatum was reduced in participants with subthreshold and clinical depression relative to healthy comparison subjects. Low ventral striatum activation predicted transition to subthreshold or clinical depression in previously healthy adolescents at 2-year follow-up. Brain responses during reward anticipation decreased in a graded manner between healthy adolescents, adolescents with current or future subthreshold depression, and adolescents with current or future clinical depression. Low ventral striatum activity was associated with anhedonia but not low mood; however, the combined presence of both symptoms showed the strongest reductions in the ventral striatum in all analyses. Conclusions: The findings suggest that reduced striatal activation operates as a mechanism across the risk spectrum for depression. It is associated with anhedonia in healthy adolescents and is a behavioral indicator of positive valence systems, consistent with predictions based on the Research Domain Criteria.}, - number = {12}, - journal = {AMERICAN JOURNAL OF PSYCHIATRY}, - author = {Stringaris, Argyris and Belil, Pablo Vidal-Ribas and Artiges, Eric and Lemaitre, Herve and Gollier-Briant, Fanny and Wotke, Selina and Vulser, Helene and Miranda, Ruben and Penttilae, Jani and Struve, Maren and Fadai, Tahmine and Kappel, Viola and Grimmer, Yvonne and Goodman, Robert and Poustka, Luise and Conrod, Patricia and Cattrell, Anna and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Buechel, Christian and Flor, Herta and Frouin, Vincent and Gattinat, Juergen and Garavan, Hugh and Gowtand, Penny and Heinz, Andreas and Ittermann, Bernd and Nees, Frauke and Papadopoulos, Dimitri and Paus, Tomas and Smolka, Michael N. and Walter, Henrik and Whelan, Rob and Martinot, Jean-Luc and Schumann, Gunter and Paillere-Martinot, Marie-Laure}, - month = dec, - year = {2015}, - pages = {1215--1223}, - annote = {The following values have no corresponding Zotero field:number: 12label: ACL}, - annote = {UnatiPMID: 26085042}, -} - -@article{ewald_role_2016, - title = {The role of the cannabinoid receptor in adolescents' processing of facial expressions.}, - volume = {43}, - copyright = {All rights reserved}, - abstract = {The processing of emotional faces is an important prerequisite for adequate social interactions in daily life, and might thus specifically be altered in adolescence, a period marked by significant changes in social emotional processing. Previous research has shown that the cannabinoid receptor CB1R is associated with longer gaze duration and increased brain responses in the striatum to happy faces in adults, yet, for adolescents, it is not clear whether an association between CBR1 and face processing exists. In the present study we investigated genetic effects of the two CB1R polymorphisms, rs1049353 and rs806377, on the processing of emotional faces in healthy adolescents. They participated in functional magnetic resonance imaging during a Faces Task, watching blocks of video clips with angry and neutral facial expressions, and completed a Morphed Faces Task in the laboratory where they looked at different facial expressions that switched from anger to fear or sadness or from happiness to fear or sadness, and labelled them according to these four emotional expressions. A-allele versus GG-carriers in rs1049353 displayed earlier recognition of facial expressions changing from anger to sadness or fear, but not for expressions changing from happiness to sadness or fear, and higher brain responses to angry, but not neutral, faces in the amygdala and insula. For rs806377 no significant effects emerged. This suggests that rs1049353 is involved in the processing of negative facial expressions with relation to anger in adolescence. These findings add to our understanding of social emotion-related mechanisms in this life period.}, - journal = {Eur J Neurosci.}, - author = {Ewald, A. and Becker, S. and Heinrich, A. and Banaschewski, T. and Poustka, L. and Bokde, A. and Büchel, C. and Bromberg, U. and Cattrell, A. and Conrod, P. and Desrivières, S. and Frouin, V. and Papadopoulos-Orfanos, D. and Gallinat, J. and Garavan, H. and Heinz, A. and Walter, H. and Ittermann, B. and Gowland, P. and Paus, T. and Martinot, J.-L. and Paillère Martinot, M.-L. and Smolka, M.-N. and Vetter, N. and Whelan, R. and Schumann, G. and Flor, H. and Nees, F.}, - month = jan, - year = {2016}, - keywords = {Amygdala, cannabinoid, emotion, limbic System/*anatomy \& histology}, - pages = {98--105}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unati PMID: 26527537}, -} - -@article{bragulat_dopaminergic_2007, - title = {Dopaminergic function in depressed patients with affective flattening or with impulsivity: [{18F}]fluoro-{L}-dopa positron emission tomography study with voxel-based analysis}, - volume = {154}, - copyright = {All rights reserved}, - abstract = {A decreased striatal presynaptic dopaminergic function has been reported in depressed patients with affective flattening and psychomotor retardation, using (18)F-fluorodopa positron emission tomography and regions-of-interest. The present study aimed to investigate regional ;[(18)F]dopa uptake in mesolimbic and mesocortical dopaminergic projections with the hypothesis that there should be a decrease in mesolimbic [(18)F]dopa uptake associated with affective flattening and psychomotor retardation. [(18)F]Dopa-positron emission tomography and anatomical magnetic resonance imaging datasets from 12 screened depressed patients with either marked affective flattening and psychomotor retardation (n=6) or with marked impulsivity (n=6), and from eight healthy subjects, were analyzed using a voxel-based approach. Regional differences in [(18)F]dopa uptake rate constant (K(i)) values between the healthy group and the two depression subgroups were compared using both statistical parametric mapping and cluster-based regions-of-interest. Patients with affective flattening and psychomotor retardation had [(18)F]dopa K(i) decreases in the left caudate, bilateral putamen and nucleus accumbens, left parahippocampus and dorsal brainstem. Impulsive depressives had [(18)F]dopa K(i) decreases in the anterior cingulate and hypothalamus, and an increase in the right parahippocampal gyrus. These findings support distinct regional dysfunctions of monoamines depending on the depressive symptomatology.}, - journal = {Psychiatry Res}, - author = {Bragulat, Véronique and Paillère-Martinot, Marie-Laure and Artiges, Eric and Frouin, Vincent and Poline, Jean-Baptiste and Martinot, Jean-Luc}, - month = feb, - year = {2007}, - keywords = {Humans, Adult, Female, Male, Affect, Positron-Emission Tomography, Fluorodeoxyglucose F18, Depressive Disorder, Major, Gyrus Cinguli, Diagnostic and Statistical Manual of Mental Disorders, Severity of Illness Index, Hippocampus, Fluoxetine, Caudate Nucleus, Putamen, Radiopharmaceuticals, Hypothalamus, Biogenic Monoamines, Brain Stem, Cyclohexanols, Impulse Control Disorders, Psychomotor Disorders, Serotonin Uptake Inhibitors}, - pages = {115--124}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - articlejb}, -} - -@inproceedings{poline_imaging_2010, - address = {Heidelberg}, - title = {Imaging {Genetics}: {Bio}-{Informatics} and {Bio}-{Statistics} {Challenges}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-3-7908-2603-6}, - url = {http://www.springerlink.com/index/10.1007/978-3-7908-2604-3}, - doi = {10.1007/978-3-7908-2604-3}, - booktitle = {compstat}, - publisher = {Physica-Verlag HD}, - author = {Poline, Jean-Baptiste and Lalanne, Christophe and Tenenhaus, Arthur and Duchesnay, Edouard and Thirion, Bertrand and Frouin, Vincent}, - editor = {Lechevallier, Yves and Saporta, Gilbert}, - year = {2010}, - keywords = {conference}, - pages = {101--110}, - file = {Poline et al. - 2010 - Imaging Genetics Bio-Informatics and Bio-Statisti.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HB7SW2DG/Poline et al. - 2010 - Imaging Genetics Bio-Informatics and Bio-Statisti.pdf:application/pdf}, -} - -@article{maroy_segmentation_2008, - title = {Segmentation of rodent whole-body dynamic {PET} images: an unsupervised method based on voxel dynamics}, - volume = {27}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {0278-0062}, - shorttitle = {Segmentation of rodent whole-body dynamic {PET} images}, - doi = {10.1109/TMI.2007.905106}, - abstract = {Positron emission tomography (PET) is a useful tool for pharmacokinetics studies in rodents during the preclinical phase of drug and tracer development. However, rodent organs are small as compared to the scanner's intrinsic resolution and are affected by physiological movements. We present a new method for the segmentation of rodent whole-body PET images that takes these two difficulties into account by estimating the pharmacokinetics far from organ borders. The segmentation method proved efficient on whole-body numerical rat phantom simulations, including 3-14 organs, together with physiological movements (heart beating, breathing, and bladder filling). The method was resistant to spillover and physiological movements, while other methods failed to obtain a correct segmentation. The radioactivity concentrations calculated with this method also showed an excellent correlation with the manual delineation of organs in a large set of preclinical images. In addition, it was faster, detected more organs, and extracted organs' mean time activity curves with a better confidence on the measure than manual delineation.}, - language = {eng}, - number = {3}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Maroy, Renaud and Boisgard, Raphaël and Comtat, Claude and Frouin, Vincent and Cathier, Pascal and Duchesnay, Edouard and Dollé, Frédéric and Nielsen, Peter E. and Trébossen, Régine and Tavitian, Bertrand}, - month = mar, - year = {2008}, - pmid = {18334430}, - keywords = {Algorithms, Artificial Intelligence, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Animals, Rats, Phantoms, Imaging, Positron-Emission Tomography, Whole Body Imaging}, - pages = {342--354}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Maroy-TMI08.pdfarticle}, -} - -@incollection{lofstedt_structured_2016, - series = {The {Multiple} {Facets} of {Partial} {Least} {Squares} and {Related} {Methods}}, - title = {Structured {Variable} {Selection} for {Regularized} {Generalized} {Canonical} {Correlation} {Analysis}, {The} {Multiple} {Facets} of {Partial} {Least} {Squares} and {Related} {Methods}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - url = {https://hal-centralesupelec.archives-ouvertes.fr/hal-01396614}, - language = {en}, - urldate = {2017-01-10}, - booktitle = {Springer {Proceedings} in {Mathematics} and {Statistics}}, - author = {Lofstedt, Tommy and Hadj-Selem, Fouad and Guillemot, Vincent and Philippe, Cathy and Duchesnay, Edouard and Frouin, Vincent and Tenenhaus, Arthur}, - year = {2016}, - pages = {129--139}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A3HTWHWC/hal-01396614.html:text/html}, -} - -@inproceedings{le_floch_bridging_2011, - title = {Bridging the gap between imaging and genetics : a multivariate statistical investigation}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Human brain mapping}, - author = {Le Floch, Edith and Lalanne, Christophe and Pinel, Philippe and Moreno, Antonio and Trinchera, Laura and Tenenhaus, Arthur and Thirion, Bertrand and Poline, Jean-Baptiste and Frouin, Vincent and Duchesnay, Edouard}, - year = {2011}, - keywords = {conference}, -} - -@inproceedings{le_floch_cluster-level_2010, - title = {Cluster-level {Inference} and {Resampling}-{Based} {Multiple} {Testing} applied to {Imaging} {Genetics} {Studies}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Human brain mapping}, - author = {Le Floch, Edith and Keller, Merlin and Frouin, Vincent and Lalanne, Christophe and Pinel, Philippe and Poline, Jean-Baptiste and Duchesnay, Edouard}, - year = {2010}, - keywords = {conference}, - file = {Le Floc, Edith et al. - 2010 - Cluster-level Inference and Resampling-Based Multi.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WIMFRYVC/Le Floc, Edith et al. - 2010 - Cluster-level Inference and Resampling-Based Multi.pdf:application/pdf}, -} - -@article{le_floch_significant_2012, - title = {Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse {Partial} {Least} {Squares}}, - volume = {63}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2012.06.061}, - abstract = {Brain imaging is increasingly recognised as an intermediate phenotype to understand the complex path between genetics and behavioural or clinical phenotypes. In this context, a first goal is to propose methods to identify the part of genetic variability that explains some neuroimaging variability. Classical univariate approaches often ignore the potential joint effects that may exist between genes or the potential covariations between brain regions. In this paper, we propose instead to investigate an exploratory multivariate method in order to identify a set of Single Nucleotide Polymorphisms (SNPs) covarying with a set of neuroimaging phenotypes derived from functional Magnetic Resonance Imaging (fMRI). Recently, Partial Least Squares (PLS) regression or Canonical Correlation Analysis (CCA) have been proposed to analyse DNA and transcriptomics. Here, we propose to transpose this idea to the DNA vs. imaging context. However, in very high-dimensional settings like in imaging genetics studies, such multivariate methods may encounter overfitting issues. Thus we investigate the use of different strategies of regularisation and dimension reduction techniques combined with PLS or CCA to face the very high dimensionality of imaging genetics studies. We propose a comparison study of the different strategies on a simulated dataset first and then on a real dataset composed of 94 subjects, around 600,000 SNPs and 34 functional MRI lateralisation indexes computed from reading and speech comprehension contrast maps. We estimate the generalisability of the multivariate association with a cross-validation scheme and demonstrate the significance of this link, using a permutation procedure. Univariate selection appears to be necessary to reduce the dimensionality. However, the significant association uncovered by this two-step approach combining univariate filtering and L1-regularised PLS suggests that discovering meaningful genetic associations calls for a multivariate approach.}, - language = {eng}, - number = {1}, - journal = {NeuroImage}, - author = {Le Floch, Edith and Guillemot, Vincent and Frouin, Vincent and Pinel, Philippe and Lalanne, Christophe and Trinchera, Laura and Tenenhaus, Arthur and Moreno, Antonio and Zilbovicius, Monica and Bourgeron, Thomas and Dehaene, Stanislas and Thirion, Bertrand and Poline, Jean-Baptiste and Duchesnay, Edouard}, - month = oct, - year = {2012}, - pmid = {22781162}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Brain Mapping, Data Interpretation, Statistical, Adult, Female, Male, Young Adult, Cognition, Least-Squares Analysis, Nerve Net, Polymorphism, Single Nucleotide}, - pages = {11--24}, - annote = {Times Cited: 14}, -} - -@inproceedings{le_floch_dimension_2012, - title = {Dimension reduction and regularisation combined with {Partial} {Least} {Squares} in high dimensional imaging-genetics studies}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Partial {Least} {Squares}}, - author = {Le Floch, E. and Trinchera, L. and Tenenhaus, A. and Poline, J.B. and Frouin, V. and Duchesnay, E.}, - year = {2012}, - keywords = {conference}, -} - -@misc{hadj-selem_supplementary_2018, - title = {Supplementary material: {Continuation} of {Nesterov}'s {Smoothing} for {Regression} with {Structured} {Sparsity} in {High}-{Dimensional} {Neuroimaging}}, - copyright = {All rights reserved}, - shorttitle = {Supplementary material}, - url = {https://hal-cea.archives-ouvertes.fr/cea-01324021/document}, - abstract = {Predictive models can be used on high-dimensional brain images for diagnosis of a clinical condition. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total Variation (TV) enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties but reasonable precision requires a small smoothing parameter, which slows down the convergence speed. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed towards any globally desired precision. Our main contributions are: To propose an expression of the duality gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the convergence speed. We provide a convergence rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.}, - language = {en}, - urldate = {2018-04-23}, - author = {Hadj-Selem, Fouad and Löfstedt, Tommy and Dohmatob, Elvis and Frouin, Vincent and Dubois, Mathieu and Guillemot, Vincent and Duchesnay, Edouard and Lofstedt, Tommy}, - year = {2018}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/4Y4QZ9X6/Hadj-Selem et al. - 2016 - Supplementary material Continuation of Nesterov's.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CAUV2ZBV/cea-01324021.html:text/html}, -} - -@inproceedings{guillemot_multi-block_2013, - title = {A multi-block approach in imaging genetics}, - copyright = {All rights reserved}, - booktitle = {9th {International} {Imaging} {Genetics} {Conference}}, - author = {Guillemot, Vincent and Tenenhaus, Arthur and Duchesnay, Edouard and Poline, Jean-Baptiste and Frouin, Vincent}, - year = {2013}, - pages = {Poster--13}, -} - -@article{dubois_quantitative_2008, - title = {Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes: application to unilateral visual stimulation}, - volume = {40}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - shorttitle = {Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes}, - doi = {10.1016/j.neuroimage.2007.11.054}, - abstract = {PET scanners devoted to in vivo functional study have recently been developed, but autoradiography remains the reference technique for assessing cerebral glucose metabolism (CMRGlu) in rodents. Autoradiographs are conventionally subjected to region of interest (ROI) analysis, which is intrinsically hypothesis-driven and therefore not suitable for whole-brain investigation. Voxel-wise statistical methods of analysis have long been used to determine differences in brain activity during in vivo functional neuroimaging experiments. They have also recently been applied to 3D reconstructed autoradiographic volume images from rat brains. We present here a fully automated analysis for autoradiographic data combining (1) computerized procedures for the acquisition and 3D reconstruction of postmortem volume images and (2) spatial normalization followed by classical whole-brain voxel-wise statistical analysis. We also describe an additional procedure for characterizing functional differences between the right and left hemispheres of the brain. We compared two spatial normalization techniques and evaluated how the effect of choosing a particular normalization technique impacted on the statistical analysis. We also propose a small volume correction analysis to address the problem of multiple statistical comparisons. Lastly, we investigated the reliability of such analyses, by comparing their results qualitatively and quantitatively with those previously obtained with our semiautomated ROI-based analysis [Dubois, A., Dauguet, J., Herard, A.-S., Besret, L., Duchesnay, E., Frouin, V., Hantraye, P., Bonvento, G., Delzescaux, T., 2007. Automated three-dimensional analysis of histologic and autoradiographic rat brain sections: application to an activation study. J. Cereb. Blood Flow Metab. 27 (10), 1742-1755.]. Both voxel-wise statistical analyses led to the detection of consistent interhemispheric differences in CMRGlu. This work demonstrates the potential value and robustness of voxel-wise statistical methods for analyzing autoradiographic data sets.}, - language = {eng}, - number = {2}, - journal = {NeuroImage}, - author = {Dubois, Albertine and Hérard, Anne-Sophie and Flandin, Guillaume and Duchesnay, Edouard and Besret, Laurent and Frouin, Vincent and Hantraye, Philippe and Bonvento, Gilles and Delzescaux, Thierry}, - month = apr, - year = {2008}, - pmid = {18234520}, - keywords = {Brain, Animals, Autoradiography, Rats, Organ Size, Photic Stimulation, glucose}, - pages = {482--494}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/ADubois-NI08.pdfarticle}, -} - -@article{lobon-iglesias_diffuse_2018, - title = {Diffuse intrinsic pontine gliomas ({DIPG}) at recurrence: is there a window to test new therapies in some patients?}, - volume = {137}, - issn = {1573-7373}, - shorttitle = {Diffuse intrinsic pontine gliomas ({DIPG}) at recurrence}, - doi = {10.1007/s11060-017-2702-7}, - abstract = {Children with diffuse intrinsic pontine glioma (DIPG) need new and more efficient treatments. They can be developed at relapse or at diagnosis, but therefore they must be combined with radiotherapy. Survival of children after recurrence and its predictors were studied to inform the possibility to design early phase clinical trials for DIPG at this stage. Among 142 DIPG patients treated between 1998 and 2014, 114 had biopsy-proven DIPG with histone H3 status available for 83. We defined as long survivors' patients who survived more than 3 months after relapse which corresponds to the minimal life expectancy requested for phase I/II trials. Factors influencing post-relapse survival were accordingly compared between short and long-term survivors after relapse. Fifty-seven percent of patients were considered long survivors and 70\% of them had a Lansky Play Scale (LPS) above 50\% at relapse. Patients who became steroids-independent after initial treatment for at least 2 months had better survival after relapse (3.7 versus 2.6 months, p = 0.001). LPS above 50\% at relapse was correlated with better survival after relapse (3.8 versus 1.8 months, p {\textless} 0.001). Patients with H3.1 mutation survived longer after relapse (4.9 versus 2.7 months, p = 0.007). Patients who received a second radiotherapy at the time of relapse had an improved survival (7.5 versus 4 months, p = 0.001). In the two-way ANOVA analysis, steroid-independence and LPS predicted survival best and the type of histone H3 (H3.1 or H3.3) mutated did not improve prediction. Survival of many DIPG patients after relapse over 3 months would make possible to propose specific trials for this condition. Steroid-independence, H3 mutation status and LPS should be considered to predict eligibility.}, - language = {eng}, - number = {1}, - journal = {Journal of Neuro-Oncology}, - author = {Lobon-Iglesias, M. J. and Giraud, G. and Castel, D. and Philippe, C. and Debily, M. A. and Briandet, C. and Fouyssac, F. and de Carli, E. and Dufour, C. and Valteau-Couanet, D. and Sainte-Rose, C. and Blauwblomme, T. and Beccaria, K. and Zerah, M. and Puget, S. and Calmon, R. and Boddaert, N. and Bolle, S. and Varlet, P. and Grill, J.}, - month = mar, - year = {2018}, - pmid = {29198053}, - keywords = {Brainstem glioma, H3K27M mutation, Midline infiltrative glioma, Steroid-independence}, - pages = {111--118}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FUE52H8P/10.html:text/html}, -} - -@article{charman_eu-aims_2017, - title = {The {EU}-{AIMS} {Longitunal} {European} {Autism} {Project} ({LEAP}): clinical characterisation}, - volume = {8}, - copyright = {All rights reserved}, - journal = {Molecular Autism}, - author = {Charman, T. and Loth, E. and Tillmann, J. and Crawley, D. and Wooldridge, C. and Goyard, D. and Ahmad, J. and Auyeung, B. and Ambrosino, S. and Banaschewski, T. and Baron-Cohen, S. and Baumeister, S. and Beckmann, C. and Bolte, S. and Bourgeron, T. and Bours, C. and Brammer, M. and Brandeis, D. and Brogna, C. and de Bruijn, Y. and Chakrabarti, B. and Cornelissen, I. and Acqua, F. D. and Dumas, G. and Durston, S. and Ecker, C. and Faulkner, J. and Frouin, V. and Garces, P. and Ham, L. and Hayward, H. and Hipp, J. and Holt, R. J. and Isaksson, J. and Johnson, M. H. and Jones, E. J. H. and Kundu, P. and Lai, M. C. and D'ardhuy, X. L. and Lombardo, M. V. and Lythgoe, D. J. and Mandl, R. and Mason, L. and Meyer-Lindenberg, A. and Moessnang, C. and Mueller, N. and O'Dwyer, L. and Oldehinkel, M. and Oranje, B. and Pandina, G. and Persico, A. M. and Ruggeri, B. and Ruigrok, A. N. V. and Sabet, J. and Sacco, R. and Caceres, A. S. J. and Simonoff, E. and Toro, R. and Tost, H. and Waldman, J. and Williams, S. C. R. and Zwiers, M. P. and Spooren, W. and Murphy, D. G. M. and Buitelaar, J. K.}, - month = dec, - year = {2017}, - pages = {27}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unati}, -} - -@article{stacey_translational_2016, - title = {A translational systems biology approach in both animals and humans identifies a functionally related module of accumbal genes involved in the regulation of reward processing and binge drinking in males}, - volume = {41}, - issn = {1180-4882}, - doi = {10.1503/jpn.150138}, - number = {3}, - journal = {JOURNAL OF PSYCHIATRY \& NEUROSCIENCE}, - author = {Stacey, David and Lourdusamy, Anbarasu and Ruggeri, Barbara and Maroteaux, Matthieu and Jia, Tianye and Cattrell, Anna and Nymberg, Charlotte and Banaschewski, Tobias and Bhattacharyya, Sohinee and Band, Hamid and Barker, Gareth and Bokde, Arun and Buchel, Christian and Carvalho, Fabiana and Conrod, Patricia and Desrivieres, Sylvane and Easton, Alanna and Fauth-Buehler, Mira and Fernandez-Medarde, Alberto and Flor, Herta and Frouin, Vincent and Gallinat, Jurgen and Garavanh, Hugh and Heinz, Andreas and Ittermann, Bernd and Lathrop, Mark and Lawrence, Claire and Loth, Eva and Mann, Karl and Martinot, Jean-Luc and Nees, Frauke and Paus, Tomas and Pausova, Zdenka and Rietschel, Marcella and Rotter, Andrea and Santos, Eugenio and Smolka, Michael and Sommer, Wolfgang and Mameli, Manuel and Spanagel, Rainer and Girault, Jean-Antoine and Mueller, Christian and Schumann, Gunter and Consortium, IMAGEN}, - month = may, - year = {2016}, - pages = {192--202}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {UnatiPMID: 26679926}, -} - -@article{jurk_personality_2015, - title = {Personality and {Substance} {Use}: {Psychometric} {Evaluation} and {Validation} of the {Substance} {Use} {Risk} {Profile} {Scale} ({SURPS}) in {English}, {Irish}, {French}, and {German} {Adolescents}}, - volume = {39}, - issn = {0145-6008}, - doi = {10.1111/acer.12886}, - number = {11}, - journal = {ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH}, - author = {Jurk, Sarah and Kuitunen-Paul, Soeren and Kroemer, Nils B. and Artiges, Eric and Banaschewski, Tobias and Bokde, Arun L. W. and Buechel, Christian and Conrod, Patricia and Fauth-Buehler, Mira and Flor, Herta and Frouin, Vincent and Gallinat, Juergen and Garavan, Hugh and Heinz, Andreas and Mann, Karl F. and Nees, Frauke and Paus, Tomas and Pausova, Zdenka and Poustka, Luise and Rietschel, Marcella and Schumann, Gunter and Struve, Maren and Smolka, Michael N. and Consortium, IMAGEN}, - month = nov, - year = {2015}, - keywords = {Psychometrics, Confirmatory Factor Analysis, Personality, Substance Use}, - pages = {2234--2248}, - annote = {The following values have no corresponding Zotero field:number: 11label: ACL}, - annote = {UnatiPMID: 26463560}, -} - -@article{loth_eu-aims_2017, - title = {The {EU}-{AIMS} {Longitudinal} {European} {Autism} {Project} ({LEAP}): design and methodologies to identify and validate stratification biomarkers for autism spectrum disorders}, - volume = {8}, - issn = {2040-2392}, - shorttitle = {The {EU}-{AIMS} {Longitudinal} {European} {Autism} {Project} ({LEAP})}, - doi = {10.1186/s13229-017-0146-8}, - abstract = {BACKGROUND: The tremendous clinical and aetiological diversity among individuals with autism spectrum disorder (ASD) has been a major obstacle to the development of new treatments, as many may only be effective in particular subgroups. Precision medicine approaches aim to overcome this challenge by combining pathophysiologically based treatments with stratification biomarkers that predict which treatment may be most beneficial for particular individuals. However, so far, we have no single validated stratification biomarker for ASD. This may be due to the fact that most research studies primarily have focused on the identification of mean case-control differences, rather than within-group variability, and included small samples that were underpowered for stratification approaches. The EU-AIMS Longitudinal European Autism Project (LEAP) is to date the largest multi-centre, multi-disciplinary observational study worldwide that aims to identify and validate stratification biomarkers for ASD. -METHODS: LEAP includes 437 children and adults with ASD and 300 individuals with typical development or mild intellectual disability. Using an accelerated longitudinal design, each participant is comprehensively characterised in terms of clinical symptoms, comorbidities, functional outcomes, neurocognitive profile, brain structure and function, biochemical markers and genomics. In addition, 51 twin-pairs (of which 36 had one sibling with ASD) are included to identify genetic and environmental factors in phenotypic variability. -RESULTS: Here, we describe the demographic characteristics of the cohort, planned analytic stratification approaches, criteria and steps to validate candidate stratification markers, pre-registration procedures to increase transparency, standardisation and data robustness across all analyses, and share some 'lessons learnt'. A clinical characterisation of the cohort is given in the companion paper (Charman et al., accepted). -CONCLUSION: We expect that LEAP will enable us to confirm, reject and refine current hypotheses of neurocognitive/neurobiological abnormalities, identify biologically and clinically meaningful ASD subgroups, and help us map phenotypic heterogeneity to different aetiologies.}, - language = {eng}, - journal = {Molecular Autism}, - author = {Loth, Eva and Charman, Tony and Mason, Luke and Tillmann, Julian and Jones, Emily J. H. and Wooldridge, Caroline and Ahmad, Jumana and Auyeung, Bonnie and Brogna, Claudia and Ambrosino, Sara and Banaschewski, Tobias and Baron-Cohen, Simon and Baumeister, Sarah and Beckmann, Christian and Brammer, Michael and Brandeis, Daniel and Bölte, Sven and Bourgeron, Thomas and Bours, Carsten and de Bruijn, Yvette and Chakrabarti, Bhismadev and Crawley, Daisy and Cornelissen, Ineke and Acqua, Flavio Dell' and Dumas, Guillaume and Durston, Sarah and Ecker, Christine and Faulkner, Jessica and Frouin, Vincent and Garces, Pilar and Goyard, David and Hayward, Hannah and Ham, Lindsay M. and Hipp, Joerg and Holt, Rosemary J. and Johnson, Mark H. and Isaksson, Johan and Kundu, Prantik and Lai, Meng-Chuan and D'ardhuy, Xavier Liogier and Lombardo, Michael V. and Lythgoe, David J. and Mandl, René and Meyer-Lindenberg, Andreas and Moessnang, Carolin and Mueller, Nico and O'Dwyer, Laurence and Oldehinkel, Marianne and Oranje, Bob and Pandina, Gahan and Persico, Antonio M. and Ruigrok, Amber N. V. and Ruggeri, Barbara and Sabet, Jessica and Sacco, Roberto and Cáceres, Antonia San José and Simonoff, Emily and Toro, Roberto and Tost, Heike and Waldman, Jack and Williams, Steve C. R. and Zwiers, Marcel P. and Spooren, Will and Murphy, Declan G. M. and Buitelaar, Jan K.}, - year = {2017}, - pmid = {28649312}, - pmcid = {PMC5481887}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, MRI, Neuroimaging, Phenotype, Adult, Child, Female, Male, Longitudinal Studies, Cognition, Genetics, Individuality, Patient Selection, Biomarkers, Precision Medicine, Autism Spectrum Disorder, EEG, Eye Movement Measurements, Eye-tracking, Genetic Heterogeneity, Hair, Saliva, Siblings, ABNORMAL-DEVELOPMENT, ANIMATED SHAPES, Author Keywords:Biomarkers, DEVELOPMENTAL TRAJECTORIES, EXECUTIVE DYSFUNCTION, FUNCTIONING AUTISM, GENETIC-VARIATION, KeyWords Plus:ASPERGER-SYNDROME, REPETITIVE BEHAVIOR, SEX-DIFFERENCES, SOCIAL-BEHAVIOR}, - pages = {24}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UnatiDOI: 10.1186/s13229-017-0146-8}, - annote = {WOS:000404099400001}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZJEIKTF4/Loth et al. - 2017 - The EU-AIMS Longitudinal European Autism Project (.pdf:application/pdf}, -} - -@article{orlhac_postreconstruction_2018, - title = {A {Postreconstruction} {Harmonization} {Method} for {Multicenter} {Radiomic} {Studies} in {PET}}, - volume = {59}, - issn = {1535-5667}, - doi = {10.2967/jnumed.117.199935}, - abstract = {Several reports have shown that radiomic features are affected by acquisition and reconstruction parameters, thus hampering multicenter studies. We propose a method that, by removing the center effect while preserving patient-specific effects, standardizes features measured from PET images obtained using different imaging protocols. Methods: Pretreatment 18F-FDG PET images of patients with breast cancer were included. In one nuclear medicine department (department A), 63 patients were scanned on a time-of-flight PET/CT scanner, and 16 lesions were triple-negative (TN). In another nuclear medicine department (department B), 74 patients underwent PET/CT on a different brand of scanner and a different reconstruction protocol, and 15 lesions were TN. The images from department A were smoothed using a gaussian filter to mimic data from a third department (department A-S). The primary lesion was segmented to obtain a lesion volume of interest (VOI), and a spheric VOI was set in healthy liver tissue. Three SUVs and 6 textural features were computed in all VOIs. A harmonization method initially described for genomic data was used to estimate the department effect based on the observed feature values. Feature distributions in each department were compared before and after harmonization. Results: In healthy liver tissue, the distributions significantly differed for 4 of 9 features between departments A and B and for 6 of 9 between departments A and A-S (P {\textless} 0.05, Wilcoxon test). After harmonization, none of the 9 feature distributions significantly differed between 2 departments (P {\textgreater} 0.1). The same trend was observed in lesions, with a realignment of feature distributions between the departments after harmonization. Identification of TN lesions was largely enhanced after harmonization when the cutoffs were determined on data from one department and applied to data from the other department. Conclusion: The proposed harmonization method is efficient at removing the multicenter effect for textural features and SUVs. The method is easy to use, retains biologic variations not related to a center effect, and does not require any feature recalculation. Such harmonization allows for multicenter studies and for external validation of radiomic models or cutoffs and should facilitate the use of radiomic models in clinical practice.}, - language = {eng}, - number = {8}, - journal = {Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine}, - author = {Orlhac, Fanny and Boughdad, Sarah and Philippe, Cathy and Stalla-Bourdillon, Hugo and Nioche, Christophe and Champion, Laurence and Soussan, Michaël and Frouin, Frédérique and Frouin, Vincent and Buvat, Irène}, - month = aug, - year = {2018}, - pmid = {29301932}, - keywords = {PET, harmonization, radiomics, texture analysis, tumor heterogeneity}, - pages = {1321--1328}, - annote = {MEDLINE:29301932}, - annote = {MEDLINE:29301932}, -} - -@article{de_pierrefeu_structured_2018, - title = {Structured {Sparse} {Principal} {Components} {Analysis} {With} the {TV}-{Elastic} {Net} {Penalty}}, - volume = {37}, - issn = {1558-254X}, - doi = {10.1109/TMI.2017.2749140}, - abstract = {Principal component analysis (PCA) is an exploratory tool widely used in data analysis to uncover the dominant patterns of variability within a population. Despite its ability to represent a data set in a low-dimensional space, PCA's interpretability remains limited. Indeed, the components produced by PCA are often noisy or exhibit no visually meaningful patterns. Furthermore, the fact that the components are usually non-sparse may also impede interpretation, unless arbitrary thresholding is applied. However, in neuroimaging, it is essential to uncover clinically interpretable phenotypic markers that would account for the main variability in the brain images of a population. Recently, some alternatives to the standard PCA approach, such as sparse PCA (SPCA), have been proposed, their aim being to limit the density of the components. Nonetheless, sparsity alone does not entirely solve the interpretability problem in neuroimaging, since it may yield scattered and unstable components. We hypothesized that the incorporation of prior information regarding the structure of the data may lead to improved relevance and interpretability of brain patterns. We therefore present a simple extension of the popular PCA framework that adds structured sparsity penalties on the loading vectors in order to identify the few stable regions in the brain images that capture most of the variability. Such structured sparsity can be obtained by combining, e.g., and total variation (TV) penalties, where the TV regularization encodes information on the underlying structure of the data. This paper presents the structured SPCA (denoted SPCA-TV) optimization framework and its resolution. We demonstrate SPCA-TV's effectiveness and versatility on three different data sets. It can be applied to any kind of structured data, such as, e.g., -dimensional array images or meshes of cortical surfaces. The gains of SPCA-TV over unstructured approaches (such as SPCA and ElasticNet PCA) or structured approach (such as GraphNet PCA) are significant, since SPCA-TV reveals the variability within a data set in the form of intelligible brain patterns that are easier to interpret and more stable across different samples.}, - language = {eng}, - number = {2}, - journal = {IEEE Transactions on Medical Imaging}, - author = {de Pierrefeu, Amicie and Lofstedt, Tommy and Hadj-Selem, Fouad and Dubois, Mathieu and Jardri, Renaud and Fovet, Thomas and Ciuciu, Philippe and Frouin, Vincent and Duchesnay, Edouard}, - year = {2018}, - pmid = {28880163}, - keywords = {Loading, Minimization, MRI, Optimization, PCA, Principal Component Analysis, Sociology, total variation, TV, unsupervisedmachine learning}, - pages = {396--407}, - annote = {WOS:000424467000006}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VFGT57HH/de Pierrefeu et al. - 2018 - Structured Sparse Principal Components Analysis Wi.pdf:application/pdf;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BPA4ESHX/8025614.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TIGGBPKW/Pierrefeu et al. - 2018 - Structured Sparse Principal Components Analysis Wi.pdf:application/pdf}, -} - -@article{hadj-selem_continuation_2018, - title = {Continuation of {Nesterov}'s {Smoothing} for {Regression} {With} {Structured} {Sparsity} in {High}-{Dimensional} {Neuroimaging}}, - volume = {37}, - issn = {1558-254X}, - doi = {10.1109/TMI.2018.2829802}, - abstract = {Predictive models can be used on high-dimensional brain images to decode cognitive states or diagnosis/prognosis of a clinical condition/evolution. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total variation (TV) is a promising candidate for structured penalization: it enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties. However, reasonable precision requires a small smoothing parameter, which slows down the convergence speed to unacceptable levels. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed toward any globally desired precision. Our main contributions are: gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the To propose an expression of the duality convergence speed. This expression is applicable to many penalties and can be used with other solvers than CONESTA. We also propose an expression for the particular smoothing parameter that minimizes the number of iterations required to reach a given precision. Furthermore, we provide a convergence proof and its rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.}, - language = {eng}, - number = {11}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Hadj-Selem, Fouad and Lofstedt, Tommy and Dohmatob, Elvis and Frouin, Vincent and Dubois, Mathieu and Guillemot, Vincent and Duchesnay, Edouard}, - month = nov, - year = {2018}, - pmid = {29993684}, - keywords = {TV, Prediction, Statistics - Machine Learning, Machine Learning, Convergence, Smoothing methods, Convex Optimization, Signature, Structured Sparsity, Three-dimensional displays}, - pages = {2403--2413}, - annote = {arXiv: 1605.09658}, - annote = {Comment: 11 pages, 6 figures, preprint}, - annote = {Comment: 34 pages, 4 figures, preprint}, - file = {arXiv\:1605.09658 PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7HU2Q2HU/Hadj-Selem et al. - 2016 - Iterative Smoothing Proximal Gradient for Regressi.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BM7TDIAZ/1605.html:text/html;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GY6AU69K/1605.html:text/html;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7PKLCQVW/8345691.html:text/html;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ULK3JG9T/Hadj-Selem et al. - 2018 - Continuation of Nesterov's Smoothing for Regressio.pdf:application/pdf}, -} - -@inproceedings{dubois_predictive_2014, - title = {Predictive support recovery with {TV}-{Elastic} {Net} penalty and logistic regression: {An} application to structural {MRI}}, - copyright = {All rights reserved}, - shorttitle = {Predictive support recovery with {TV}-{Elastic} {Net} penalty and logistic regression}, - doi = {10.1109/PRNI.2014.6858517}, - abstract = {The use of machine-learning in neuroimaging offers new perspectives in early diagnosis and prognosis of brain diseases. Although such multivariate methods can capture complex relationships in the data, traditional approaches provide irregular (ℓ2 penalty) or scattered (ℓ1 penalty) predictive pattern with a very limited relevance. A penalty like Total Variation (TV) that exploits the natural 3D structure of the images can increase the spatial coherence of the weight map. However, TV penalization leads to non-smooth optimization problems that are hard to minimize. We propose an optimization framework that minimizes any combination of ℓ1, ℓ2, and TV penalties while preserving the exact ℓ1 penalty. This algorithm uses Nesterov's smoothing technique to approximate the TV penalty with a smooth function such that the loss and the penalties are minimized with an exact accelerated proximal gradient algorithm. We propose an original continuation algorithm that uses successively smaller values of the smoothing parameter to reach a prescribed precision while achieving the best possible convergence rate. This algorithm can be used with other losses or penalties. The algorithm is applied on a classification problem on the ADNI dataset. We observe that the TV penalty does not necessarily improve the prediction but provides a major breakthrough in terms of support recovery of the predictive brain regions.}, - author = {Dubois, M. and Hadj-Selem, F. and Löfstedt, T. and Perrot, M. and Fischer, C. and Frouin, V. and Duchesnay, E.}, - month = jun, - year = {2014}, - note = {tex.ids: dubois2014predictive -tex.organization: IEEE}, - keywords = {biomedical MRI, Brain, diseases, image classification, learning (artificial intelligence), Machine learning, medical image processing, structural MRI, machine learning, Neuroimaging, logistic regression, Prognosis, regression analysis, optimisation, Vectors, Approximation algorithms, Prediction algorithms, ADNI dataset, brain, brain diseases, classification problem, complex data relationships, Convergence, diagnosis, exact accelerated proximal gradient algorithm, irregular ℓ2 penalty, irregular ℓ2penalty, Logistics, multivariate methods, natural 3D structure, Nesterov smoothing technique, neuroimaging, neurophysiology, nonsmooth optimization problems, penalty-like total variation, predictive brain regions, predictive support recovery, prognosis, scattered l1 penalty, scattered ℓ1 penalty, scattered ℓ1penalty, smoothing methods, Smoothing methods, spatial coherence, TV-elastic net penalty}, - pages = {1--4}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QXSFJSQN/6858517.html:text/html;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZHPJBMRV/6858517.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NZC9QLSH/Dubois et al. - 2014 - Predictive support recovery with TV-Elastic Net pe.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/247ZIIIT/Dubois et al. - 2014 - Predictive support recovery with TV-Elastic Net pe.pdf:application/pdf}, -} - -@inproceedings{fouque_comparison_2013, - title = {Comparison of {Features} for {Voxel}-{Based} {Analysis} and {Classification} of {Anatomical} {Neuroimaging} {Data}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-0-7695-5061-9}, - url = {http://dl.acm.org/citation.cfm?id=2552484.2552547}, - doi = {10.1109/PRNI.2013.55}, - booktitle = {2013 {International} {Workshop} on {Pattern} {Recognition} in {Neuroimaging}}, - publisher = {IEEE}, - author = {Fouque, Anne-Laure and Fischer, Clara and Frouin, Vincent and Ciuciu, Philippe and Duchesnay, Edouard}, - month = jun, - year = {2013}, - keywords = {MRI, conference, classification, group analysis}, - pages = {186--189}, -} - -@inproceedings{le_floch_discovering_2012, - title = {Discovering associations in high dimensional imaging-genetics data: {A} comparison study of dimension reduction and regularisation strategies combined with partial least squares}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {International {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Le Floch, Edith and Pinel, Philippe and Tenenhaus, Arthur and Trinchera, Laura and Poline, Jean-Baptiste and Frouin, Vincent and Duchesnay, Edouard}, - year = {2012}, - keywords = {conference}, - pages = {1503--1506}, -} - -@article{dubois_automated_2007, - title = {Automated three-dimensional analysis of histological and autoradiographic rat brain sections: application to an activation study}, - volume = {27}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {0271-678X}, - shorttitle = {Automated three-dimensional analysis of histological and autoradiographic rat brain sections}, - doi = {10.1038/sj.jcbfm.9600470}, - abstract = {Besides the newly developed positron emission tomography scanners (microPET) dedicated to the in vivo functional study of small animals, autoradiography remains the reference technique widely used for functional brain imaging and the gold standard for the validation of in vivo results. The analysis of autoradiographic data is classically achieved in two dimensions (2D) using a section-by-section approach, is often limited to few sections and the delineation of the regions of interest to be analysed is directly performed on autoradiographic sections. In addition, such approach of analysis does not accommodate the possible anatomical shifts linked to dissymmetry associated with the sectioning process. This classic analysis is time-consuming, operator-dependent and can therefore lead to non-objective and non-reproducible results. In this paper, we have developed an automated and generic toolbox for processing of autoradiographic and corresponding histological rat brain sections based on a three-step approach, which involves: (1) an optimized digitization dealing with hundreds of autoradiographic and histological sections; (2) a robust reconstruction of the volumes based on a reliable registration method; and (3) an original 3D-geometry-based approach to analysis of anatomical and functional post-mortem data. The integration of the toolbox under a unified environment (in-house software BrainVISA, http://brainvisa.info) with a graphic interface enabled a robust and operator-independent exploitation of the overall anatomical and functional information. We illustrated the substantial qualitative and quantitative benefits obtained by applying our methodology to an activation study (rats, n=5, under unilateral visual stimulation).}, - language = {eng}, - number = {10}, - journal = {Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism}, - author = {Dubois, Albertine and Dauguet, Julien and Herard, Anne-Sophie and Besret, Laurent and Duchesnay, Edouard and Frouin, Vincent and Hantraye, Philippe and Bonvento, Gilles and Delzescaux, Thierry}, - month = oct, - year = {2007}, - pmid = {17377517}, - keywords = {Brain, Imaging, Three-Dimensional, Animals, Autoradiography, Rats}, - pages = {1742--1755}, - annote = {The following values have no corresponding Zotero field:number: 10label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/ADubois-JCBFM07.pdfarticle}, -} - -@article{habert_evaluation_2018, - title = {Evaluation of amyloid status in a cohort of elderly individuals with memory complaints: validation of the method of quantification and determination of positivity thresholds}, - volume = {32}, - issn = {1864-6433}, - shorttitle = {Evaluation of amyloid status in a cohort of elderly individuals with memory complaints}, - url = {https://doi.org/10.1007/s12149-017-1221-0}, - doi = {10.1007/s12149-017-1221-0}, - abstract = {Our aim is to validate the process steps implemented by the French CATI platform to assess amyloid status, obtained from 18F-Florbetapir PET scans, in a cohort of 318 cognitively normal subjects participating in the INSIGHT-preAD study. Our objective was to develop a method with partial volume effect correction (PVEC) on untransformed PET images, using an automated pipeline (“RACHEL”) adapted to large series of patients and including quality checks of results.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Annals of Nuclear Medicine}, - author = {Habert, Marie-Odile and Bertin, Hugo and Labit, Mickael and Diallo, Mamadou and Marie, Sullivan and Martineau, Kelly and Kas, Aurélie and Causse-Lemercier, Valérie and Bakardjian, Hovagim and Epelbaum, Stéphane and Chételat, Gael and Houot, Marion and Hampel, Harald and Dubois, Bruno and Mangin, Jean-François and Audrain, C. and Bakardjian, H. and Benali, H. and Bertin, H. and Boukadida, L. and Cacciamani, F. and Causse-Lemercier, V. and Cavedo, E. and Chiesa, P. and Colliot, O. and Dos Santos, A. and Dubois, B. and Durrleman, S. and Epelbaum, S. and Gagliardi, G. and Genthon, R. and Habert, M.-O. and Hampel, H. and Jungalee, N. and Kas, A. and Lehericy, S. and Lamari, F. and Letondor, C. and Levy, M. and Lista, S. and Mochel, F. and Nyasse, F. and Poisson, C. and Potier, M. C. and Revillon, M. and Rojkova, K. and Roy, P. and Santos-Andrade, K. and Santos, A. and Simon, V. and Sole, M. and Tandetnik, C. and Thiebaud De Schotten, M. and {INSIGHT-AD study group}}, - month = feb, - year = {2018}, - keywords = {Humans, Software, Neuroimaging, Image Processing, Computer-Assisted, Reference Values, Adolescent, Child, Female, Male, Reaction Time, Positron-Emission Tomography, Aged, Cognition, Attention Deficit Disorder with Hyperactivity, Memory, Prefrontal Cortex, Alzheimer’s disease, Amyloid, 18F-Florbetapir, Amyloid burden quantification, Brain PET, Aniline Compounds, Ethylene Glycols, Attention-deficit/hyperactivity disorder, Inattention, Multi-informant, Reaction time variability, Ventromedial prefrontal cortex}, - pages = {75--86}, - annote = {MEDLINE:29633962}, - annote = {MEDLINE:29633962}, - file = {Accepted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/42XN2KUL/Albaugh et al. - 2017 - Inattention and Reaction Time Variability Are Link.pdf:application/pdf}, -} - -@article{le_guen_genetic_2018, - title = {Genetic {Influence} on the {Sulcal} {Pits}: {On} the {Origin} of the {First} {Cortical} {Folds}}, - volume = {28}, - issn = {1047-3211}, - shorttitle = {Genetic {Influence} on the {Sulcal} {Pits}}, - url = {https://doi.org/10.1093/cercor/bhx098}, - doi = {10.1093/cercor/bhx098}, - abstract = {The influence of genes on cortical structures has been assessed through various phenotypes. The sulcal pits, which are the putative first cortical folds, have for long been assumed to be under tight genetic control, but this was never quantified. We estimated the pit depth heritability in various brain regions using the high quality and large sample size of the Human Connectome Project pedigree cohort. Analysis of additive genetic variance indicated that their heritability ranges between 0.2 and 0.5 and displays a regional genetic control with an overall symmetric pattern between hemispheres. However, a noticeable asymmetry of heritability estimates is observed in the superior temporal sulcus and could thus be related to language lateralization. The heritability range estimated in this study reinforces the idea that cortical shape is determined primarily by nongenetic factors, which is consistent with the important increase of cortical folding from birth to adult life and thus predominantly constrained by environmental factors. Nevertheless, the genetic cues, implicated with various local levels of heritability in the formation of sulcal pits, play a fundamental role in the normal gyral pattern development. Quantifying their influence and identifying the underlying genetic variants would provide insight into neurodevelopmental disorders.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Le Guen, Yann and Auzias, Guillaume and Leroy, François and Noulhiane, Marion and Dehaene-Lambertz, Ghislaine and Duchesnay, Edouard and Mangin, Jean-François and Coulon, Olivier and Frouin, Vincent}, - month = jun, - year = {2018}, - keywords = {imaging-genetic, sulcal pits, STS, brain asymmetry}, - pages = {1922--1933}, - annote = {MEDLINE:28444225}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati}, - annote = {UnicogPMID: 28444225}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/54XH832D/Le Guen et al. - 2018 - Genetic Influence on the Sulcal Pits On the Origi.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IW6UP4ZS/Genetic-Influence-on-the-Sulcal-Pits-On-the-Origin.html:text/html}, -} - -@inproceedings{le_guen_heritability_2019, - title = {Heritability of surface area and cortical thickness: a comparison between the {Human} {Connectome} {Project} and the {UK} {Biobank} dataset}, - shorttitle = {Heritability of surface area and cortical thickness}, - url = {https://ieeexplore.ieee.org/abstract/document/8759539}, - doi = {10.1109/ISBI.2019.8759539}, - abstract = {Heritability of the regional thickness/surface in human cortex is established. Yet the estimates vary substantially depending on cohorts or the information they are derived from: pedigree or genotyping. Here we present three heritability studies of the cortex phenotype in two cohorts showing: i) both pedigree and genotyping or ii) genotyping only. We obtained clearly correlated heritability values between studies with a shift appearing between cohorts. Spatial pattern of heritability remains highly consistent across cohorts.}, - urldate = {2024-03-12}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Le Guen, Yann and Karkar, Slim and Grigis, Antoine and Philippe, Cathy and Mangin, Jean-François and Frouin, Vincent}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {Sociology, Statistics, Magnetic resonance imaging, heritability, imaging-genetic, cortical thickness, Genomics, Bioinformatics, surface area}, - pages = {1887--1890}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FC8YYEQ4/Le Guen et al. - 2019 - Heritability of surface area and cortical thicknes.pdf:application/pdf}, -} - -@article{karkar_genome-wide_2021, - title = {Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 {UK} {Biobank} subjects}, - volume = {29}, - copyright = {2021 The Author(s)}, - issn = {1476-5438}, - url = {https://www.nature.com/articles/s41431-021-00827-8}, - doi = {10.1038/s41431-021-00827-8}, - abstract = {Neuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome-wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a single block, while the last approach considers each haplotype independently. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {European Journal of Human Genetics}, - author = {Karkar, Slim and Dandine-Roulland, Claire and Mangin, Jean-François and Le Guen, Yann and Philippe, Cathy and Deleuze, Jean-François and Pierre-Jean, Morgane and Le Floch, Edith and Frouin, Vincent}, - month = sep, - year = {2021}, - note = {Publisher: Nature Publishing Group}, - keywords = {Magnetic resonance imaging, Predictive markers, Genetics of the nervous system, Genome-wide association studies, Haplotypes}, - pages = {1424--1437}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RD2URD5E/Karkar et al. - 2021 - Genome-wide haplotype association study in imaging.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/2RCWDAQX/Karkar et al. - 2021 - Genome-wide haplotype association study in imaging.pdf:application/pdf}, -} - -@article{chegraoui_integrating_2023, - title = {Integrating multiomics and prior knowledge: a study of the {Graphnet} penalty impact}, - volume = {39}, - issn = {1367-4811}, - shorttitle = {Integrating multiomics and prior knowledge}, - url = {https://doi.org/10.1093/bioinformatics/btad454}, - doi = {10.1093/bioinformatics/btad454}, - abstract = {In the field of oncology, statistical models are used for the discovery of candidate factors that influence the development of the pathology or its outcome. These statistical models can be designed in a multiblock framework to study the relationship between different multiomic data, and variable selection is often achieved by imposing constraints on the model parameters. A priori graph constraints have been used in the literature as a way to improve feature selection in the model, yielding more interpretability. However, it is still unclear how these graphs interact with the models and how they impact the feature selection. Additionally, with the availability of different graphs encoding different information, one can wonder how the choice of the graph meaningfully impacts the results obtained.We proposed to study the graph penalty impact on a multiblock model. Specifically, we used the SGCCA as the multiblock framework. We studied the effect of the penalty on the model using the TCGA-LGG dataset. Our findings are 3-fold. We showed that the graph penalty increases the number of selected genes from this dataset, while selecting genes already identified in other works as pertinent biomarkers in the pathology. We demonstrated that using different graphs leads to different though consistent results, but that graph density is the main factor influencing the obtained results. Finally, we showed that the graph penalty increases the performance of the survival prediction from the model-derived components and the interpretability of the results.Source code is freely available at https://github.com/neurospin/netSGCCA}, - number = {8}, - urldate = {2023-09-07}, - journal = {Bioinformatics}, - author = {Chegraoui, Hamza and Guillemot, Vincent and Rebei, Amine and Gloaguen, Arnaud and Grill, Jacques and Philippe, Cathy and Frouin, Vincent}, - month = aug, - year = {2023}, - pages = {btad454}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/85U67P26/Chegraoui et al. - 2023 - Integrating multiomics and prior knowledge a stud.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EQ53VG6M/7230780.html:text/html}, -} - -@article{khalid_multimodal_2023, - title = {Multimodal {MRI} radiomic models to predict genomic mutations in diffuse intrinsic pontine glioma with missing imaging modalities}, - volume = {10}, - issn = {2296-858X}, - url = {https://www.frontiersin.org/articles/10.3389/fmed.2023.1071447}, - abstract = {PurposePredicting H3.1, TP53, and ACVR1 mutations in DIPG could aid in the selection of therapeutic options. The contribution of clinical data and multi-modal MRI were studied for these three predictive tasks. To keep the maximum number of subjects, which is essential for a rare disease, missing data were considered. A multi-modal model was proposed, collecting all available data for each patient, without performing any imputation.MethodsA retrospective cohort of 80 patients with confirmed DIPG and at least one of the four MR modalities (T1w, T1c, T2w, and FLAIR), acquired with two different MR scanners was built. A pipeline including standardization of MR data and extraction of radiomic features within the tumor was applied. The values of radiomic features between the two MR scanners were realigned using the ComBat method. For each prediction task, the most robust features were selected based on a recursive feature elimination with cross-validation. Five different models, one based on clinical data and one per MR modality, were developed using logistic regression classifiers. The prediction of the multi-modal model was defined as the average of all possible prediction results among five for each patient. The performances of the models were compared using a leave-one-out approach.ResultsThe percentage of missing modalities ranged from 6 to 11\% across modalities and tasks. The performance of each individual model was dependent on each specific task, with an AUC of the ROC curve ranging from 0.63 to 0.80. The multi-modal model outperformed the clinical model for each prediction tasks, thus demonstrating the added value of MRI. Furthermore, regardless of performance criteria, the multi-modal model came in the first place or second place (very close to first). In the leave-one-out approach, the prediction of H3.1 (resp. ACVR1 and TP53) mutations achieved a balanced accuracy of 87.8\% (resp. 82.1 and 78.3\%).ConclusionCompared with a single modality approach, the multi-modal model combining multiple MRI modalities and clinical features was the most powerful to predict H3.1, ACVR1, and TP53 mutations and provided prediction, even in the case of missing modality. It could be proposed in the absence of a conclusive biopsy.}, - urldate = {2023-09-07}, - journal = {Frontiers in Medicine}, - author = {Khalid, Fahad and Goya-Outi, Jessica and Escobar, Thibault and Dangouloff-Ros, Volodia and Grigis, Antoine and Philippe, Cathy and Boddaert, Nathalie and Grill, Jacques and Frouin, Vincent and Frouin, Frédérique}, - year = {2023}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/V2SE87HW/Khalid et al. - 2023 - Multimodal MRI radiomic models to predict genomic .pdf:application/pdf}, -} - -@article{mekki_genetic_2022, - title = {The genetic architecture of language functional connectivity}, - volume = {249}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921010661}, - doi = {10.1016/j.neuroimage.2021.118795}, - abstract = {Language is a unique trait of the human species, of which the genetic architecture remains largely unknown. Through language disorders studies, many candidate genes were identified. However, such complex and multifactorial trait is unlikely to be driven by only few genes and case-control studies, suffering from a lack of power, struggle to uncover significant variants. In parallel, neuroimaging has significantly contributed to the understanding of structural and functional aspects of language in the human brain and the recent availability of large scale cohorts like UK Biobank have made possible to study language via image-derived endophenotypes in the general population. Because of its strong relationship with task-based fMRI (tbfMRI) activations and its easiness of acquisition, resting-state functional MRI (rsfMRI) have been more popularised, making it a good surrogate of functional neuronal processes. Taking advantage of such a synergistic system by aggregating effects across spatially distributed traits, we performed a multivariate genome-wide association study (mvGWAS) between genetic variations and resting-state functional connectivity (FC) of classical brain language areas in the inferior frontal (pars opercularis, triangularis and orbitalis), temporal and inferior parietal lobes (angular and supramarginal gyri), in 32,186 participants from UK Biobank. Twenty genomic loci were found associated with language FCs, out of which three were replicated in an independent replication sample. A locus in 3p11.1, regulating EPHA3 gene expression, is found associated with FCs of the semantic component of the language network, while a locus in 15q14, regulating THBS1 gene expression is found associated with FCs of the perceptual-motor language processing, bringing novel insights into the neurobiology of language.}, - language = {en}, - urldate = {2023-02-06}, - journal = {NeuroImage}, - author = {Mekki, Yasmina and Guillemot, Vincent and Lemaître, Hervé and Carrión-Castillo, Amaia and Forkel, Stephanie and Frouin, Vincent and Philippe, Cathy}, - month = apr, - year = {2022}, - keywords = {GWAS, Imaging-genetics, Language, Multivariate analysis, Resting-state functional MRI, UK Biobank}, - pages = {118795}, -} - -@article{gloaguen_multiway_2022, - title = {Multiway generalized canonical correlation analysis}, - volume = {23}, - issn = {1465-4644}, - url = {https://doi.org/10.1093/biostatistics/kxaa010}, - doi = {10.1093/biostatistics/kxaa010}, - abstract = {Regularized generalized canonical correlation analysis (RGCCA) is a general multiblock data analysis framework that encompasses several important multivariate analysis methods such as principal component analysis, partial least squares regression, and several versions of generalized canonical correlation analysis. In this article, we extend RGCCA to the case where at least one block has a tensor structure. This method is called multiway generalized canonical correlation analysis (MGCCA). Convergence properties of the MGCCA algorithm are studied, and computation of higher-level components are discussed. The usefulness of MGCCA is shown on simulation and on the analysis of a cognitive study in human infants using electroencephalography (EEG).}, - number = {1}, - urldate = {2023-02-06}, - journal = {Biostatistics}, - author = {Gloaguen, Arnaud and Philippe, Cathy and Frouin, Vincent and Gennari, Giulia and Dehaene-Lambertz, Ghislaine and Le Brusquet, Laurent and Tenenhaus, Arthur}, - month = jan, - year = {2022}, - pages = {240--256}, -} - -@article{lemaitre_genetic_2023, - title = {Genetic variations within human gained enhancer elements affect human brain sulcal morphology}, - volume = {265}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922008941}, - doi = {10.1016/j.neuroimage.2022.119773}, - abstract = {The expansion of the cerebral cortex is one of the most distinctive changes in the evolution of the human brain. Cortical expansion and related increases in cortical folding may have contributed to emergence of our capacities for high-order cognitive abilities. Molecular analysis of humans, archaic hominins, and non-human primates has allowed identification of chromosomal regions showing evolutionary changes at different points of our phylogenetic history. In this study, we assessed the contributions of genomic annotations spanning 30 million years to human sulcal morphology measured via MRI in more than 18,000 participants from the UK Biobank. We found that variation within brain-expressed human gained enhancers, regulatory genetic elements that emerged since our last common ancestor with Old World monkeys, explained more trait heritability than expected for the left and right calloso-marginal posterior fissures and the right central sulcus. Intriguingly, these are sulci that have been previously linked to the evolution of locomotion in primates and later on bipedalism in our hominin ancestors.}, - language = {en}, - urldate = {2023-02-06}, - journal = {NeuroImage}, - author = {Lemaitre, Herve and Le Guen, Yann and Tilot, Amanda K. and Stein, Jason L. and Philippe, Cathy and Mangin, Jean-François and Fisher, Simon E. and Frouin, Vincent}, - month = jan, - year = {2023}, - keywords = {Neuroimaging, Evolution, Genome-wide association, Human gained enhancers, Sulcal morphology}, - pages = {119773}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Q5CPE88S/Lemaitre et al. - 2023 - Genetic variations within human gained enhancer el.pdf:application/pdf}, -} - -@inproceedings{beaudoin_etude_2022, - title = {Etude de la {Pénalisation} {GraphNet} en {Analyse} de {Données} {Multi}-blocs}, - url = {https://pasteur.hal.science/pasteur-04131938}, - abstract = {L'intégration de données multiblocs est maintenant incontournable pour analyser des données complexes allant, par exemple, des données multi-omiques, aux données d'imagerie génétique. Par ailleurs, les bases de données biologiques de référence contiennent maintenant une information très riche qu'il convient d'intégrer dans de telles analyses. Nous proposons d'explorer la méthode netSGCCA qui permet l'intégration de réseaux dans le cadre de l'Analyse des Corrélations Canonique Généralisée pénalisée à l'aide d'une pénalité GraphNet. Plus particulièrement, nous souhaitons mettre en lumière un des désavantages de cette pénalité, qui est d'introduire des composantes ``haute-fréquence''. L'exemple que nous étudions est issu d'une étude clinique sur la Spondylarthrite ankylosante et comprend trois blocs : deux blocs de données d'expression, et un bloc de données cliniques. Le réseau de référence que nous utilisons est extrait de la base de données STRING-DB. Nous montrons sur cet exemple un moyen de ne conserver que les éléments ``basse fréquence'' induits par l'introduction de la pénalité GraphNet.}, - language = {fr}, - urldate = {2023-09-07}, - author = {Beaudoin, Annabelle and Pietrosemoli, Natalia and Philippe, Cathy and Abdi, Hervé and Guillemot, Vincent}, - month = jun, - year = {2022}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/E4TBVVG7/pasteur-04131938.html:text/html}, -} - -@article{calmon_radiogenomics_2021, - title = {Radiogenomics of diffuse intrinsic pontine gliomas ({DIPGs}): correlation of histological and biological characteristics with multimodal {MRI} features}, - volume = {31}, - issn = {1432-1084}, - shorttitle = {Radiogenomics of diffuse intrinsic pontine gliomas ({DIPGs})}, - url = {https://doi.org/10.1007/s00330-021-07991-x}, - doi = {10.1007/s00330-021-07991-x}, - abstract = {The diffuse intrinsic pontine gliomas (DIPGs) are now defined by the type of histone H3 mutated at lysine 27. We aimed to correlate the multimodal MRI features of DIPGs, H3K27M mutant, with their histological and molecular characteristics.}, - language = {en}, - number = {12}, - urldate = {2023-02-06}, - journal = {European Radiology}, - author = {Calmon, Raphaël and Dangouloff-Ros, Volodia and Varlet, Pascale and Deroulers, Christophe and Philippe, Cathy and Debily, Marie-Anne and Castel, David and Beccaria, Kevin and Blauwblomme, Thomas and Grevent, David and Levy, Raphael and Roux, Charles-Joris and Purcell, Yvonne and Saitovitch, Ana and Zilbovicius, Monica and Dufour, Christelle and Puget, Stéphanie and Grill, Jacques and Boddaert, Nathalie}, - month = dec, - year = {2021}, - pages = {8913--8924}, -} - -@inproceedings{rebei_contribution_2021, - title = {Contribution {Of} {Imaging}-{Genetics} {To} {Overall} {Survival} {Prediction} {Compared} {To} {Clinical} {Status} {For} {Pcnsl} {Patients}}, - doi = {10.1109/ISBI48211.2021.9433785}, - abstract = {Accurately predicting the survival of patients with cancer has the potential to substantially enhance and customize the treatment strategies. Integrating and using all the patients' available data is essential to make the most accurate predictions. In this work, we gather clinical, imaging and genetic data into one mono-block multivariate survival analysis for patients with primary central nervous system lymphoma (PCNSL). As a first step, we select the best features from each pre-processed dataset. Then we assemble and use the resulting block to predict overall survival with a survival random forest algorithm. The assessment of the proposed method yielded a C-index of 0.776. We thus conclude that multimodal data integration significantly improves prediction performance.}, - booktitle = {2021 {IEEE} 18th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Rebei, Amine and Alentorn, Agusti and Chegraoui, Hamza and Frouin, Vincent and Philippe, Cathy}, - month = apr, - year = {2021}, - note = {ISSN: 1945-8452}, - keywords = {MRI, Survival analysis, Genetics, Prediction algorithms, Central nervous system, Cancer, Data integration, Brain Tumor, Focusing, imaging genetics, Tumors}, - pages = {832--835}, -} - -@inproceedings{chegraoui_prediction_2021, - title = {Prediction {Performance} of {Radiomic} {Features} {When} {Obtained} using an {Object} {Detection} {Framework}}, - doi = {10.1109/ISBI48211.2021.9434148}, - abstract = {Radiomic features analysis is a non invasive method for disease profiling. In the case of brain tumour studies, the quality of these features depends on the quality of tumour segmentation. However, these segmentations are not available for most cohorts. One way to address this issue is using object detection frameworks to automatically extract the area where the tumour is located in. The purpose of this study is to compare the quality of bounding-boxes based radiomics with manual segmentation, with regards to their performance in patient stratification and survival prediction.}, - booktitle = {2021 {IEEE} 18th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Chegraoui, Hamza and Rebei, Amine and Philippe, Cathy and Frouin, Vincent}, - month = apr, - year = {2021}, - note = {ISSN: 1945-8452}, - keywords = {Reliability, Image segmentation, Feature extraction, Object detection, Shape, Stability analysis, Tuning}, - pages = {1382--1385}, -} - -@inproceedings{guillemot_introducing_2021, - address = {Nice, France}, - title = {Introducing group-sparsity and orthogonality constraints in {RGCCA}}, - url = {https://hal.science/hal-03264640}, - abstract = {RGCCA-a fast and flexible method-generalizes many other well-known methods in order to analyze data-sets comprising multiple blocks of variables. Here we extend RGCCA by adding two new constraints to the RCCCA optimization problem: 1) group sparsity and 2) orthogonality of the block weight vectors. These two constraints facilitate the interpretability of the results when analyzing high dimensional data with a group structure. We illustrate this new method-called gSGCCA-with the analysis of pediatric high-grade glioma data: a set comprising three data blocks. This analysis shows that these new constraints greatly improve the interpretability of the statistical analysis.}, - urldate = {2023-09-07}, - booktitle = {{JdS2021} : 52èmes {Journées} de {Statistique}}, - author = {Guillemot, Vincent and Gloaguen, Arnaud and Tenenhaus, Arthur and Philippe, Cathy and Abdi, Hervé}, - month = jun, - year = {2021}, - keywords = {sparsity, RGCCA, group-sparsity, structure}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/KQN76C2N/Guillemot et al. - 2021 - Introducing group-sparsity and orthogonality const.pdf:application/pdf}, -} - -@article{chegraoui_object_2021, - title = {Object {Detection} {Improves} {Tumour} {Segmentation} in {MR} {Images} of {Rare} {Brain} {Tumours}}, - volume = {13}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - issn = {2072-6694}, - url = {https://www.mdpi.com/2072-6694/13/23/6113}, - doi = {10.3390/cancers13236113}, - abstract = {Tumour lesion segmentation is a key step to study and characterise cancer from MR neuroradiological images. Presently, numerous deep learning segmentation architectures have been shown to perform well on the specific tumour type they are trained on (e.g., glioblastoma in brain hemispheres). However, a high performing network heavily trained on a given tumour type may perform poorly on a rare tumour type for which no labelled cases allows training or transfer learning. Yet, because some visual similarities exist nevertheless between common and rare tumours, in the lesion and around it, one may split the problem into two steps: object detection and segmentation. For each step, trained networks on common lesions could be used on rare ones following a domain adaptation scheme without extra fine-tuning. This work proposes a resilient tumour lesion delineation strategy, based on the combination of established elementary networks that achieve detection and segmentation. Our strategy allowed us to achieve robust segmentation inference on a rare tumour located in an unseen tumour context region during training. As an example of a rare tumour, Diffuse Intrinsic Pontine Glioma (DIPG), we achieve an average dice score of 0.62 without further training or network architecture adaptation.}, - language = {en}, - number = {23}, - urldate = {2023-02-06}, - journal = {Cancers}, - author = {Chegraoui, Hamza and Philippe, Cathy and Dangouloff-Ros, Volodia and Grigis, Antoine and Calmon, Raphael and Boddaert, Nathalie and Frouin, Frédérique and Grill, Jacques and Frouin, Vincent}, - month = jan, - year = {2021}, - keywords = {segmentation, deep learning, brain tumour, DIPG, domain adaptation, object-detection}, - pages = {6113}, -} - -@article{di_stefano_clinical_2020, - title = {Clinical, molecular, and radiomic profile of gliomas with {FGFR3}-{TACC3} fusions}, - volume = {22}, - issn = {1522-8517}, - url = {https://doi.org/10.1093/neuonc/noaa121}, - doi = {10.1093/neuonc/noaa121}, - abstract = {Actionable fibroblast growth factor receptor 3 (FGFR3)–transforming acidic coiled-coil protein 3 fusions (F3T3) are found in approximately 3\% of gliomas, but their characteristics and prognostic significance are still poorly defined. Our goal was to characterize the clinical, radiological, and molecular profile of F3T3 positive diffuse gliomas.We screened F3T3 fusion by real-time (RT)-PCR and FGFR3 immunohistochemistry in a large series of gliomas, characterized for main genetic alterations, histology, and clinical evolution. We performed a radiological and radiomic case control study, using an exploratory and a validation cohort.We screened 1162 diffuse gliomas (951 unselected cases and 211 preselected for FGFR3 protein immunopositivity), identifying 80 F3T3 positive gliomas. F3T3 was mutually exclusive with IDH mutation (P \< 0.001) and EGFR amplification (P = 0.01), defining a distinct molecular cluster associated with CDK4 (P = 0.04) and MDM2 amplification (P = 0.03). F3T3 fusion was associated with longer survival for the whole series and for glioblastomas (median overall survival was 31.1 vs 19.9 mo, P = 0.02) and was an independent predictor of better outcome on multivariate analysis.F3T3 positive gliomas had specific MRI features, affecting preferentially insula and temporal lobe, and with poorly defined tumor margins. F3T3 fusion was correctly predicted by radiomics analysis on both the exploratory (area under the curve [AUC] = 0.87) and the validation MRI (AUC = 0.75) cohort. Using Cox proportional hazards models, radiomics predicted survival with a high C-index (0.75, SD 0.04), while the model combining clinical, genetic, and radiomic data showed the highest C-index (0.81, SD 0.04).F3T3 positive gliomas have distinct molecular and radiological features, and better outcome.}, - number = {11}, - urldate = {2023-09-07}, - journal = {Neuro-Oncology}, - author = {Di Stefano, Anna Luisa and Picca, Alberto and Saragoussi, Edouard and Bielle, Franck and Ducray, Francois and Villa, Chiara and Eoli, Marica and Paterra, Rosina and Bellu, Luisa and Mathon, Bertrand and Capelle, Laurent and Bourg, Véronique and Gloaguen, Arnaud and Philippe, Cathy and Frouin, Vincent and Schmitt, Yohann and Lerond, Julie and Leclerc, Julie and Lasorella, Anna and Iavarone, Antonio and Mokhtari, Karima and Savatovsky, Julien and Alentorn, Agusti and Sanson, Marc and {TARGET study group}}, - month = nov, - year = {2020}, - pages = {1614--1624}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/F298AVGG/Di Stefano et al. - 2020 - Clinical, molecular, and radiomic profile of gliom.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JMIIK3EH/5837595.html:text/html}, -} - -@article{le_guen_enhancer_2020, - title = {Enhancer {Locus} in ch14q23.1 {Modulates} {Brain} {Asymmetric} {Temporal} {Regions} {Involved} in {Language} {Processing}}, - volume = {30}, - issn = {1047-3211}, - url = {https://doi.org/10.1093/cercor/bhaa112}, - doi = {10.1093/cercor/bhaa112}, - abstract = {Identifying the genes that contribute to the variability in brain regions involved in language processing may shed light on the evolution of brain structures essential to the emergence of language in Homo sapiens. The superior temporal asymmetrical pit (STAP), which is not observed in chimpanzees, represents an ideal phenotype to investigate the genetic variations that support human communication. The left STAP depth was significantly associated with a predicted enhancer annotation located in the 14q23.1 locus, between DACT1 and KIAA0586, in the UK Biobank British discovery sample (N = 16 515). This association was replicated in the IMAGEN cohort (N = 1726) and the UK Biobank non-British validation sample (N = 2161). This genomic region was also associated to a lesser extent with the right STAP depth and the formation of sulcal interruptions, “plis de passage,” in the bilateral STAP but not with other structural brain MRI phenotypes, highlighting its notable association with the superior temporal regions. Diffusion MRI emphasized an association with the fractional anisotropy of the left auditory fibers of the corpus callosum and with networks involved in linguistic processing in resting-state functional MRI. Overall, this evidence demonstrates a specific relationship between this locus and the establishment of the superior temporal regions that support human communication.}, - number = {10}, - urldate = {2023-02-06}, - journal = {Cerebral Cortex}, - author = {Le Guen, Yann and Leroy, François and Philippe, Cathy and {IMAGEN Consortium} and Mangin, Jean-François and Dehaene-Lambertz, Ghislaine and Frouin, Vincent}, - month = sep, - year = {2020}, - pages = {5322--5332}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SCDV84MH/Le Guen et al. - 2020 - Enhancer Locus in ch14q23.1 Modulates Brain Asymme.pdf:application/pdf}, -} - -@article{mihailov_cortical_2020, - title = {Cortical signatures in behaviorally clustered autistic traits subgroups: a population-based study}, - volume = {10}, - copyright = {2020 The Author(s)}, - issn = {2158-3188}, - shorttitle = {Cortical signatures in behaviorally clustered autistic traits subgroups}, - url = {https://www.nature.com/articles/s41398-020-00894-3}, - doi = {10.1038/s41398-020-00894-3}, - abstract = {Extensive heterogeneity in autism spectrum disorder (ASD) has hindered the characterization of consistent biomarkers, which has led to widespread negative results. Isolating homogenized subtypes could provide insight into underlying biological mechanisms and an overall better understanding of ASD. A total of 1093 participants from the population-based “Healthy Brain Network” cohort (Child Mind Institute in the New York City area, USA) were selected based on score availability in behaviors relevant to ASD, aged 6–18 and IQ {\textgreater}= 70. All participants underwent an unsupervised clustering analysis on behavioral dimensions to reveal subgroups with ASD traits, identified by the presence of social deficits. Analysis revealed three socially impaired ASD traits subgroups: (1) high in emotionally dysfunctional traits, (2) high in ADHD-like traits, and (3) high in anxiety and depressive symptoms. 527 subjects had good quality structural MRI T1 data. Site effects on cortical features were adjusted using the ComBat method. Neuroimaging analyses compared cortical thickness, gyrification, and surface area, and were controlled for age, gender, and IQ, and corrected for multiple comparisons. Structural neuroimaging analyses contrasting one combined heterogeneous ASD traits group against controls did not yield any significant differences. Unique cortical signatures, however, were observed within each of the three individual ASD traits subgroups versus controls. These observations provide evidence of ASD traits subtypes, and confirm the necessity of applying dimensional approaches to extract meaningful differences, thus reducing heterogeneity and paving the way to better understanding ASD traits.}, - language = {en}, - number = {1}, - urldate = {2023-02-06}, - journal = {Translational Psychiatry}, - author = {Mihailov, Angeline and Philippe, Cathy and Gloaguen, Arnaud and Grigis, Antoine and Laidi, Charles and Piguet, Camille and Houenou, Josselin and Frouin, Vincent}, - month = jun, - year = {2020}, - keywords = {Neuroscience, Diagnostic markers, Prognostic markers, Human behaviour, Autism spectrum disorders}, - pages = {1--12}, -} - -@article{karkar_alzheimers_2020, - title = {Alzheimer's polygenic risk score in general population reveals new biomarkers for early diagnosis}, - volume = {16}, - issn = {1552-5279}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/alz.043396}, - doi = {10.1002/alz.043396}, - abstract = {Background In aging population, Alzheimer's disease (AD) with its different stages (preclinical, prodromal, mild to severe) has a strong genetic component. For a given individual and using summary statistics available from powerful reference GWAS in Alzheimer’s disease (IGAP, Lambert, 2013), one can compute a Polygenic Risk Score (PRS) for AD, that is a cumulative genetic risk computed with one subject’s genome variants. Using individual's PRS and MRI images in an aging general population like UK Biobank, we could point at imaging markers (endophenotypes) associated with early stages of AD. Method 16,549 subjects aged 47-74 from UK Biobank were included in the analysis. Using anatomical T1 MRI images (3T), opening measurements in 123 sulci were extracted with BrainVisa/Morphologist pipeline. Individual's PRS were computed using PRSice and summary statistics from IGAP study and then have been tested for an association with sulcal opening measurements. Result We obtained 24 sulci for which opening measurements was either positively or negatively associated with PRS (p {\textless} 0.05 after FDR correction). 17 sulcal opening showed increased widening w.r.t PRS with a main focus around the precuneus region, with superior parietal and central sulci. 7 sulcal opening showed opposite effect w.r.t the PRS and are located mostly in the orbital and insula region. See Figure for details. Conclusion For neurological disease like AD that have a strong genetic background, the combination of genetics and imaging data in large, aging general population studies like UK Biobank, provides powerful tools to identify new possible early markers of neurodegeneration. Focus on early risk patterns as the ones presented here with a main result on parietal sulcal alterations might facilitate identification of individuals at risk for cognitive decline and possibly support diagnostic procedures for AD.}, - language = {en}, - number = {S3}, - urldate = {2023-02-06}, - journal = {Alzheimer's \& Dementia}, - author = {Karkar, Slim and Philippe, Cathy and Hager, Alexa and Mangin, Jean-Francois and Frouin, Vincent}, - year = {2020}, - pages = {e043396}, -} - -@inproceedings{mekki_heritability_2019, - title = {Heritability of the language network using resting state {fMRI} data}, - url = {https://hal-cea.archives-ouvertes.fr/cea-02289470}, - abstract = {Background: Language is a singularity of the human species. It is expected to have a genetic constituent. Estimation of the part of variance attributable to genetic variation across subjects in functional brain imaging within the regions of the language, provide us a quantification of the genetic influence. This part of variance -which corresponds to heritability- is important to prioritize the structural and functional brain features. Language specific tasks fMRI are generally used to achieve this decomposition of variance, but resting state fMRI remains also a valid alternative. Indeed, a growing evidence suggest that resting state functional connectivity pattern could be identified during cognitive task activation. UK Biobank with 19,336 subjects that underwent a rsfMRI, as well as Human Connectome Project (HCP) with 1113 subjects are a unique opportunity to study such a question. Methods: The present work consists in estimating the heritability of the language network, using region of interest, identified by (Pallier, 2011) during a task fMRI experience, based on resting state fMRI connectivity analysis. Imaging genetics data for both cohorts underwent a stringent quality control protocol, yielding 18,851 and 739 samples for UKB and HCP respectively. Results: Significant heritability, estimated via GCTA for UKB and SOLAR for HCP, were observed (UKB: h²=10\%-14\%, HCP: h²=22\%-43\%). Multiple test were corrected with Bonferroni correction. Conclusions: The obtained results suggest some genetic influence on the phenotype chosen which indicates that the human language brain organization is under relatively strong genetic control, strong enough to consider association studies with genotyping data.}, - language = {en}, - urldate = {2023-02-06}, - author = {Mekki, Yasmina and Philippe, Cathy and Guillemot, Vincent and Lemaître, Hervé and Frouin, Vincent}, - month = sep, - year = {2019}, -} - -@article{labreche_genome-wide_2019, - title = {A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a {LOC} {Network} study}, - volume = {21}, - issn = {1522-8517}, - shorttitle = {A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1}, - url = {https://doi.org/10.1093/neuonc/noz088}, - doi = {10.1093/neuonc/noz088}, - abstract = {Primary central nervous system lymphoma (PCNSL) is a rare form of extra-nodal non-Hodgkin lymphoma. PCNSL is a distinct subtype of non-Hodgkin lymphoma, with over 95\% of tumors belonging to the diffuse large B-cell lymphoma (DLBCL) group. We have conducted a genome-wide association study (GWAS) on immunocompetent patients to address the possibility that common genetic variants influence the risk of developing PCNSL.We performed a meta-analysis of 2 new GWASs of PCNSL totaling 475 cases and 1134 controls of European ancestry. To increase genomic resolution, we imputed \>10 million single nucleotide polymorphisms using the 1000 Genomes Project combined with UK10K as reference. In addition we performed a transcription factor binding disruption analysis and investigated the patterns of local chromatin by Capture Hi-C data.We identified independent risk loci at 3p22.1 (rs41289586, ANO10, P = 2.17 × 10−8) and 6p25.3 near EXOC2 (rs116446171, P = 1.95 x 10−13). In contrast, the lack of an association between rs41289586 and DLBCL suggests distinct germline predisposition to PCNSL and DLBCL. We found looping chromatin interactions between noncoding regions at 6p25.3 (rs11646171) with the IRF4 promoter and at 8q24.21 (rs13254990) with the MYC promoter, both genes with strong relevance to B-cell tumorigenesis.To our knowledge this is the first study providing insight into the genetic predisposition to PCNSL. Our findings represent an important step in defining the contribution of common genetic variation to the risk of developing PCNSL.}, - number = {8}, - urldate = {2023-02-06}, - journal = {Neuro-Oncology}, - author = {Labreche, Karim and Daniau, Mailys and Sud, Amit and Law, Philip J and Royer-Perron, Louis and Holroyd, Amy and Broderick, Peter and Went, Molly and Benazra, Marion and Ahle, Guido and Soubeyran, Pierre and Taillandier, Luc and Chinot, Olivier L and Casasnovas, Olivier and Bay, Jacques-Olivier and Jardin, Fabrice and Oberic, Lucie and Fabbro, Michel and Damaj, Gandhi and Brion, Annie and Mokhtari, Karima and Philippe, Cathy and Sanson, Marc and Houillier, Caroline and Soussain, Carole and Hoang-Xuan, Khê and Houlston, Richard S and Alentorn, Agusti and {LOC Network}}, - month = aug, - year = {2019}, - pages = {1039--1048}, -} - -@inproceedings{goya-outi_can_2019, - title = {Can {Structural} {MRI} {Radiomics} {Predict} {DIPG} {Histone} {H3} {Mutation} and {Patient} {Overall} {Survival} at {Diagnosis} {Time}?}, - doi = {10.1109/BHI.2019.8834524}, - abstract = {Radiomics was proposed to identify tumor phenotypes noninvasively from quantitative imaging features. The present study aimed at investigating if radiomic features measured at diagnosis time from structural MRI can predict histone H3 mutations and overall survival of patients with diffuse intrinsic pontine glioma. To this end, 316 radiomic features from multimodal diagnostic MRI of 38 patients were extracted, and three clinical parameters were added. Two approaches for computing radiomic features were proposed: a global estimation from a spherical region of interest defined inside the tumor and a local estimation where features are computed inside the previously defined region from fixed size spherical patches and the mean of these features is considered. A feature selection pipeline was then developed. Three machine learning models for H3 mutation classification and three regression models for overall survival prediction were used. Leave-one-out F1-weighted scores for SVM model combining imaging and clinical features reached 0.83, showing a good prediction of H3 mutation using structural MRI. Results on overall survival prediction are not conclusive and suggest the need of a larger number of patients.}, - booktitle = {2019 {IEEE} {EMBS} {International} {Conference} on {Biomedical} \& {Health} {Informatics} ({BHI})}, - author = {Goya-Outi, Jessica and Calmon, Raphael and Orlhac, Fanny and Philippe, Cathy and Boddaert, Nathalie and Puget, Stéphanie and Buvat, Irène and Frouin, Vincent and Grill, Jacques and Frouin, Frédérique}, - month = may, - year = {2019}, - note = {ISSN: 2641-3604}, - keywords = {Machine Learning, Magnetic resonance imaging, Predictive models, Feature extraction, Structural MRI, Computational modeling, Tumors, Image Standardization, Radiomics, Rare Cancer}, - pages = {1--4}, -} - -@inproceedings{karkar_multivariate_2019, - title = {Multivariate {Haplotype} {Analysis} {Of} 96 {Sulci} {Opening} {For} 15,612 {UK}-{Biobank} {Sujects}}, - doi = {10.1109/ISBI.2019.8759497}, - abstract = {Imaging genetic studies of large control cohorts such as UK Biobank enable to assess the range of normal variations in brain structures. Previous studies by our group have shown that the width of several cortical sulci is associated with a variant in the upstream region of KCNK2 gene even if this effect is corrected with age. Here we propose to analyze in a multivariate setup the associations between sets of genetic variants and multiple sulci widths. The genetic variants we consider are sets of SNPs of known phase called haplotypes, taken from the upstream region of KCNK2 gene. To the best of our knowledge, multivariate analysis in imaging genetics has never been used in haplotype studies. Our method was able to recover the expected association signal and uncover new associations between imaging data and genetic variants.}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Karkar, S. and Gloaguen, A. and Le Guen, Y. and Pierre-Jean, M. and Dandine-Roulland, C. and Le Floch, E. and Philippe, C. and Tenenhaus, A. and Frouin, V.}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {Imaging, Aging, Imaging genetics, Grey matter, Genomics, Bioinformatics, Analytical models, haplotype, multivariate analysis}, - pages = {392--395}, -} - -@inproceedings{guigui_network_2019, - title = {Network {Regularization} in {Imaging} {Genetics} {Improves} {Prediction} {Performances} and {Model} {Interpretability} on {Alzheimer}’s {Disease}}, - doi = {10.1109/ISBI.2019.8759593}, - abstract = {Imaging genetics is a growing popular research avenue which aims to find genetic variants associated with quantitative phenotypes that characterize a disease. In this work, we combine structural MRI with genetic data structured by prior knowledge of interactions in a Canonical Correlation Analysis (CCA) model with graph regularization. This results in improved prediction performance and yields a more interpretable model.}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Guigui, N. and Philippe, C. and Gloaguen, A. and Karkar, S. and Guillemot, V. and Löfstedt, T. and Frouin, V.}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {Imaging, Diseases, Brain modeling, Imaging genetics, Data models, Genomics, Bioinformatics, Generalized Canonical Correlation Analysis, Networks, Structured constraints}, - pages = {1403--1406}, -} - -@article{le_guen_eqtl_2019, - title = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening: evidence from 15,597 {UK} {Biobank} participants with neuroimaging data}, - volume = {224}, - issn = {1863-2661}, - shorttitle = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening}, - url = {https://doi.org/10.1007/s00429-018-1808-9}, - doi = {10.1007/s00429-018-1808-9}, - abstract = {The grey and white matter volumes are known to reduce with age. This cortical shrinkage is visible on magnetic resonance images and is conveniently identified by the increased volume of cerebrospinal fluid in the sulci between two gyri. Here, we replicated this finding using the UK Biobank dataset and studied the genetic influence on these cortical features of aging. We divided all individuals genetically confirmed of British ancestry into two sub-cohorts (12,162 and 3435 subjects for discovery and replication samples, respectively). We found that the heritability of the sulcal opening ranges from 15 to 45\% (SE = 4.8\%). We identified 4 new loci that contribute to this opening, including one that also affects the sulci grey matter thickness. We identified the most significant variant (rs864736) on this locus as being an expression quantitative trait locus (eQTL) for the KCNK2 gene. This gene regulates the immune-cell into the central nervous system (CNS) and controls the CNS inflammation, which is implicated in cortical atrophy and cognitive decline. These results expand our knowledge of the genetic contribution to cortical shrinking and promote further investigation into these variants and genes in pathological context such as Alzheimer’s disease in which brain shrinkage is a key biomarker.}, - language = {en}, - number = {2}, - urldate = {2023-02-06}, - journal = {Brain Structure and Function}, - author = {Le Guen, Yann and Philippe, Cathy and Riviere, Denis and Lemaitre, Hervé and Grigis, Antoine and Fischer, Clara and Dehaene-Lambertz, Ghislaine and Mangin, Jean-François and Frouin, Vincent}, - month = mar, - year = {2019}, - keywords = {Brain ageing, Imaging genetics, CSF, GM thickness, GWAS, Sulci widening}, - pages = {847--857}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VJK7LZXH/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DBSB6Y6V/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf}, -} - -@article{alentorn_p0588_2018, - title = {P05.88 {Radiomics} analysis of brain metastases from non-small cell lung cancer brings relevant supplementary information to clinical scores}, - volume = {20}, - issn = {1522-8517}, - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144734/}, - doi = {10.1093/neuonc/noy139.414}, - abstract = {Background -Lung cancer, and more precisely, non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality due to its high prevalence. Likewise, brain metastases from lung cancer are the most frequent type of secondary brain tumors. Different prognostic scores have been proposed to better stratify the treatment of brain metastases. More recently, lung GPA has been updated considering two frequent molecular characteristics in lung adenocarcinoma: EGFR and ALK alterations. However, to the best of our knowledge, the crosstalk between imaging features and the currently used prognostic scores is unknown.We sought to analyze the clinical value of radiomics data in the prediction of survival in patients with brain mets from NSCLC. - -Material and Methods -We have selected 29 patients with brain metastases of NSCLC treated during 2015–2016 at Pitié-Salpêtrière Hospital. We selected patients with neither previous history of brain mets nor brain surgery and high-quality structural MRI.We extracted 1428 radiomic features per patient, including: first-order statistics, volume, shape, texture and wavelet analysis using pyradiomics on Gadolinium enhanced T1 and FLAIR RM images. Using the plsRcox package, several Cox models were constructed with either clinical (GPA score, EGFR mutation and ALK fusion status) or radiomics features or both. The goodness of fit was assessed with the Harrell’s concordance index using 5 fold cross-validation. - -Results -The performance of the radiomics model (mean Harrell’s C-index 0.88, SD 0.08) to predict OS was the best compared to the prediction using clinical data (mean Harrell’s C-index 0.77, SD 0.25). Surprisingly, the addition of clinical data to the radiomics model decreased the performance of OS prediction (mean Harrell’s C-index 0.83, SD 0.17). - -Conclusion -Radiomics analysis of brain mets from NSCLC may provide additional clinically relevant data on the survival, in a non-invasive way. The results of this small cohort are currently being validated in a larger dataset of patients.}, - number = {Suppl 3}, - urldate = {2023-09-07}, - journal = {Neuro-Oncology}, - author = {Alentorn, A and Philippe, C and Grigis, A and Ibañez-Julia, M and Younan, N and Duran-Peña, A and Royer-Perron, L and Goya-Outi, J and Buvat, I and Frouin, F and Jacob, J and Conforti, R and Hoang-Xuan, K and Frouin, V}, - month = sep, - year = {2018}, - pmid = {null}, - pmcid = {PMC6144734}, - pages = {iii324}, -} - -@inproceedings{karkar_study_2018, - title = {A study of feasibility for genome-wide haplotype association of complex traits in imaging genetics}, - doi = {10.1109/BIBM.2018.8621306}, - abstract = {Imaging-genetics cohorts allow to find associations between genotyped variants and brain imaging features. They are invaluable tools to evaluate the part of genetics and environment in the brain characteristic variance observed in normal and pathological populations. The present analyses were conducted using the 2018 UK Biobank (UKB) data release, and included 15,040 subjects for which sulcal opening, a measure of sulcus width, are extracted for 126 sulci using BrainVisa/Morphologist pipeline. Based on genetic maps, continuous blocks of high-confidence phase are extracted using the haplotype dataset of UK Biobank. The feasibility study analyzes 13,942 haplotypes of 1,756 blocks on chromosome 21, obtained with a stringent block definition, and shows that block-based test seems underpowered compared to haplotype-based association test.}, - booktitle = {2018 {IEEE} {International} {Conference} on {Bioinformatics} and {Biomedicine} ({BIBM})}, - author = {Karkar, Slim and Guen, Yann Le and Philippe, Cathy and Dandine-Roulland, Claire and Pierre-Jean, Morgane and Mangin, Jean-FranÇois and Floch, Edith Le and Frouin, Vincent}, - month = dec, - year = {2018}, - keywords = {Brain, Imaging, Genomics, Pathology, Bioinformatics, Biological cells}, - pages = {2764--2766}, -} - -@article{castel_transcriptomic_2018, - title = {Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, {H3} {K27M}-mutant’ discriminate two subgroups based on the type of histone {H3} mutated and not supratentorial or infratentorial location}, - volume = {6}, - issn = {2051-5960}, - url = {https://doi.org/10.1186/s40478-018-0614-1}, - doi = {10.1186/s40478-018-0614-1}, - abstract = {Diffuse midline glioma (DMG), H3 K27M-mutant, is a new entity in the updated WHO classification grouping together diffuse intrinsic pontine gliomas and infiltrating glial neoplasms of the midline harboring the same canonical mutation at the Lysine 27 of the histones H3 tail.}, - language = {en}, - number = {1}, - urldate = {2023-02-06}, - journal = {Acta Neuropathologica Communications}, - author = {Castel, David and Philippe, Cathy and Kergrohen, Thomas and Sill, Martin and Merlevede, Jane and Barret, Emilie and Puget, Stéphanie and Sainte-Rose, Christian and Kramm, Christof M. and Jones, Chris and Varlet, Pascale and Pfister, Stefan M. and Grill, Jacques and Jones, David T. W. and Debily, Marie-Anne}, - month = nov, - year = {2018}, - pages = {117}, -} - -@inproceedings{tenenhaus_three-way_2018, - address = {Hong-Kong, China}, - title = {Three-{Way} {Generalized} {Canonical} {Correlation} {Analysis}}, - url = {https://hal.science/hal-03111188}, - urldate = {2023-09-07}, - booktitle = {{SIAM} {Conference} on {Applied} {Linear} {Algebra}}, - author = {Tenenhaus, Arthur and Gloaguen, Arnaud and Le Brusquet, Laurent and Philippe, Cathy and Frouin, Vincent}, - month = may, - year = {2018}, -} diff --git a/bibutils/data/ginkgo_v-20240621.bib b/bibutils/data/ginkgo_v-20240621.bib deleted file mode 100644 index 4dd1462..0000000 --- a/bibutils/data/ginkgo_v-20240621.bib +++ /dev/null @@ -1,2440 +0,0 @@ - -@article{gori_bayesian_2017, - title = {A {Bayesian} framework for joint morphometry of surface and curve meshes in multi-object complexes}, - volume = {35}, - issn = {1361-8423}, - doi = {10.1016/j.media.2016.08.011}, - abstract = {We present a Bayesian framework for atlas construction of multi-object shape complexes comprised of both surface and curve meshes. It is general and can be applied to any parametric deformation framework and to all shape models with which it is possible to define probability density functions (PDF). Here, both curve and surface meshes are modelled as Gaussian random varifolds, using a finite-dimensional approximation space on which PDFs can be defined. Using this framework, we can automatically estimate the parameters balancing data-terms and deformation regularity, which previously required user tuning. Moreover, it is also possible to estimate a well-conditioned covariance matrix of the deformation parameters. We also extend the proposed framework to data-sets with multiple group labels. Groups share the same template and their deformation parameters are modelled with different distributions. We can statistically compare the groups'distributions since they are defined on the same space. We test our algorithm on 20 Gilles de la Tourette patients and 20 control subjects, using three sub-cortical regions and their incident white matter fiber bundles. We compare their morphological characteristics and variations using a single diffeomorphism in the ambient space. The proposed method will be integrated with the Deformetrica software package, publicly available at www.deformetrica.org.}, - language = {eng}, - journal = {Medical Image Analysis}, - author = {Gori, Pietro and Colliot, Olivier and Marrakchi-Kacem, Linda and Worbe, Yulia and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - month = jan, - year = {2017}, - pmid = {27607468}, - keywords = {Algorithms, Humans, Software, Normal Distribution, Case-Control Studies, Bayes Theorem, Shape, Atlas, Bayesian, Complex, Fiber bundle, Morphometry, Multi-object, Tourette Syndrome, Varifolds}, - pages = {458--474}, -} - -@article{favre_white_2016, - title = {White {Matter} {Plasticity} {Induced} by {Psychoeducation} in {Bipolar} {Patients}: {A} {Controlled} {Diffusion} {Tensor} {Imaging} {Study}}, - volume = {85}, - issn = {1423-0348}, - shorttitle = {White {Matter} {Plasticity} {Induced} by {Psychoeducation} in {Bipolar} {Patients}}, - doi = {10.1159/000441009}, - language = {eng}, - number = {1}, - journal = {Psychotherapy and Psychosomatics}, - author = {Favre, Pauline and Houenou, Josselin and Baciu, Monica and Pichat, Cédric and Poupon, Cyril and Bougerol, Thierry and Polosan, Mircea}, - year = {2016}, - pmid = {26610264}, - keywords = {Humans, Adult, Female, Male, Neuronal Plasticity, Limbic System, Endorphins, Patient Education as Topic, Self-Help Groups}, - pages = {58--60}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {UniactPMID: 26610264}, -} - -@article{pardo_study_2013, - title = {Study of the variability of short association bundles on a {HARDI} database}, - volume = {2013}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2013.6609441}, - abstract = {The construction of an atlas of the human brain connectome, in particular, the cartography of fiber bundles of superficial white matter (SWM) is a complex and unachieved task. Its description is essential for the understanding of human brain function and the study of several pathologies. In this work we applied an automatic white matter bundle segmentation method proposed in the literature for the analysis of the variability of a big amount of superficial white matter bundles. The method was applied to 30 subjects of a high quality HARDI database, adding several processing steps in order to improve the results. Then we calculated some indices for studying the variability of 40 SWM fiber bundles from each hemisphere, and we constructed a model of these bundles in the MNI standard space.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Pardo, Edison and Guevara, Pamela and Duclap, Delphine and Houenou, Josselin and Lebois, Alice and Schmitt, Benoît and Le Bihan, Denis and Mangin, Jean-François and Poupon, Cyril}, - year = {2013}, - pmid = {24109628}, - keywords = {Humans, Automatic Data Processing, Diffusion Magnetic Resonance Imaging, Databases, Factual, Connectome, Radiography}, - pages = {77--80}, -} - -@article{georget_stacked_2017, - title = {Stacked magnetic resonators for {MRI} {RF} coils decoupling}, - volume = {275}, - issn = {1096-0856}, - doi = {10.1016/j.jmr.2016.11.012}, - abstract = {Parallel transmission is a very promising method to tackle B1+ field inhomogeneities at ultrahigh field in magnetic resonant imaging (MRI). This technique is however limited by the mutual coupling between the radiating elements. Here we propose to solve this problem by designing a passive magneto-electric resonator that we here refer to as stacked magnetic resonator (SMR). By combining numerical and experimental methodologies, we prove that this novelty passive solution allows an efficient decoupling of elements of a phased-array coil. We demonstrate the ability of this technique to significantly reduce by more than 10dB the coupling preserving the quality of images compared to ideally isolated linear resonators on a spherical salty agar gel phantom in a 7T MRI scanner.}, - language = {eng}, - journal = {Journal of Magnetic Resonance (San Diego, Calif.: 1997)}, - author = {Georget, Elodie and Luong, Michel and Vignaud, Alexandre and Giacomini, Eric and Chazel, Edouard and Ferrand, Guillaume and Amadon, Alexis and Mauconduit, Franck and Enoch, Stefan and Tayeb, Gérard and Bonod, Nicolas and Poupon, Cyril and Abdeddaim, Redha}, - month = feb, - year = {2017}, - pmid = {27951426}, - keywords = {7T, ARRAY, Author Keywords:High-field RF coils, COMPONENTS, DESIGN, KeyWords Plus:WALL DISTRIBUTED FILTERS, Linear resonator, Metamaterial, Passive decoupling, Phased array coil, High-field RF coils}, - pages = {11--18}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unirs}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YU3JS8VL/Georget et al. - 2017 - Stacked magnetic resonators for MRI RF coils decou.pdf:application/pdf}, -} - -@article{mangin_spatial_2016, - title = {Spatial normalization of brain images and beyond}, - volume = {33}, - issn = {1361-8423}, - doi = {10.1016/j.media.2016.06.008}, - abstract = {The deformable atlas paradigm has been at the core of computational anatomy during the last two decades. Spatial normalization is the variant endowing the atlas with a coordinate system used for voxel-based aggregation of images across subjects and studies. This framework has largely contributed to the success of brain mapping. Brain spatial normalization, however, is still ill-posed because of the complexity of the human brain architecture and the lack of architectural landmarks in standard morphological MRI. Multi-atlas strategies have been developed during the last decade to overcome some difficulties in the context of segmentation. A new generation of registration algorithms embedding architectural features inferred for instance from diffusion or functional MRI is on the verge to improve the architectural value of spatial normalization. A better understanding of the architectural meaning of the cortical folding pattern will lead to use some sulci as complementary constraints. Improving the architectural compliance of spatial normalization may impose to relax the diffeomorphic constraint usually underlying atlas warping. A two-level strategy could be designed: in each region, a dictionary of templates of incompatible folding patterns would be collected and matched in a way or another using rare architectural information, while individual subjects would be aligned using diffeomorphisms to the closest template. Manifold learning could help to aggregate subjects according to their morphology. Connectivity-based strategies could emerge as an alternative to deformation-based alignment leading to match the connectomes of the subjects rather than images.}, - language = {eng}, - journal = {Medical Image Analysis}, - author = {Mangin, J.-F. and Lebenberg, J. and Lefranc, S. and Labra, N. and Auzias, G. and Labit, M. and Guevara, M. and Mohlberg, H. and Roca, P. and Guevara, P. and Dubois, J. and Leroy, F. and Dehaene-Lambertz, G. and Cachia, A. and Dickscheid, T. and Coulon, O. and Poupon, C. and Rivière, D. and Amunts, K. and Sun, Z. Y.}, - month = oct, - year = {2016}, - pmid = {27344104}, - keywords = {Algorithms, Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Connectome, Diffeomorphism, Spatial normalization, Cortical folding pattern}, - pages = {127--133}, -} - -@article{katz_similar_2016, - title = {Similar white matter but opposite grey matter changes in schizophrenia and high-functioning autism}, - volume = {134}, - issn = {1600-0447}, - doi = {10.1111/acps.12579}, - abstract = {OBJECTIVE: High-functioning autism (HFA) and schizophrenia (SZ) are two of the main neurodevelopmental disorders, sharing several clinical dimensions and risk factors. Their exact relationship is poorly understood, and few studies have directly compared both disorders. Our aim was thus to directly compare neuroanatomy of HFA and SZ using a multimodal MRI design. -METHODS: We scanned 79 male adult subjects with 3T MRI (23 with HFA, 24 with SZ and 32 healthy controls, with similar non-verbal IQ). We compared them using both diffusion-based whole-brain tractography and T1 voxel-based morphometry. -RESULTS: HFA and SZ groups exhibited similar white matter alterations in the left fronto-occipital inferior fasciculus with a decrease in generalized fractional anisotropy compared with controls. In grey matter, the HFA group demonstrated bilateral prefrontal and anterior cingulate increases in contrast with prefrontal and left temporal reductions in SZ. -CONCLUSION: HFA and SZ may share common white matter deficits in long-range connections involved in social functions, but opposite grey matter abnormalities in frontal regions that subserve complex cognitive functions. Our results are consistent with the fronto-occipital underconnectivity theory of HFA and the altered connectivity hypothesis of SZ and suggest the existence of both associated and diametrical liabilities to these two conditions.}, - language = {eng}, - number = {1}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Katz, J. and d'Albis, M.-A. and Boisgontier, J. and Poupon, C. and Mangin, J.-F. and Guevara, P. and Duclap, D. and Hamdani, N. and Petit, J. and Monnet, D. and Le Corvoisier, P. and Leboyer, M. and Delorme, R. and Houenou, J.}, - month = jul, - year = {2016}, - pmid = {27105136}, - keywords = {Humans, MRI, Brain Mapping, Adult, Male, Autistic Disorder, Young Adult, Anisotropy, Gray Matter, Cross-Sectional Studies, Multimodal Imaging, autism, connectivity}, - pages = {31--39}, -} - -@article{sun_shape_2017, - title = {Shape analysis of the cingulum, uncinate and arcuate fasciculi in patients with bipolar disorder}, - volume = {42}, - issn = {1488-2434}, - abstract = {BACKGROUND: Abnormal maturation of brain connectivity is supposed to underlie the dysfunctional emotion regulation in patients with bipolar disorder (BD). To test this hypothesis, white matter integrity is usually investigated using measures of water diffusivity provided by MRI. Here we consider a more intuitive aspect of the morphometry of the white matter tracts: the shape of the fibre bundles, which is associated with neurodevelopment. We analyzed the shape of 3 tracts involved in BD: the cingulum (CG), uncinate fasciculus (UF) and arcuate fasciculus (AF). -METHODS: We analyzed diffusion MRI data in patients with BD and healthy controls. The fibre bundles were reconstructed using Q-ball-based tractography and automated segmentation. Using Isomap, a manifold learning method, the differences in the shape of the reconstructed bundles were visualized and quantified. -RESULTS: We included 112 patients and 82 controls in our analysis. We found the left AF of patients to be further extended toward the temporal pole, forming a tighter hook than in controls. We found no significant difference in terms of shape for the left UF, the left CG or the 3 right fasciculi. However, in patients compared with controls, the ventrolateral branch of the left UF in the orbitofrontal region had a tendency to be larger, and the left CG of patients had a tendency to be smaller in the frontal lobe and larger in the parietal lobe. -LIMITATIONS: This was a cross-sectional study. -CONCLUSION: Our results suggest neurodevelopmental abnormalities in the left AF in patients with BD. The statistical tendencies observed for the left UF and left CG deserve further study.}, - language = {eng}, - number = {1}, - journal = {Journal of psychiatry \& neuroscience: JPN}, - author = {Sun, Zhong Yi and Houenou, Josselin and Duclap, Delphine and Sarrazin, Samuel and Linke, Julia and Daban, Claire and Hamdani, Nora and d'Albis, Marc-Antoine and Le Corvoisier, Philippe and Guevara, Pamela and Delavest, Marine and Bellivier, Frank and Bellivier, Frank and Almeida, Jorge and Versace, Amelia and Poupon, Cyril and Leboyer, Marion and Phillips, Mary and Wessa, Michèle and Mangin, Jean-François}, - year = {2017}, - pmid = {28234596}, - pmcid = {PMC5373709}, - keywords = {Brain, Humans, Image Processing, Computer-Assisted, Adult, Adolescent, Female, Male, Young Adult, Bipolar Disorder, Middle Aged, Diffusion Magnetic Resonance Imaging, Neural Pathways, Aged, Machine Learning, Cross-Sectional Studies, ABNORMALITIES, CORPUS-CALLOSUM, I DISORDER, INDIVIDUALS, KeyWords Plus:SPATIAL STATISTICS, NERVOUS-SYSTEM, RATING-SCALE}, - pages = {27--36}, - annote = {The following values have no corresponding Zotero field:number: 1}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unirs}, - annote = {UnirsPMID: 28234596 PMCID: PMC5373709}, -} - -@article{marrakchi-kacem_robust_2016, - title = {Robust imaging of hippocampal inner structure at {7T}: in vivo acquisition protocol and methodological choices}, - volume = {29}, - issn = {1352-8661}, - shorttitle = {Robust imaging of hippocampal inner structure at {7T}}, - doi = {10.1007/s10334-016-0552-5}, - abstract = {OBJECTIVE: Motion-robust multi-slab imaging of hippocampal inner structure in vivo at 7T. -MATERIALS AND METHODS: Motion is a crucial issue for ultra-high resolution imaging, such as can be achieved with 7T MRI. An acquisition protocol was designed for imaging hippocampal inner structure at 7T. It relies on a compromise between anatomical details visibility and robustness to motion. In order to reduce acquisition time and motion artifacts, the full slab covering the hippocampus was split into separate slabs with lower acquisition time. A robust registration approach was implemented to combine the acquired slabs within a final 3D-consistent high-resolution slab covering the whole hippocampus. Evaluation was performed on 50 subjects overall, made of three groups of subjects acquired using three acquisition settings; it focused on three issues: visibility of hippocampal inner structure, robustness to motion artifacts and registration procedure performance. -RESULTS: Overall, T2-weighted acquisitions with interleaved slabs proved robust. Multi-slab registration yielded high quality datasets in 96 \% of the subjects, thus compatible with further analyses of hippocampal inner structure. -CONCLUSION: Multi-slab acquisition and registration setting is efficient for reducing acquisition time and consequently motion artifacts for ultra-high resolution imaging of the inner structure of the hippocampus.}, - language = {eng}, - number = {3}, - journal = {Magma (New York, N.Y.)}, - author = {Marrakchi-Kacem, Linda and Vignaud, Alexandre and Sein, Julien and Germain, Johanne and Henry, Thomas R. and Poupon, Cyril and Hertz-Pannier, Lucie and Lehéricy, Stéphane and Colliot, Olivier and Van de Moortele, Pierre-François and Chupin, Marie}, - month = jun, - year = {2016}, - pmid = {27138193}, - keywords = {Anatomical contrasts, Hippocampal formation, Inner structure of the hippocampus, Registration, Ultra-high field imaging}, - pages = {475--489}, -} - -@article{guevara_reproducibility_2017, - title = {Reproducibility of superficial white matter tracts using diffusion-weighted imaging tractography}, - volume = {147}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2016.11.066}, - abstract = {Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of pathogenesis triggered by abnormal connectivity. In this work we automatically created a multi-subject atlas of SWM diffusion-based bundles of the whole brain. For each subject, the complete cortico-cortical tractogram is first split into sub-tractograms connecting pairs of gyri. Then intra-subject shape-based fiber clustering performs compression of each sub-tractogram into a set of bundles. Proceeding further with shape-based clustering provides a match of the bundles across subjects. Bundles found in most of the subjects are instantiated in the atlas. To increase robustness, this procedure was performed with two independent groups of subjects, in order to discard bundles without match across the two independent atlases. Finally, the resulting intersection atlas was projected on a third independent group of subjects in order to filter out bundles without reproducible and reliable projection. The final multi-subject diffusion-based U-fiber atlas is composed of 100 bundles in total, 50 per hemisphere, from which 35 are common to both hemispheres.}, - language = {eng}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Román, Claudio and Houenou, Josselin and Duclap, Delphine and Poupon, Cyril and Mangin, Jean François and Guevara, Pamela}, - month = feb, - year = {2017}, - pmid = {28034765}, - keywords = {Brain, Humans, Reproducibility of Results, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Diffusion Tensor Imaging, White Matter, Segmentation, Atlases as Topic, Bundle atlas, Fiber clustering, Short association fibers, Tractography segmentation, White matter tracts, ATLAS, Author Keywords:Diffusion MRI, CONNECTIONS, DATASETS, DISSECTION, FIBERS, IMAGES, KeyWords Plus:HUMAN BRAIN, RECONSTRUCTION, Diffusion MRI}, - pages = {703--725}, - annote = {The following values have no corresponding Zotero field:section: label: ACL}, - annote = {Unirs}, -} - -@article{gallea_rad51_2013, - title = {{RAD51} deficiency disrupts the corticospinal lateralization of motor control}, - volume = {136}, - issn = {1460-2156}, - doi = {10.1093/brain/awt258}, - abstract = {Mirror movements are involuntary symmetrical movements of one side of the body that mirror voluntary movements of the other side. Congenital mirror movement disorder is a rare condition characterized by mirror movements that persist throughout adulthood in subjects with no other clinical abnormalities. The affected individuals have mirror movements predominating in the muscles that control the fingers and are unable to perform purely unimanual movements. Congenital mirror movement disorder thus provides a unique paradigm for studying the lateralization of motor control. We conducted a multimodal, controlled study of patients with congenital mirror movements associated with RAD51 haploinsufficiency (n = 7, mean age 33.3 ± 16.8 years) by comparison with age- and gender-matched healthy volunteers (n = 14, mean age 33.9 ± 16.1 years). We showed that patients with congenital mirror movements induced by RAD51 deficiency had: (i) an abnormal decussation of the corticospinal tract; (ii) abnormal interhemispheric inhibition and bilateral cortical activation of primary motor areas during intended unimanual movements; and (iii) an abnormal involvement of the supplementary motor area during both unimanual and bimanual movements. The lateralization of motor control thus requires a fine interplay between interhemispheric communication and corticospinal wiring. This fine interplay determines: (i) the delivery of appropriate motor plans from the supplementary motor area to the primary motor cortex; (ii) the lateralized activation of the primary motor cortex; and (iii) the unilateral transmission of the motor command to the limb involved in the intended movement. Our results also unveil an unexpected function of RAD51 in corticospinal development of the motor system.}, - language = {eng}, - number = {Pt 11}, - journal = {Brain: A Journal of Neurology}, - author = {Gallea, Cécile and Popa, Traian and Hubsch, Cécile and Valabregue, Romain and Brochard, Vanessa and Kundu, Prantik and Schmitt, Benoît and Bardinet, Eric and Bertasi, Eric and Flamand-Roze, Constance and Alexandre, Nicolas and Delmaire, Christine and Méneret, Aurélie and Depienne, Christel and Poupon, Cyril and Hertz-Pannier, Lucie and Cincotta, Massimo and Vidailhet, Marie and Lehericy, Stéphane and Meunier, Sabine and Roze, Emmanuel}, - month = nov, - year = {2013}, - pmid = {24056534}, - keywords = {Humans, Adult, Adolescent, Female, Male, Young Adult, Middle Aged, Functional Laterality, genetics, Transcranial Magnetic Stimulation, Multimodal Imaging, corticospinal pathways, Dyskinesias, Efferent Pathways, Evoked Potentials, Motor, Hand, Haploinsufficiency, Magnetoencephalography, Motor Cortex, motor disorders, movement coordination, Rad51 Recombinase, transcallosal inhibition}, - pages = {3333--3346}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UniactPMID: 24056534}, -} - -@article{gallea_pedunculopontine_2017, - title = {Pedunculopontine network dysfunction in {Parkinson}'s disease with postural control and sleep disorders}, - volume = {32}, - issn = {1531-8257}, - doi = {10.1002/mds.26923}, - abstract = {BACKGROUND: The objective of this study was to investigate pedunculopontine nucleus network dysfunctions that mediate impaired postural control and sleep disorder in Parkinson's disease. -METHODS: We examined (1) Parkinson's disease patients with impaired postural control and rapid eye movement sleep behavior disorder (further abbreviated as sleep disorder), (2) Parkinson's disease patients with sleep disorder only, (3) Parkinson's disease patients with neither impaired postural control nor sleep disorder, and (4) healthy volunteers. We assessed postural control with clinical scores and biomechanical recordings during gait initiation. Participants had video polysomnography, daytime sleepiness self-evaluation, and resting-state functional MRIs. -RESULTS: Patients with impaired postural control and sleep disorder had longer duration of anticipatory postural adjustments during gait initiation and decreased functional connectivity between the pedunculopontine nucleus and the supplementary motor area in the locomotor network that correlated negatively with the duration of anticipatory postural adjustments. Both groups of patients with sleep disorder had decreased functional connectivity between the pedunculopontine nucleus and the anterior cingulate cortex in the arousal network that correlated with daytime sleepiness. The degree of dysfunction in the arousal network was related to the degree of connectivity in the locomotor network in all patients with sleep disorder, but not in patients without sleep disorder or healthy volunteers. -CONCLUSIONS: These results shed light on the functional neuroanatomy of pedunculopontine nucleus networks supporting the clinical manifestation and the interdependence between sleep and postural control impairments in Parkinson's disease. © 2016 International Parkinson and Movement Disorder Society.}, - language = {eng}, - number = {5}, - journal = {Movement Disorders: Official Journal of the Movement Disorder Society}, - author = {Gallea, Cecile and Ewenczyk, Claire and Degos, Bertrand and Welter, Marie-Laure and Grabli, David and Leu-Semenescu, Smaranda and Valabregue, Romain and Berroir, Pierre and Yahia-Cherif, Lydia and Bertasi, Eric and Fernandez-Vidal, Sara and Bardinet, Eric and Roze, Emmanuel and Benali, Habib and Poupon, Cyril and François, Chantal and Arnulf, Isabelle and Lehéricy, Stéphane and Vidailhet, Marie}, - month = may, - year = {2017}, - pmid = {28164375}, - keywords = {Brain, Humans, Female, Male, Middle Aged, Neural Pathways, Aged, Case-Control Studies, Gyrus Cinguli, Functional Neuroimaging, Motor Cortex, anticipatory postural adjustments, Author Keywords : anticipatory postural adjustments, BALANCE DISORDERS, BEHAVIOR DISORDER, GAIT, KeyWords Plus : EYE-MOVEMENT SLEEP, MODULATION, NUCLEUS AREA, ORGANIZATION, Parkinson Disease, Pedunculopontine Tegmental Nucleus, Postural Balance, rapid eye movement behavioral disorder, REM Sleep Behavior Disorder, REM-SLEEP, Sleep Wake Disorders, STIMULATION, supplementary motor area}, - pages = {693--704}, - annote = {ACL}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {UNirs}, - annote = {UnirsPMID: 28164375}, -} - -@article{gori_parsimonious_2016, - title = {Parsimonious {Approximation} of {Streamline} {Trajectories} in {White} {Matter} {Fiber} {Bundles}}, - volume = {35}, - issn = {1558-254X}, - doi = {10.1109/TMI.2016.2591080}, - abstract = {Fiber bundles stemming from tractography algorithms contain many streamlines. They require therefore a great amount of computer memory and computational resources to be stored, visualised and processed. We propose an approximation scheme for fiber bundles which results in a parsimonious representation of weighted prototypes. Prototypes are chosen among the streamlines and they represent groups of similar streamlines. Their weight is related to the number of approximated streamlines. Both streamlines and prototypes are modelled as weighted currents. This computational model does not need point-to-point correspondences and two streamlines are considered similar if their endpoints are close to each other and if their pathways follow similar trajectories. Moreover, the space of weighted currents is a vector space with a closed-form metric. This permits easy computation of the approximation error and the selection of the prototypes is based on the minimisation of this error. We propose an iterative algorithm which approximates independently and simultaneously all the fascicles of the bundle in a fast and accurate way. We show that the resulting representation preserves the shape of the bundle and it can be used to accurately reconstruct the original structural connectivity. We evaluate our algorithm on bundles obtained from both deterministic and probabilistic tractography algorithms. The resulting approximations use on average only 2\% of the original streamlines as prototypes. This drastically reduces the computational burden of the processes where the geometry of the streamlines is considered. We demonstrate its effectiveness using as example the registration between two fiber bundles.}, - language = {eng}, - number = {12}, - journal = {IEEE transactions on medical imaging}, - author = {Gori, Pietro and Colliot, Olivier and Marrakchi-Kacem, Linda and Worbe, Yulia and De Vico Fallani, Fabrizio and Chavez, Mario and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - year = {2016}, - pmid = {27416589}, - keywords = {Algorithms, Brain, Humans, Image Processing, Computer-Assisted, Computer Simulation, Nerve Fibers}, - pages = {2609--2619}, - annote = {The following values have no corresponding Zotero field:number: 12}, -} - -@article{benezit_organising_2015, - title = {Organising white matter in a brain without corpus callosum fibres}, - volume = {63}, - issn = {1973-8102}, - doi = {10.1016/j.cortex.2014.08.022}, - abstract = {Isolated corpus callosum dysgenesis (CCD) is a congenital malformation which occurs during early development of the brain. In this study, we aimed to identify and describe its consequences beyond the lack of callosal fibres, on the morphology, microstructure and asymmetries of the main white matter bundles with diffusion imaging and fibre tractography. Seven children aged between 9 and 13 years old and seven age- and gender-matched control children were studied. First, we focused on bundles within the mesial region of the cerebral hemispheres: the corpus callosum, Probst bundles and cingulum which were selected using a conventional region-based approach. We demonstrated that the Probst bundles have a wider connectivity than the previously described rostrocaudal direction, and a microstructure rather distinct from the cingulum but relatively close to callosal remnant fibres. A sigmoid bundle was found in two partial ageneses. Second, the corticospinal tract, thalamic radiations and association bundles were extracted automatically via an atlas of adult white matter bundles to overcome bias resulting from a priori knowledge of the bundles' anatomical morphology and trajectory. Despite the lack of callosal fibres and the colpocephaly observed in CCD, all major white matter bundles were identified with a relatively normal morphology, and preserved microstructure (i.e. fractional anisotropy, mean diffusivity) and asymmetries. Consequently the bundles' organisation seems well conserved in brains with CCD. These results await further investigations with functional imaging before apprehending the cognition variability in children with isolated dysgenesis.}, - language = {eng}, - journal = {Cortex; a Journal Devoted to the Study of the Nervous System and Behavior}, - author = {Bénézit, Audrey and Hertz-Pannier, Lucie and Dehaene-Lambertz, Ghislaine and Monzalvo, Karla and Germanaud, David and Duclap, Delphine and Guevara, Pamela and Mangin, Jean-François and Poupon, Cyril and Moutard, Marie-Laure and Dubois, Jessica}, - month = feb, - year = {2015}, - pmid = {25282054}, - keywords = {Brain, Humans, MRI, Adolescent, Child, Female, Male, Corpus Callosum, Nerve Fibers, Tractography, Atlas, Diffusion magnetic resonance imaging, agenesis, Agenesis of Corpus Callosum, Corpus callosum dysgenesis, Hypoplasia, Probst bundle, White matter bundles}, - pages = {155--171}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Times Cited: 3}, - annote = {Unati - Unirs - UniactPMID: 25282054 }, -} - -@article{leroy_new_2015, - title = {New human-specific brain landmark: the depth asymmetry of superior temporal sulcus}, - volume = {112}, - issn = {1091-6490}, - shorttitle = {New human-specific brain landmark}, - doi = {10.1073/pnas.1412389112}, - abstract = {Identifying potentially unique features of the human cerebral cortex is a first step to understanding how evolution has shaped the brain in our species. By analyzing MR images obtained from 177 humans and 73 chimpanzees, we observed a human-specific asymmetry in the superior temporal sulcus at the heart of the communication regions and which we have named the "superior temporal asymmetrical pit" (STAP). This 45-mm-long segment ventral to Heschl's gyrus is deeper in the right hemisphere than in the left in 95\% of typical human subjects, from infanthood till adulthood, and is present, irrespective of handedness, language lateralization, and sex although it is greater in males than in females. The STAP also is seen in several groups of atypical subjects including persons with situs inversus, autistic spectrum disorder, Turner syndrome, and corpus callosum agenesis. It is explained in part by the larger number of sulcal interruptions in the left than in the right hemisphere. Its early presence in the infants of this study as well as in fetuses and premature infants suggests a strong genetic influence. Because this asymmetry is barely visible in chimpanzees, we recommend the STAP region during midgestation as an important phenotype to investigate asymmetrical variations of gene expression among the primate lineage. This genetic target may provide important insights regarding the evolution of the crucial cognitive abilities sustained by this sulcus in our species, namely communication and social cognition.}, - language = {eng}, - number = {4}, - journal = {Proceedings of the National Academy of Sciences of the United States of America}, - author = {Leroy, François and Cai, Qing and Bogart, Stephanie L. and Dubois, Jessica and Coulon, Olivier and Monzalvo, Karla and Fischer, Clara and Glasel, Hervé and Van der Haegen, Lise and Bénézit, Audrey and Lin, Ching-Po and Kennedy, David N. and Ihara, Aya S. and Hertz-Pannier, Lucie and Moutard, Marie-Laure and Poupon, Cyril and Brysbaert, Marc and Roberts, Neil and Hopkins, William D. and Mangin, Jean-François and Dehaene-Lambertz, Ghislaine}, - month = jan, - year = {2015}, - pmid = {25583500}, - pmcid = {PMC4313811}, - keywords = {anatomy, Humans, Adult, Child, Child Development Disorders, Pervasive, Female, Male, Temporal Lobe, Middle Aged, Infant, Animals, Cognition, Radiography, Agenesis of Corpus Callosum, human-specific, Pan troglodytes, Situs Inversus, STS, Turner Syndrome}, - pages = {1208--1213}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACL}, - annote = {Times Cited: 7}, - annote = {Unicog - Unati - UnirsPMID: 25583500 }, -} - -@article{kulikova_multi-parametric_2015, - title = {Multi-parametric evaluation of the white matter maturation}, - volume = {220}, - issn = {1863-2661}, - doi = {10.1007/s00429-014-0881-y}, - abstract = {In vivo evaluation of the brain white matter maturation is still a challenging task with no existing gold standards. In this article we propose an original approach to evaluate the early maturation of the white matter bundles, which is based on comparison of infant and adult groups using the Mahalanobis distance computed from four complementary MRI parameters: quantitative qT1 and qT2 relaxation times, longitudinal λ║ and transverse λ⊥ diffusivities from diffusion tensor imaging. Such multi-parametric approach is expected to better describe maturational asynchrony than conventional univariate approaches because it takes into account complementary dependencies of the parameters on different maturational processes, notably the decrease in water content and the myelination. Our approach was tested on 17 healthy infants (aged 3- to 21-week old) for 18 different bundles. It finely confirmed maturational asynchrony across the bundles: the spino-thalamic tract, the optic radiations, the cortico-spinal tract and the fornix have the most advanced maturation, while the superior longitudinal and arcuate fasciculi, the anterior limb of the internal capsule and the external capsule have the most delayed maturation. Furthermore, this approach was more reliable than univariate approaches as it revealed more maturational relationships between the bundles and did not violate a priori assumptions on the temporal order of the bundle maturation. Mahalanobis distances decreased exponentially with age in all bundles, with the only difference between them explained by different onsets of maturation. Estimation of these relative delays confirmed that the most dramatic changes occur during the first post-natal year.}, - language = {eng}, - number = {6}, - journal = {Brain Structure \& Function}, - author = {Kulikova, S. and Hertz-Pannier, L. and Dehaene-Lambertz, G. and Buzmakov, A. and Poupon, C. and Dubois, J.}, - month = nov, - year = {2015}, - pmid = {25183543}, - pmcid = {PMC4575699}, - keywords = {Brain, Humans, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Infant, Signal Processing, Computer-Assisted, Infant, Newborn, Diffusion magnetic resonance imaging, Bundles, Diffusion tensor Imaging DTI, Infants, Mahalanobis distance, T1 and T2 relaxometry}, - pages = {3657--3672}, - annote = {The following values have no corresponding Zotero field:number: 6label: ACL}, - annote = {UniactPMID: 25183543 }, -} - -@article{pyatigorskaya_medulla_2016, - title = {Medulla oblongata damage and cardiac autonomic dysfunction in {Parkinson} disease}, - volume = {87}, - issn = {1526-632X}, - doi = {10.1212/WNL.0000000000003426}, - abstract = {OBJECTIVE: To characterize medulla oblongata damage using diffusion tensor imaging (DTI) in Parkinson disease (PD) and correlate it with dysfunction of the cardiac sympathetic/vagal balance. -METHODS: Fifty-two patients with PD and 24 healthy controls were included in the study. All participants underwent clinical examination and 3T MRI using 3D T1-weighted imaging and DTI. DTI metrics were calculated within manually drawn regions of interest. Heart rate variability was evaluated using spectral analysis of the R-R cardiac interval during REM and slow-wave sleep based on continuous overnight electrocardiographic monitoring. Respiratory frequency was measured in 30-second contiguous epochs of REM and slow-wave sleep. The relationships between imaging and cardiac variables were calculated using partial correlations followed by the multiple comparisons permutation approach. -RESULTS: The changes in heart rate and respiratory frequency variability from slow-wave sleep to REM sleep in healthy controls were no longer detectable in patients with PD. There were significant increases in the mean (p = 0.006), axial (p = 0.006), and radial diffusivities (p = 0.005) in the medulla oblongata of patients with PD. In PD, diffusion changes were specifically correlated with a lower heart rate and respiratory frequency variability during REM sleep. -CONCLUSIONS: This study provides evidence that medulla oblongata damage underlies cardiac sympathetic/vagal balance and respiratory dysfunction in patients with PD.}, - language = {eng}, - number = {24}, - journal = {Neurology}, - author = {Pyatigorskaya, Nadya and Mongin, Marie and Valabregue, Romain and Yahia-Cherif, Lydia and Ewenczyk, Claire and Poupon, Cyril and Debellemaniere, Eden and Vidailhet, Marie and Arnulf, Isabelle and Lehéricy, Stephane}, - month = dec, - year = {2016}, - pmid = {27837003}, - keywords = {Humans, Adult, Adolescent, Female, Male, Young Adult, Middle Aged, Aged, Wakefulness, Parkinson Disease, Autonomic Nervous System Diseases, Heart Diseases, Heart Rate, Medulla Oblongata, Sleep}, - pages = {2540--2545}, - annote = {The following values have no corresponding Zotero field:number: 24}, -} - -@article{marrakchi-kacem_mapping_2013, - title = {Mapping cortico-striatal connectivity onto the cortical surface: a new tractography-based approach to study {Huntington} disease}, - volume = {8}, - issn = {1932-6203}, - shorttitle = {Mapping cortico-striatal connectivity onto the cortical surface}, - doi = {10.1371/journal.pone.0053135}, - abstract = {Huntington disease (HD) is associated with early and severe damage to the basal ganglia and particularly the striatum. We investigated cortico-striatal connectivity modifications occurring in HD patients using a novel approach which focuses on the projection of the connectivity profile of the basal ganglia onto the cortex. This approach consists in computing, for each subcortical structure, surface connectivity measures representing its strength of connections to the cortex and comparing these measures across groups. In this study, we focused on Huntington disease as an application of this new approach. First, surface cortico-striatal connectivity measures of a group of healthy subjects were averaged in order to infer the "normal" connectivity profile of the striatum to the cortex. Second, a statistical analysis was performed from the surface connectivity measures of healthy subjects and HD patients in order to detect the cortical gyri presenting altered cortico-striatal connectivity in HD. Lastly, percentage differences of connectivity between healthy subjects and patients were inferred, for each nucleus of the striatum, from the connectivity measures of the cortical gyri presenting a significant connectivity difference between the two groups. These percentage differences characterize the axonal disruptions between the striatum and the cortex occurring in HD. We found selective region-specific degeneration of cortical connections predominating for associative and primary sensorimotor connections and with relative preservation of limbic connections. Our method can be used to infer novel connectivity-based markers of HD pathological process.}, - language = {eng}, - number = {2}, - journal = {PloS One}, - author = {Marrakchi-Kacem, Linda and Delmaire, Christine and Guevara, Pamela and Poupon, Fabrice and Lecomte, Sophie and Tucholka, Alan and Roca, Pauline and Yelnik, Jérôme and Durr, Alexandra and Mangin, Jean-François and Lehéricy, Stéphane and Poupon, Cyril}, - year = {2013}, - pmid = {23405066}, - pmcid = {PMC3566172}, - keywords = {Humans, Brain Mapping, Female, Male, Middle Aged, Diffusion Tensor Imaging, Limbic System, Corpus Striatum, Huntington Disease, Motor Cortex, Sensory Receptor Cells}, - pages = {e53135}, -} - -@article{gori_joint_2015, - title = {Joint {Morphometry} of {Fiber} {Tracts} and {Gray} {Matter} {Structures} {Using} {Double} {Diffeomorphisms}}, - volume = {24}, - issn = {1011-2499}, - abstract = {This work proposes an atlas construction method to jointly analyse the relative position and shape of fiber tracts and gray matter structures. It is based on a double diffeomorphism which is a composition of two diffeomorphisms. The first diffeomorphism acts only on the white matter keeping fixed the gray matter of the atlas. The resulting white matter, together with the gray matter, are then deformed by the second diffeomorphism. The two diffeomorphisms are related and jointly optimised. In this way, the, first diffeomorphisms explain the variability in structural connectivity within the population, namely both changes in the connected areas of the gray matter and in the geometry of the pathway of the tracts. The second diffeomorphisms put into correspondence the homologous anatomical structures across subjects. Fiber bundles are approximated with weighted prototypes using the metric of weighted currents. The atlas, the covariance matrix of deformation parameters and the noise variance of each structure are automatically estimated using a Bayesian approach. This method is applied to patients with Tourette syndrome and controls showing a variability in the structural connectivity of the left cortico-putamen circuit.}, - language = {eng}, - journal = {Information Processing in Medical Imaging: Proceedings of the ... Conference}, - author = {Gori, Pietro and Colliot, Olivier and Marrakchi-Kacem, Linda and Worbe, Yulia and Routier, Alexandre and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - year = {2015}, - pmid = {26221680}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Models, Statistical, Subtraction Technique, Nerve Fibers, Myelinated, Gray Matter}, - pages = {275--287}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unirs - MetricPMID: 26221680}, -} - -@article{wessa_impaired_2016, - title = {Impaired and preserved aspects of feedback learning in {aMCI}: contributions of structural connectivity}, - volume = {221}, - issn = {1863-2661}, - shorttitle = {Impaired and preserved aspects of feedback learning in {aMCI}}, - doi = {10.1007/s00429-015-1075-y}, - abstract = {Distinct lines of research demonstrated that patients with amnestic mild cognitive impairment (aMCI), a potential precursor of Alzheimer disease (AD), are particularly impaired in remembering relations between items and that the use of emotional targets can facilitate memory in patients with AD. We link these findings by examining learning through positive and negative feedback in patients with aMCI, and explore its anatomic underpinnings with diffusion tensor imaging and tractography. Compared to healthy controls, patients with single-domain aMCI were impaired in learning from positive feedback, while learning from negative outcomes was preserved. Among pathways within the brain circuit involved in feedback learning, abnormal white matter microstructure was observed in tracts, which connect left-hemispheric amygdala with hippocampus and entorhinal cortex. In all participants, reduced white matter integrity in this left fiber tract was specifically associated with learning from positive outcomes. Microstructure of right-hemispheric tracts between amygdala and entorhinal cortex was related to learning from negative feedback, and was not compromised in aMCI patients. Our results provide new insight into how anatomical connections might contribute to impaired and preserved aspects of learning behaviors in the early AD process and indicate potential compensatory mechanisms.}, - language = {eng}, - number = {5}, - journal = {Brain Structure \& Function}, - author = {Wessa, Michèle and King, Andrea V. and Meyer, Patric and Frölich, Lutz and Flor, Herta and Poupon, Cyril and Hoppstädter, Michael and Linke, Julia}, - year = {2016}, - pmid = {26084875}, - keywords = {Brain, Humans, Female, Male, Middle Aged, Neural Pathways, Functional Laterality, Aged, Amnesia, Hippocampus, Cognitive Dysfunction, Amygdala, Tractography, Amnestic mild cognitive impairment, Entorhinal cortex, Formative Feedback}, - pages = {2831--2846}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unirs - MetricPMID: 26084875 }, -} - -@article{labra_gpu-based_2013, - title = {{GPU}-based acceleration of an automatic white matter segmentation algorithm using {CUDA}}, - volume = {2013}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2013.6609444}, - abstract = {This paper presents a parallel implementation of an algorithm for automatic segmentation of white matter fibers from tractography data. We execute the algorithm in parallel using a high-end video card with a Graphics Processing Unit (GPU) as a computation accelerator, using the CUDA language. By exploiting the parallelism and the properties of the memory hierarchy available on the GPU, we obtain a speedup in execution time of 33.6 with respect to an optimized sequential version of the algorithm written in C, and of 240 with respect to the original Python/C++ implementation. The execution time is reduced from more than two hours to only 35 seconds for a subject dataset of 800,000 fibers, thus enabling applications that use interactive segmentation and visualization of small to medium-sized tractography datasets.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Labra, Nicole and Figueroa, Miguel and Guevara, Pamela and Duclap, Delphine and Hoeunou, Josselin and Poupon, Cyril and Mangin, Jean-Francois}, - year = {2013}, - pmid = {24109631}, - keywords = {Algorithms, Humans, Software, Brain Mapping, Image Processing, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Databases, Factual, Radiography}, - pages = {89--92}, -} - -@article{bzdok_formal_2016, - title = {Formal {Models} of the {Network} {Co}-occurrence {Underlying} {Mental} {Operations}}, - volume = {12}, - issn = {1553-7358}, - doi = {10.1371/journal.pcbi.1004994}, - abstract = {Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81) by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition.}, - language = {eng}, - number = {6}, - journal = {PLoS computational biology}, - author = {Bzdok, Danilo and Varoquaux, Gaël and Grisel, Olivier and Eickenberg, Michael and Poupon, Cyril and Thirion, Bertrand}, - year = {2016}, - pmid = {27310288}, - pmcid = {PMC4911040}, - keywords = {Brain, Humans, Models, Neurological, Adult, Female, Male, Young Adult, Cognition, Nerve Net, Learning, Machine Learning, Neurons}, - pages = {e1004994}, - annote = {The following values have no corresponding Zotero field:number: 6}, -} - -@article{labra_fast_2017, - title = {Fast {Automatic} {Segmentation} of {White} {Matter} {Streamlines} {Based} on a {Multi}-{Subject} {Bundle} {Atlas}}, - volume = {15}, - issn = {1559-0089}, - doi = {10.1007/s12021-016-9316-7}, - abstract = {This paper presents an algorithm for fast segmentation of white matter bundles from massive dMRI tractography datasets using a multisubject atlas. We use a distance metric to compare streamlines in a subject dataset to labeled centroids in the atlas, and label them using a per-bundle configurable threshold. In order to reduce segmentation time, the algorithm first preprocesses the data using a simplified distance metric to rapidly discard candidate streamlines in multiple stages, while guaranteeing that no false negatives are produced. The smaller set of remaining streamlines is then segmented using the original metric, thus eliminating any false positives from the preprocessing stage. As a result, a single-thread implementation of the algorithm can segment a dataset of almost 9 million streamlines in less than 6 minutes. Moreover, parallel versions of our algorithm for multicore processors and graphics processing units further reduce the segmentation time to less than 22 seconds and to 5 seconds, respectively. This performance enables the use of the algorithm in truly interactive applications for visualization, analysis, and segmentation of large white matter tractography datasets.}, - language = {eng}, - number = {1}, - journal = {Neuroinformatics}, - author = {Labra, Nicole and Guevara, Pamela and Duclap, Delphine and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Figueroa, Miguel}, - year = {2017}, - pmid = {27722821}, - keywords = {Algorithms, Brain, Humans, Pattern Recognition, Automated, Software, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Diffusion Magnetic Resonance Imaging, Neural Pathways, Connectome, Tractography segmentation, White matter tracts, Diffusion-weighted MRI, GPU programming, HARDI data, Streamline distance}, - pages = {71--86}, -} - -@article{dubois_exploring_2016, - title = {Exploring the {Early} {Organization} and {Maturation} of {Linguistic} {Pathways} in the {Human} {Infant} {Brain}}, - volume = {26}, - issn = {1460-2199}, - doi = {10.1093/cercor/bhv082}, - abstract = {Linguistic processing is based on a close collaboration between temporal and frontal regions connected by two pathways: the "dorsal" and "ventral pathways" (assumed to support phonological and semantic processing, respectively, in adults). We investigated here the development of these pathways at the onset of language acquisition, during the first post-natal weeks, using cross-sectional diffusion imaging in 21 healthy infants (6-22 weeks of age) and 17 young adults. We compared the bundle organization and microstructure at these two ages using tractography and original clustering analyses of diffusion tensor imaging parameters. We observed structural similarities between both groups, especially concerning the dorsal/ventral pathway segregation and the arcuate fasciculus asymmetry. We further highlighted the developmental tempos of the linguistic bundles: The ventral pathway maturation was more advanced than the dorsal pathway maturation, but the latter catches up during the first post-natal months. Its fast development during this period might relate to the learning of speech cross-modal representations and to the first combinatorial analyses of the speech input.}, - language = {eng}, - number = {5}, - journal = {Cerebral Cortex (New York, N.Y.: 1991)}, - author = {Dubois, Jessica and Poupon, Cyril and Thirion, Bertrand and Simonnet, Hina and Kulikova, Sofya and Leroy, François and Hertz-Pannier, Lucie and Dehaene-Lambertz, Ghislaine}, - month = may, - year = {2016}, - pmid = {25924951}, - keywords = {Brain, Humans, Female, Male, Temporal Lobe, Infant, Neural Pathways, Cross-Sectional Studies, Frontal Lobe, Diffusion magnetic resonance imaging, interhemispheric asymmetry, Language Development, language network, Linguistics, white matter maturation and myelination}, - pages = {2283--2298}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unirs - MetricPMID: 25924951}, -} - -@article{scholz_dysfunctional_2016, - title = {Dysfunctional decision-making related to white matter alterations in bipolar {I} disorder}, - volume = {194}, - issn = {1573-2517}, - doi = {10.1016/j.jad.2015.12.019}, - abstract = {OBJECTIVE: This study investigated how frontal white matter (WM) alterations in patients with bipolar I disorder (BD-I) are linked to motivational dysregulation, often reported in the form of risk-taking and impulsivity, and whether structure-function relations in patients might differ from healthy subjects (HC). -METHOD: We acquired diffusion data from 24 euthymic BD-I patients and 24 controls, to evaluate WM integrity of selected frontal tracts. Risk-taking was assessed by the Cambridge Gambling Task and impulsivity by self-report with the Barratt-Impulsiveness Scale. -RESULTS: BD-I patients displayed significantly lower integrity in the right cingulum compared to HC. They also showed more risk-taking behavior and reported increased trait-impulsivity. Risk-taking was negatively associated with WM integrity in the right cingulum. Impulsivity was not related to WM integrity in investigated tracts. Together with age and sex, FA in the cingulum explained 25\% of variance in risk-taking scores in all study participants. The left inferior fronto-occipital fasciculus (IFOF) was specifically predictive of risk-taking behavior in BD-I patients, but not in HC. -LIMITATIONS: The employed parameters did not allow us to specify the exact origin of WM changes, nor did the method allow the analysis of specific brain subregions. Also, sample size was moderate and the sample included patients with lifetime alcohol dependence/abuse, hence effects found need replication and have to be interpreted with caution. -CONCLUSION: Our results further strengthen recent models linking structural changes in frontal networks to behavioral markers of BD-I. They extend recent findings by showing that risk-taking is also linked to the cingulum in BD-I and HC, while other prefrontal tracts (IFOF) are specifically implicated in risk-taking behavior in BD-I patients. Meanwhile, self-reported impulsivity was not associated with WM integrity of the tracts investigated in our study.}, - language = {eng}, - journal = {Journal of Affective Disorders}, - author = {Scholz, Vanessa and Houenou, Josselin and Kollmann, Bianca and Duclap, Delphine and Poupon, Cyril and Wessa, Michèle}, - month = apr, - year = {2016}, - pmid = {26803778}, - keywords = {Humans, Adult, Female, Male, Middle Aged, Nerve Net, Case-Control Studies, Impulsive Behavior, Impulsivity, Self Report, DTI, Bipolar-I disorder, Decision Making, Risk-taking}, - pages = {72--79}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Uniact}, -} - -@article{lyoubi-idrissi_diffusion_2017, - title = {Diffusion magnetic resonance imaging in cerebral small vessel disease}, - volume = {173}, - issn = {0035-3787}, - doi = {10.1016/j.neurol.2017.03.005}, - abstract = {Cerebral small vessel disease (SVD) is frequent in the elderly, and accounts for a wide spectrum of clinical and radiological manifestations. This report summarizes the most important findings obtained using diffusion MRI (DWI) in SVD. With DWI and apparent diffusion coefficient (ADC) maps, recent ischemic lesions can easily be detected after acute stroke in SVD, while even multiple simultaneous lesions may be observed. Microstructural changes are frequent in SVD, with increases in diffusivity and decreases in anisotropy being the most reliable findings observed, mainly in white matter. These tissue changes are associated with clinical severity and especially executive dysfunction. They can also precede the usual MRI markers of SVD, such as white matter hyperintensities, microbleeds and lacunes. Thus, DWI may reveal surrogate markers of SVD progression and offer a better understanding of their underlying mechanisms.}, - language = {eng}, - number = {4}, - journal = {Revue Neurologique}, - author = {Lyoubi-Idrissi, A. L. and Jouvent, E. and Poupon, C. and Chabriat, H.}, - month = apr, - year = {2017}, - pmid = {28392060}, - keywords = {Humans, Image Processing, Computer-Assisted, Diffusion Tensor Imaging, Diffusion magnetic resonance imaging, AMYLOID ANGIOPATHY, Author Keywords:Small vessel disease, AXON DIAMETER DISTRIBUTION, Diffusion-weighted imaging, HUMAN-BRAIN, ISCHEMIC LEUKOARAIOSIS, KeyWords Plus:AUTOSOMAL-DOMINANT ARTERIOPATHY, LACUNAR INFARCTS, Small vessel disease, Stroke, TENSOR MRI, TISSUE MICROSTRUCTURAL CHANGES, WEIGHTED MRI, WHITE-MATTER}, - pages = {201--210}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACL}, - annote = {UnirsDOI: 10.1016/j.neurol.2017.03.005}, - annote = {UnirsPMID: 28392060 DOI: 10.1016/j.neurol.2017.03.005}, -} - -@article{boutet_detection_2014, - title = {Detection of volume loss in hippocampal layers in {Alzheimer}'s disease using 7 {T} {MRI}: a feasibility study}, - volume = {5}, - issn = {2213-1582}, - shorttitle = {Detection of volume loss in hippocampal layers in {Alzheimer}'s disease using 7 {T} {MRI}}, - doi = {10.1016/j.nicl.2014.07.011}, - abstract = {In Alzheimer's disease (AD), the hippocampus is an early site of tau pathology and neurodegeneration. Histological studies have shown that lesions are not uniformly distributed within the hippocampus. Moreover, alterations of different hippocampal layers may reflect distinct pathological processes. 7 T MRI dramatically improves the visualization of hippocampal subregions and layers. In this study, we aimed to assess whether 7 T MRI can detect volumetric changes in hippocampal layers in vivo in patients with AD. We studied four AD patients and seven control subjects. MR images were acquired using a whole-body 7 T scanner with an eight channel transmit-receive coil. Hippocampal subregions were manually segmented from coronal T2*-weighted gradient echo images with 0.3 × 0.3 × 1.2 mm3 resolution using a protocol that distinguishes between layers richer or poorer in neuronal bodies. Five subregions were segmented in the region of the hippocampal body: alveus, strata radiatum, lacunosum and moleculare (SRLM) of the cornu Ammonis (CA), hilum, stratum pyramidale of CA and stratum pyramidale of the subiculum. We found strong bilateral reductions in the SRLM of the cornu Ammonis and in the stratum pyramidale of the subiculum (p {\textless} 0.05), with average cross-sectional area reductions ranging from -29\% to -49\%. These results show that it is possible to detect volume loss in distinct hippocampal layers using segmentation of 7 T MRI. 7 T MRI-based segmentation is a promising tool for AD research.}, - language = {eng}, - journal = {NeuroImage. Clinical}, - author = {Boutet, Claire and Chupin, Marie and Lehéricy, Stéphane and Marrakchi-Kacem, Linda and Epelbaum, Stéphane and Poupon, Cyril and Wiggins, Christopher and Vignaud, Alexandre and Hasboun, Dominique and Defontaines, Bénédicte and Hanon, Olivier and Dubois, Bruno and Sarazin, Marie and Hertz-Pannier, Lucie and Colliot, Olivier}, - year = {2014}, - pmid = {25161900}, - pmcid = {PMC4141975}, - keywords = {Humans, Image Interpretation, Computer-Assisted, Alzheimer Disease, Female, Male, Middle Aged, Aged, Hippocampus, Alzheimer's disease, Segmentation, Volumetry, 7 T, 7 Tesla, AD, Alzheimer's disease, CA, cornu Ammonis, CN, cognitively normal, DG, dentate gyrus, Hippocampal layers, Human 7 T MRI, MRI, magnetic resonance imaging, SP, stratum pyramidale, SRLM, strata radiatum, lacunosum and moleculare, 7 T, 7 Tesla, Feasibility Studies, Human 7 T MRI}, - pages = {341--348}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UniactPMID: 25161900}, -} - -@article{sarrazin_corpus_2015, - title = {Corpus callosum area in patients with bipolar disorder with and without psychotic features: an international multicentre study}, - volume = {40}, - copyright = {All rights reserved}, - issn = {1180-4882}, - doi = {10.1503/jpn.140262}, - abstract = {Background Previous studies have reported MRI abnormalities of the corpus callosum (CC) in patients with bipolar disorder (BD), although only a few studies have directly compared callosal areas in psychotic versus nonpsychotic patients with this disorder. We sought to compare regional callosal areas in a large international multicentre sample of patients with BD and healthy controls. Methods We analyzed anatomic T-1 MRI data of patients with BD-I and healthy controls recruited from 4 sites (France, Germany, Ireland and the United States). We obtained the mid-sagittal areas of 7 CC subregions using an automatic CC delineation. Differences in regional callosal areas between patients and controls were compared using linear mixed models (adjusting for age, sex, handedness, brain volume, history of alcohol abuse/dependence, lithium or antipsychotic medication status, symptomatic status and site) and multiple comparisons correction. We also compared regional areas of the CC between patients with BD with and without a history of psychotic features. Results We included 172 patients and 146 controls in our study. Patients with BD had smaller adjusted mid-sagittal CC areas than controls along the posterior body, the isthmus and the splenium of the CC. Patients with a positive history of psychotic features had greater adjusted area of the rostral CC region than those without a history of psychotic features. Limitations We found small to medium effect sizes, and there was no calibration technique among the sites. Conclusion Our results suggest that BD with psychosis is associated with a different pattern of interhemispheric connectivity than BD without psychosis and could be considered a relevant neuroimaging subtype of BD.}, - number = {5}, - journal = {JOURNAL OF PSYCHIATRY \& NEUROSCIENCE}, - author = {Sarrazin, Samuel and d'Albis, Marc-Antoine and McDonald, Colm and Linke, Julia and Wessa, Michele and Phillips, Mary and Delavest, Marine and Emsell, Louise and Versace, Amelia and Almeida, Jorge and Mangin, Jean-Francois and Poupon, Cyril and Le Dudal, Katia and Daban, Claire and Hamdani, Nora and Leboyer, Marion and Houenou, Josselin}, - month = sep, - year = {2015}, - keywords = {Humans, Image Processing, Computer-Assisted, Adult, Female, Male, Bipolar Disorder, Corpus Callosum, United States, Middle Aged, Linear Models, Antipsychotic Agents, Lithium, Diagnostic and Statistical Manual of Mental Disorders, France, Germany, Ireland}, - pages = {352--359}, - annote = {The following values have no corresponding Zotero field:number: 5label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 26151452}, -} - -@inproceedings{guevara_creation_2016, - title = {Creation of a whole brain short association bundle atlas using a hybrid approach.}, - copyright = {All rights reserved}, - doi = {10.1109/EMBC.2016.7590899}, - author = {Guevara, M. and Roman, C. and Houenou, J. and Duclap, D. and Poupon, C. and Mangin, J. F. and Guevara, P.}, - month = aug, - year = {2016}, - keywords = {Brain, Humans, Reproducibility of Results, Brain Mapping, White Matter, Cluster Analysis}, - pages = {1115--1119}, - annote = {The following values have no corresponding Zotero field:pub-location: Strasbourg, France}, - annote = {UnirsPMID: 28268521.}, -} - -@article{senova_optogenetic_2018, - title = {Optogenetic {Tractography} for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates}, - volume = {8}, - issn = {2045-2322}, - doi = {10.1038/s41598-018-21486-8}, - abstract = {Dissecting neural circuitry in non-human primates (NHP) is crucial to identify potential neuromodulation anatomical targets for the treatment of pharmacoresistant neuropsychiatric diseases by electrical neuromodulation. How targets of deep brain stimulation (DBS) and cortical targets of transcranial magnetic stimulation (TMS) compare and might complement one another is an important question. Combining optogenetics and tractography may enable anatomo-functional characterization of large brain cortico-subcortical neural pathways. For the proof-of-concept this approach was used in the NHP brain to characterize the motor cortico-subthalamic pathway (m\_CSP) which might be involved in DBS action mechanism in Parkinson's disease (PD). Rabies-G-pseudotyped and Rabies-G-VSVg-pseudotyped EIAV lentiviral vectors encoding the opsin ChR2 gene were stereotaxically injected into the subthalamic nucleus (STN) and were retrogradely transported to the layer of the motor cortex projecting to STN. A precise anatomical mapping of this pathway was then performed using histology-guided high angular resolution MRI tractography guiding accurately cortical photostimulation of m\_CSP origins. Photoexcitation of m\_CSP axon terminals or m\_CSP cortical origins modified the spikes distribution for photosensitive STN neurons firing rate in non-equivalent ways. Optogenetic tractography might help design preclinical neuromodulation studies in NHP models of neuropsychiatric disease choosing the most appropriate target for the tested hypothesis.}, - language = {eng}, - number = {1}, - journal = {Scientific Reports}, - author = {Senova, S. and Poupon, C. and Dauguet, J. and Stewart, H. J. and Dugué, G. P. and Jan, C. and Hosomi, K. and Ralph, G. S. and Barnes, L. and Drouot, X. and Pouzat, C. and Mangin, J. F. and Pain, F. and Doignon, I. and Aron-Badin, R. and Brouillet, E. and Boyden, E. S. and Mitrophanous, K. A. and Hantraye, P. and Palfi, S.}, - month = feb, - year = {2018}, - pmid = {29463867}, - pmcid = {PMC5820256}, - pages = {3362}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WG2RQFY7/Senova et al. - 2018 - Optogenetic Tractography for anatomo-functional ch.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Y4KZLJ9E/Senova et al. - 2018 - Optogenetic Tractography for anatomo-functional ch.pdf:application/pdf}, -} - -@article{gramfort_denoising_2014, - title = {Denoising and fast diffusion imaging with physically constrained sparse dictionary learning}, - volume = {18}, - issn = {1361-8423}, - doi = {10.1016/j.media.2013.08.006}, - abstract = {Diffusion-weighted imaging (DWI) allows imaging the geometry of water diffusion in biological tissues. However, DW images are noisy at high b-values and acquisitions are slow when using a large number of measurements, such as in Diffusion Spectrum Imaging (DSI). This work aims to denoise DWI and reduce the number of required measurements, while maintaining data quality. To capture the structure of DWI data, we use sparse dictionary learning constrained by the physical properties of the signal: symmetry and positivity. The method learns a dictionary of diffusion profiles on all the DW images at the same time and then scales to full brain data. Its performance is investigated with simulations and two real DSI datasets. We obtain better signal estimates from noisy measurements than by applying mirror symmetry through the q-space origin, Gaussian denoising or state-of-the-art non-local means denoising. Using a high-resolution dictionary learnt on another subject, we show that we can reduce the number of images acquired while still generating high resolution DSI data. Using dictionary learning, one can denoise DW images effectively and perform faster acquisitions. Higher b-value acquisitions and DSI techniques are possible with approximately 40 measurements. This opens important perspectives for the connectomics community using DSI.}, - language = {eng}, - number = {1}, - journal = {Medical Image Analysis}, - author = {Gramfort, A. and Poupon, C. and Descoteaux, M.}, - month = jan, - year = {2014}, - pmid = {24084469}, - keywords = {Algorithms, Artificial Intelligence, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Diffusion-weighted imaging, Signal-To-Noise Ratio, Denoising, Diffusion Spectrum Imaging (DSI), Sparse coding, Undersampling}, - pages = {36--49}, -} - -@article{linke_impaired_2013, - title = {Impaired anatomical connectivity and related executive functions: differentiating vulnerability and disease marker in bipolar disorder}, - volume = {74}, - issn = {1873-2402}, - shorttitle = {Impaired anatomical connectivity and related executive functions}, - doi = {10.1016/j.biopsych.2013.04.010}, - abstract = {BACKGROUND: Bipolar 1 disorder (BD1) has been associated with impaired set shifting, increased risk taking, and impaired integrity of frontolimbic white matter. However, it remains unknown to what extent these findings are related to each other and whether these abnormalities represent risk factors or consequences of the illness. -METHODS: We addressed the first question by comparing 19 patients with BD1 and 19 healthy control subjects (sample 1) with diffusion tensor imaging, the Intra-Extra Dimensional Set Shift Task, and the Cambridge Gambling Task. The second question we approached by applying the same protocol to 22 healthy first-degree relatives of patients with BD1 and 22 persons without a family history of mental disorders (sample 2). -RESULTS: In comparison with their control groups, BD1 patients and healthy first-degree relatives of patients with BD1 showed significantly reduced fractional anisotropy (FA) in the right anterior limb of the internal capsule and right uncinate fasciculus. White matter integrity in corpus callosum was reduced in BD1 patients only. In addition, reduced FA in anterior limb of the internal capsule correlated significantly with an increased number of errors during set shifting and increased risk taking and reduced FA in uncinate fasciculus correlated significantly with increased risk taking. -CONCLUSIONS: Similar white matter alterations in BD1 patients and healthy relatives of BD1 patients are associated with comparable behavioral abnormalities. Further, results indicate that altered frontolimbic and frontothalamic connectivity and corresponding behavioral abnormalities might be a trait and vulnerability marker of BD1, whereas interhemispheric connectivity appears to be a disease marker.}, - language = {eng}, - number = {12}, - journal = {Biological Psychiatry}, - author = {Linke, Julia and King, Andrea V. and Poupon, Cyril and Hennerici, Michael G. and Gass, Achim and Wessa, Michèle}, - month = dec, - year = {2013}, - pmid = {23684382}, - keywords = {Brain, Humans, Adult, Adolescent, Female, Male, Neuropsychological Tests, Young Adult, Corpus Callosum, Middle Aged, Anisotropy, Nerve Fibers, Myelinated, Psychiatric Status Rating Scales, Cognition Disorders, Statistics as Topic, Family, Executive Function, DTI, Diffusion magnetic resonance imaging, first-degree relatives, fractional anisotropy, risk taking, set shifting}, - pages = {908--916}, -} - -@article{garcia-lorenzo_coeruleus/subcoeruleus_2013, - title = {The coeruleus/subcoeruleus complex in rapid eye movement sleep behaviour disorders in {Parkinson}'s disease}, - volume = {136}, - issn = {1460-2156}, - doi = {10.1093/brain/awt152}, - abstract = {In Parkinson's disease, rapid eye movement sleep behaviour disorder is an early non-dopaminergic syndrome with nocturnal violence and increased muscle tone during rapid eye movement sleep that can precede Parkinsonism by several years. The neuronal origin of rapid eye movement sleep behaviour disorder in Parkinson's disease is not precisely known; however, the locus subcoeruleus in the brainstem has been implicated as this structure blocks muscle tone during normal rapid eye movement sleep in animal models and can be damaged in Parkinson's disease. Here, we studied the integrity of the locus coeruleus/subcoeruleus complex in patients with Parkinson's disease using combined neuromelanin-sensitive, structural and diffusion magnetic resonance imaging approaches. We compared 24 patients with Parkinson's disease and rapid eye movement sleep behaviour disorder, 12 patients without rapid eye movement sleep behaviour disorder and 19 age- and gender-matched healthy volunteers. All subjects underwent clinical examination and characterization of rapid eye movement sleep using video-polysomnography and multimodal imaging at 3 T. Using neuromelanin-sensitive imaging, reduced signal intensity was evident in the locus coeruleus/subcoeruleus area in patients with Parkinson's disease that was more marked in patients with than those without rapid eye movement sleep behaviour disorder. Reduced signal intensity correlated with the percentage of abnormally increased muscle tone during rapid eye movement sleep. The results confirmed that this complex is affected in Parkinson's disease and showed a gradual relationship between damage to this structure, presumably the locus subcoeruleus, and abnormal muscle tone during rapid eye movement sleep, which is the cardinal marker of rapid eye movement sleep behaviour disorder. In longitudinal studies, the technique may also provide early markers of non-dopaminergic Parkinson's disease pathology to predict the occurrence of Parkinson's disease.}, - language = {eng}, - number = {Pt 7}, - journal = {Brain: A Journal of Neurology}, - author = {García-Lorenzo, Daniel and Longo-Dos Santos, Clarisse and Ewenczyk, Claire and Leu-Semenescu, Smaranda and Gallea, Cecile and Quattrocchi, Graziella and Pita Lobo, Patricia and Poupon, Cyril and Benali, Habib and Arnulf, Isabelle and Vidailhet, Marie and Lehericy, Stéphane}, - month = jul, - year = {2013}, - pmid = {23801736}, - pmcid = {PMC3692035}, - keywords = {Humans, MRI, Brain Mapping, Image Processing, Computer-Assisted, Regression Analysis, Adult, Adolescent, Female, Male, Young Adult, Middle Aged, Aged, Retrospective Studies, Electroencephalography, Parkinson Disease, REM Sleep Behavior Disorder, Neurologic Examination, Electromyography, Locus Coeruleus, Melanins, neuromelanin-sensitive imaging, Polysomnography, RBD, VBM, Video Recording}, - pages = {2120--2129}, -} - -@article{houenou_cytomegalovirus_2014, - title = {Cytomegalovirus seropositivity and serointensity are associated with hippocampal volume and verbal memory in schizophrenia and bipolar disorder}, - volume = {48}, - issn = {1878-4216}, - doi = {10.1016/j.pnpbp.2013.09.003}, - abstract = {INTRODUCTION: Cytomegalovirus (CMV) is a member of the herpesviridae family that has a limbic and temporal gray matter tropism. It is usually latent in humans but has been associated with schizophrenia, bipolar disorder and cognitive deficits in some populations. Hippocampal decreased volume and dysfunction play a critical role in these cognitive deficits. We hypothesized that CMV seropositivity and serointensity would be associated with hippocampal volume and cognitive functioning in patients with schizophrenia or bipolar disorder. -METHODS: 102 healthy controls, 118 patients with bipolar disorder and 69 patients with schizophrenia performed the California Verbal Learning Test (CVLT) and had blood samples drawn to assess CMV IgG levels. A subgroup of 52 healthy controls, 31 patients with bipolar disorder and 27 patients with schizophrenia underwent T1 MRI for hippocampal volumetry. We analyzed the association between CMV serointensity and seropositivity with hippocampal volume. We also explored the correlation between CMV serointensity and seropositivity and CVLT scores. -RESULTS: In both patient groups but not in controls, higher CMV serointensity was significantly associated with smaller right hippocampal volume. Further, in the group of patients with schizophrenia but not bipolar disorder, CMV serointensity was negatively correlated with CVLT scores. -CONCLUSION: CMV IgG titers are associated with decreased hippocampal volume and poorer episodic verbal memory in patients with schizophrenia or bipolar disorder. The mechanism of this association warrants further exploration.}, - language = {eng}, - journal = {Progress in Neuro-Psychopharmacology \& Biological Psychiatry}, - author = {Houenou, J. and d'Albis, M.-A. and Daban, C. and Hamdani, N. and Delavest, M. and Lepine, J. P. and Vederine, F.-E. and Carde, S. and Lajnef, M. and Cabon, C. and Dickerson, F. and Yolken, R. H. and Tamouza, R. and Poupon, C. and Leboyer, M.}, - month = jan, - year = {2014}, - pmid = {24083998}, - keywords = {Humans, Adult, Female, Male, Neuropsychological Tests, Middle Aged, Hippocampus, bipolar disorder, Memory Disorders, BD, California Verbal Learning Test, CMV, CVLT, CVLT Recall score for list A, CVLT-RC-A, cytomegalovirus, Cytomegalovirus Infections, HC, healthy controls, Immunoglobulin G, MADRS, Montgomery–Asberg Depression Scale, PANSS, Positive and Negative Syndrome Scale, Verbal Learning, Verbal memory, Viral Proteins, YMRS, Young Mania Rating Scale}, - pages = {142--148}, -} - -@article{dubois_correction_2014, - title = {Correction strategy for diffusion-weighted images corrupted with motion: application to the {DTI} evaluation of infants' white matter}, - volume = {32}, - issn = {1873-5894}, - shorttitle = {Correction strategy for diffusion-weighted images corrupted with motion}, - doi = {10.1016/j.mri.2014.05.007}, - abstract = {OBJECTIVE: Diffusion imaging techniques such as DTI and HARDI are difficult to implement in infants because of their sensitivity to subject motion. A short acquisition time is generally preferred, at the expense of spatial resolution and signal-to-noise ratio. Before estimating the local diffusion model, most pre-processing techniques only register diffusion-weighted volumes, without correcting for intra-slice artifacts due to motion or technical problems. Here, we propose a fully automated strategy, which takes advantage of a high orientation number and is based on spherical-harmonics decomposition of the diffusion signal. -MATERIAL AND METHODS: The correction strategy is based on two successive steps: 1) automated detection and resampling of corrupted slices; 2) correction for eddy current distortions and realignment of misregistered volumes. It was tested on DTI data from adults and non-sedated healthy infants. -RESULTS: The methodology was validated through simulated motions applied to an uncorrupted dataset and through comparisons with an unmoved reference. Second, we showed that the correction applied to an infant group enabled to improve DTI maps and to increase the reliability of DTI quantification in the immature cortico-spinal tract. -CONCLUSION: This automated strategy performed reliably on DTI datasets and can be applied to spherical single- and multiple-shell diffusion imaging.}, - language = {eng}, - number = {8}, - journal = {Magnetic Resonance Imaging}, - author = {Dubois, Jessica and Kulikova, Sofya and Hertz-Pannier, Lucie and Mangin, Jean-François and Dehaene-Lambertz, Ghislaine and Poupon, Cyril}, - month = oct, - year = {2014}, - pmid = {24960369}, - keywords = {Algorithms, Brain, Humans, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, MRI, Models, Statistical, Adult, Infant, Artifacts, Automation, Fourier Analysis, Motion, Diffusion magnetic resonance imaging, Diffusion imaging, Movement, Artifact, Vibration, Signal-To-Noise Ratio}, - pages = {981--992}, -} - -@article{dubois_early_2014, - title = {The early development of brain white matter: a review of imaging studies in fetuses, newborns and infants}, - volume = {276}, - issn = {1873-7544}, - shorttitle = {The early development of brain white matter}, - doi = {10.1016/j.neuroscience.2013.12.044}, - abstract = {Studying how the healthy human brain develops is important to understand early pathological mechanisms and to assess the influence of fetal or perinatal events on later life. Brain development relies on complex and intermingled mechanisms especially during gestation and first post-natal months, with intense interactions between genetic, epigenetic and environmental factors. Although the baby's brain is organized early on, it is not a miniature adult brain: regional brain changes are asynchronous and protracted, i.e. sensory-motor regions develop early and quickly, whereas associative regions develop later and slowly over decades. Concurrently, the infant/child gradually achieves new performances, but how brain maturation relates to changes in behavior is poorly understood, requiring non-invasive in vivo imaging studies such as magnetic resonance imaging (MRI). Two main processes of early white matter development are reviewed: (1) establishment of connections between brain regions within functional networks, leading to adult-like organization during the last trimester of gestation, (2) maturation (myelination) of these connections during infancy to provide efficient transfers of information. Current knowledge from post-mortem descriptions and in vivo MRI studies is summed up, focusing on T1- and T2-weighted imaging, diffusion tensor imaging, and quantitative mapping of T1/T2 relaxation times, myelin water fraction and magnetization transfer ratio.}, - language = {eng}, - journal = {Neuroscience}, - author = {Dubois, J. and Dehaene-Lambertz, G. and Kulikova, S. and Poupon, C. and Hüppi, P. S. and Hertz-Pannier, L.}, - month = sep, - year = {2014}, - pmid = {24378955}, - keywords = {Brain, Humans, Infant, Myelin Sheath, Infant, Newborn, fetus and infant, myelination, Fetus, white matter bundles}, - pages = {48--71}, -} - -@article{gori_bayesian_2013, - title = {Bayesian atlas estimation for the variability analysis of shape complexes}, - volume = {16}, - abstract = {In this paper we propose a Bayesian framework for multiobject atlas estimation based on the metric of currents which permits to deal with both curves and surfaces without relying on point correspondence. This approach aims to study brain morphometry as a whole and not as a set of different components, focusing mainly on the shape and relative position of different anatomical structures which is fundamental in neuro-anatomical studies. We propose a generic algorithm to estimate templates of sets of curves (fiber bundles) and closed surfaces (sub-cortical structures) which have the same "form" (topology) of the shapes present in the population. This atlas construction method is based on a Bayesian framework which brings to two main improvements with respect to previous shape based methods. First, it allows to estimate from the data set a parameter specific to each object which was previously fixed by the user: the trade-off between data-term and regularity of deformations. In a multi-object analysis these parameters balance the contributions of the different objects and the need for an automatic estimation is even more crucial. Second, the covariance matrix of the deformation parameters is estimated during the atlas construction in a way which is less sensitive to the outliers of the population.}, - language = {eng}, - number = {Pt 1}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {Gori, Pietro and Colliot, Olivier and Worbe, Yulia and Marrakchi-Kacem, Linda and Lecomte, Sophie and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - year = {2013}, - pmid = {24505675}, - keywords = {Algorithms, Artificial Intelligence, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Models, Anatomic, Bayes Theorem}, - pages = {267--274}, -} - -@article{gori_prototype_2014, - title = {A prototype representation to approximate white matter bundles with weighted currents}, - volume = {17}, - abstract = {Quantitative and qualitative analysis of white matter fibers resulting from tractography algorithms is made difficult by their huge number. To this end, we propose an approximation scheme which gives as result a more concise but at the same time exhaustive representation of a fiber bundle. It is based on a novel computational model for fibers, called weighted currents, characterised by a metric that considers both the pathway and the anatomical locations of the endpoints of the fibers. Similarity has therefore a twofold connotation: geometrical and related to the connectivity. The core idea is to use this metric for approximating a fiber bundle with a set of weighted prototypes, chosen among the fibers, which represent ensembles of similar fibers. The weights are related to the fibers represented b y t he prototypes. The algorithm is divided into two steps. First, the main modes of the fiber bundle are detected using a modularity based clustering algorithm. Second, a prototype fiber selection process is carried on in each cluster separately. This permits to explain the main patterns of the fiber bundle in a fast and accurate way.}, - language = {eng}, - number = {Pt 3}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {Gori, Pietro and Colliot, Olivier and Marrakchi-Kacem, Linda and Worbe, Yulia and De Vico, Fallani Fabrizio and Chavez, Mario and Lecomte, Sophie and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - year = {2014}, - pmid = {25320811}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Reproducibility of Results, Sensitivity and Specificity, Models, Statistical, Nerve Fibers, Myelinated, Computer Simulation, Numerical Analysis, Computer-Assisted, Connectome}, - pages = {289--296}, -} - -@article{thirion_principal_2014, - title = {Principal component regression predicts functional responses across individuals}, - volume = {17}, - abstract = {Inter-subject variability is a major hurdle for neuroimaging group-level inference, as it creates complex image patterns that are not captured by standard analysis models and jeopardizes the sensitivity of statistical procedures. A solution to this problem is to model random subjects effects by using the redundant information conveyed by multiple imaging contrasts. In this paper, we introduce a novel analysis framework, where we estimate the amount of variance that is fit by a random effects subspace learned on other images; we show that a principal component regression estimator outperforms other regression models and that it fits a significant proportion (10\% to 25\%) of the between-subject variability. This proves for the first time that the accumulation of contrasts in each individual can provide the basis for more sensitive neuroimaging group analyzes.}, - language = {eng}, - number = {Pt 2}, - journal = {Medical image computing and computer-assisted intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention}, - author = {Thirion, Bertrand and Varoquaux, Gaël and Grisel, Olivier and Poupon, Cyril and Pinel, Philippe}, - year = {2014}, - pmid = {25485446}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Principal Component Analysis, Brain Mapping, Data Interpretation, Statistical, Nerve Net}, - pages = {741--748}, -} - -@article{lehericy_7_2014, - title = {7 {Tesla} magnetic resonance imaging: a closer look at substantia nigra anatomy in {Parkinson}'s disease}, - volume = {29}, - issn = {1531-8257}, - shorttitle = {7 {Tesla} magnetic resonance imaging}, - doi = {10.1002/mds.26043}, - abstract = {A hallmark of Parkinson's disease (PD) is the progressive neurodegeneration of dopaminergic neurons in the substantia nigra pars compacta (SNc). Dopaminergic denervation is commonly imaged using radiotracer imaging in target structures such as the striatum. Until recently, imaging made only a modest contribution to detecting neurodegenerative changes in the substantia nigra (SN) directly. Histologically, the SN is subdivided into the ventral pars reticulata and the dorsal pars compacta, which is composed of dopaminergic neurons. In humans, dopaminergic neurons, which are known to accumulate neuromelanin, form clusters of cells (nigrosomes) that penetrate deep into the SN pars reticulata (SNr). The SNr contains higher levels of iron than the SNc in normal subjects. Neuromelanin and T2*-weighted imaging therefore better detect the SNc and the SNr, respectively. The development of ultra-high field 7 Tesla (7T) magnetic resonance imaging (MRI) provided the increase in spatial resolution and in contrast that was needed to detect changes in SN morphology. 7T MRI allows visualization of nigrosome-1 as a hyperintense signal area on T2*-weighted images in the SNc of healthy subjects and its absence in PD patients, probably because of the loss of melanized neurons and the increase of iron deposition. This review is designed to provide a better understanding of the correspondence between the outlines and subdivisions of the SN detected using different MRI contrasts and the histological organization of the SN. The recent findings obtained at 7T will then be presented in relation to histological knowledge.}, - language = {eng}, - number = {13}, - journal = {Movement Disorders: Official Journal of the Movement Disorder Society}, - author = {Lehéricy, Stéphane and Bardinet, Eric and Poupon, Cyril and Vidailhet, Marie and François, Chantal}, - month = nov, - year = {2014}, - pmid = {25308960}, - keywords = {Humans, Image Processing, Computer-Assisted, Female, Male, Substantia Nigra, Parkinson Disease, neuromelanin, nigrosome, substantia nigra pars compacta, substantia nigra pars reticulata}, - pages = {1574--1581}, -} - -@article{labra_interactive_2014, - title = {Interactive segmentation of white-matter fibers using a multi-subject atlas}, - volume = {2014}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2014.6944099}, - abstract = {We present a fast algorithm for automatic segmentation of white matter fibers from tractography datasets based on a multi-subject bundle atlas. We describe a sequential version of the algorithm that runs on a desktop computer CPU, as well as a highly parallel version that uses a Graphics Processing Unit (GPU) as an accelerator. Our sequential implementation runs 270 times faster than a C++/Python implementation of a previous algorithm based on the same segmentation method, and 21 times faster than a highly optimized C version of the same previous algorithm. Our parallelized implementation exploits the multiple computation units and memory hierarchy of the GPU to further speed up the algorithm by a factor of 30 with respect to our sequential code. As a result, the time to segment a subject dataset of 800,000 fibers is reduced from more than 2.5 hours in the Python/C++ code, to less than one second in the GPU version.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Labra, Nicole and Figueroa, Miguel and Guevara, Pamela and Duclap, Delphine and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-Francois}, - year = {2014}, - pmid = {25570467}, - keywords = {Algorithms, Humans, Image Processing, Computer-Assisted, Computer Graphics, Time Factors, Nerve Fibers, Databases as Topic}, - pages = {2376--2379}, -} - -@article{dubois_mri_2016, - title = {{MRI} and {M}/{EEG} studies of the {White} {Matter} {Development} in {Human} {Fetuses} and {Infants}: {Review} and {Opinion}}, - volume = {2}, - issn = {2213-6312}, - shorttitle = {{MRI} and {M}/{EEG} studies of the {White} {Matter} {Development} in {Human} {Fetuses} and {Infants}}, - doi = {10.3233/BPL-160031}, - abstract = {Already during the last trimester of gestation, functional responses are recorded in foetuses and preterm newborns, attesting an already complex cerebral architecture. Then throughout childhood, anatomical connections are further refined but at different rates and over asynchronous periods across functional networks. Concurrently, infants gradually achieve new psychomotor and cognitive skills. Only the recent use of non-invasive techniques such as magnetic resonance imaging (MRI) and magneto- and electroencephalography (M/EEG) has opened the possibility to understand the relationships between brain maturation and skills development in vivo. In this review, we describe how these techniques have been applied to study the white matter maturation. At the structural level, the early architecture and myelination of bundles have been assessed with diffusion and relaxometry MRI, recently integrated in multi-compartment models and multi-parametric approaches. Nevertheless, technical limitations prevent us to map major developmental mechanisms such as fibers growth and pruning, and the progressive maturation at the bundle scale in case of mixing trajectories. At the functional level, M/EEG have been used to record different visual, somatosensory and auditory evoked responses. Because the conduction velocity of neural impulses increases with the myelination of connections, major changes in the components latency are observed throughout development. But so far, only a few studies have related structural and functional markers of white matter myelination. Such multi-modal approaches will be a major challenge in future research, not only to understand normal development, but also to characterize early mechanisms of pathologies and the influence of fetal and perinatal interventions on later outcome.}, - language = {eng}, - number = {1}, - journal = {Brain Plasticity (Amsterdam, Netherlands)}, - author = {Dubois, Jessica and Adibpour, Parvaneh and Poupon, Cyril and Hertz-Pannier, Lucie and Dehaene-Lambertz, Ghislaine}, - month = dec, - year = {2016}, - pmid = {29765848}, - pmcid = {PMC5928537}, - keywords = {relaxometry, myelination, architecture, Brain organization, diffusion tensor imaging DTI, evoked potentials or fields, maturation, sensory modalities}, - pages = {49--69}, -} - -@article{houenou_multilevel_2017, - title = {A {Multilevel} {Functional} {Study} of a {SNAP25} {At}-{Risk} {Variant} for {Bipolar} {Disorder} and {Schizophrenia}}, - volume = {37}, - issn = {1529-2401}, - doi = {10.1523/JNEUROSCI.1040-17.2017}, - abstract = {The synaptosomal-associated protein SNAP25 is a key player in synaptic vesicle docking and fusion and has been associated with multiple psychiatric conditions, including schizophrenia, bipolar disorder, and attention-deficit/hyperactivity disorder. We recently identified a promoter variant in SNAP25, rs6039769, that is associated with early-onset bipolar disorder and a higher gene expression level in human prefrontal cortex. In the current study, we showed that this variant was associated both in males and females with schizophrenia in two independent cohorts. We then combined in vitro and in vivo approaches in humans to understand the functional impact of the at-risk allele. Thus, we showed in vitro that the rs6039769 C allele was sufficient to increase the SNAP25 transcription level. In a postmortem expression analysis of 33 individuals affected with schizophrenia and 30 unaffected control subjects, we showed that the SNAP25b/SNAP25a ratio was increased in schizophrenic patients carrying the rs6039769 at-risk allele. Last, using genetics imaging in a cohort of 71 subjects, we showed that male risk carriers had an increased amygdala-ventromedial prefrontal cortex functional connectivity and a larger amygdala than non-risk carriers. The latter association has been replicated in an independent cohort of 121 independent subjects. Altogether, results from these multilevel functional studies are bringing strong evidence for the functional consequences of this allelic variation of SNAP25 on modulating the development and plasticity of the prefrontal-limbic network, which therefore may increase the vulnerability to both early-onset bipolar disorder and schizophrenia.SIGNIFICANCE STATEMENT Functional characterization of disease-associated variants is a key challenge in understanding neuropsychiatric disorders and will open an avenue in the development of personalized treatments. Recent studies have accumulated evidence that the SNARE complex, and more specifically the SNAP25 protein, may be involved in psychiatric disorders. Here, our multilevel functional studies are bringing strong evidence for the functional consequences of an allelic variation of SNAP25 on modulating the development and plasticity of the prefrontal-limbic network. These results demonstrate a common genetically driven functional alteration of a synaptic mechanism both in schizophrenia and early-onset bipolar disorder and confirm the shared genetic vulnerability between these two disorders.}, - language = {eng}, - number = {43}, - journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, - author = {Houenou, Josselin and Boisgontier, Jennifer and Henrion, Annabelle and d'Albis, Marc-Antoine and Dumaine, Anne and Linke, Julia and Wessa, Michèle and Daban, Claire and Hamdani, Nora and Delavest, Marine and Llorca, Pierre-Michel and Lançon, Christophe and Schürhoff, Franck and Szöke, Andrei and Le Corvoisier, Philippe and Barau, Caroline and Poupon, Cyril and Etain, Bruno and Leboyer, Marion and Jamain, Stéphane}, - month = oct, - year = {2017}, - pmid = {28972123}, - keywords = {Humans, Adult, Female, Male, Young Adult, Middle Aged, Animals, Nerve Net, Mice, Genetic Predisposition to Disease, genetics, bipolar disorder, Limbic System, Prefrontal Cortex, brain imaging, Cell Line, Tumor, Genetic Variation, SNAP25, SNARE, Synaptosomal-Associated Protein 25}, - pages = {10389--10397}, -} - -@article{sarrazin_multicenter_2014, - title = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder: psychotic features and interhemispheric disconnectivity}, - volume = {71}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {2168-6238}, - shorttitle = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder}, - doi = {10.1001/jamapsychiatry.2013.4513}, - abstract = {IMPORTANCE: Tractography studies investigating white matter (WM) abnormalities in patients with bipolar disorder have yielded heterogeneous results owing to small sample sizes. The small size limits their generalizability, a critical issue for neuroimaging studies of biomarkers of bipolar I disorder (BPI). -OBJECTIVES: To study WM abnormalities using whole-brain tractography in a large international multicenter sample of BPI patients and to compare these alterations between patients with or without a history of psychotic features during mood episodes. -DESIGN, SETTING, AND PARTICIPANTS: A cross-sectional, multicenter, international, Q-ball imaging tractography study comparing 118 BPI patients and 86 healthy control individuals. In addition, among the patient group, we compared those with and without a history of psychotic features. University hospitals in France, Germany, and the United States contributed participants. -INTERVENTIONS: Participants underwent assessment using the Diagnostic Interview for Genetic Studies at the French sites or the Structured Clinical Interview for DSM-IV at the German and US sites. Diffusion-weighted magnetic resonance images were acquired using the same acquisition parameters and scanning hardware at each site. We reconstructed 22 known deep WM tracts using Q-ball imaging tractography and an automatized segmentation technique. -MAIN OUTCOMES AND MEASURES: Generalized fractional anisotropy values along each reconstructed WM tract. -RESULTS: Compared with controls, BPI patients had significant reductions in mean generalized fractional anisotropy values along the body and the splenium of the corpus callosum, the left cingulum, and the anterior part of the left arcuate fasciculus when controlling for age, sex, and acquisition site (corrected for multiple testing). Patients with a history of psychotic features had a lower mean generalized fractional anisotropy value than those without along the body of the corpus callosum (corrected for multiple testing). -CONCLUSIONS AND RELEVANCE: In this multicenter sample, BPI patients had reduced WM integrity in interhemispheric, limbic, and arcuate WM tracts. Interhemispheric pathways are more disrupted in patients with than in those without psychotic symptoms. Together these results highlight the existence of an anatomic disconnectivity in BPI and further underscore a role for interhemispheric disconnectivity in the pathophysiological features of psychosis in BPI.}, - language = {eng}, - number = {4}, - journal = {JAMA psychiatry}, - author = {Sarrazin, Samuel and Poupon, Cyril and Linke, Julia and Wessa, Michèle and Phillips, Mary and Delavest, Marine and Versace, Amelia and Almeida, Jorge and Guevara, Pamela and Duclap, Delphine and Duchesnay, Edouard and Mangin, Jean-François and Le Dudal, Katia and Daban, Claire and Hamdani, Nora and D'Albis, Marc-Antoine and Leboyer, Marion and Houenou, Josselin}, - month = apr, - year = {2014}, - pmid = {24522197}, - keywords = {Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Reference Values, Adult, Female, Male, Bipolar Disorder, Cerebral Cortex, Corpus Callosum, Anisotropy, Neural Pathways, Dominance, Cerebral, Psychiatric Status Rating Scales, Diffusion Tensor Imaging, Leukoencephalopathies, Psychotic Disorders}, - pages = {388--396}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QXSGCF5P/Sarrazin et al. - 2014 - A multicenter tractography study of deep white mat.pdf:application/pdf}, -} - -@article{souza-queiroz_childhood_2016, - title = {Childhood trauma and the limbic network: a multimodal {MRI} study in patients with bipolar disorder and controls}, - volume = {200}, - issn = {1573-2517}, - shorttitle = {Childhood trauma and the limbic network}, - doi = {10.1016/j.jad.2016.04.038}, - abstract = {BACKGROUND: Childhood trauma (CT) is a major risk factor for psychiatric conditions. It is hypothesized that CT effects are mediated by the limbic system. Few multimodal neuroimaging studies allow an integrated perspective of this impact. Our goal was thus to study the effects of CT on the limbic network. -METHODS: We acquired multimodal MRI (T1, diffusion weighted, and resting state fMRI) data from 79 subjects (47 healthy controls and 32 patients with bipolar disorder, BD). We performed correlational analyses between Childhood Trauma Questionnaire (sub)scores (physical and emotional abuse/neglect and sexual abuse) and anatomo-functional measurements of the limbic network (hippocampal and amygdala volumes, prefronto-limbic functional connectivity, uncinate fractional anisotropy). -RESULTS: We found CTQ total scores to be negatively correlated with amygdala volume, prefronto-limbic functional connectivity (FC) and uncinate fractional anisotropy in our sample. Considering subscores, neglects (physical and emotional) were the only to affect neural parameters. The patients with BD drove most of the results. -LIMITATIONS: Small sample size and low level of trauma in controls. -CONCLUSIONS: Our multimodal approach enabled an integrated view of the long-term effects of CT on the limbic system.}, - language = {eng}, - journal = {Journal of Affective Disorders}, - author = {Souza-Queiroz, Julia and Boisgontier, Jennifer and Etain, Bruno and Poupon, Cyril and Duclap, Delphine and d'Albis, Marc-Antoine and Daban, Claire and Hamdani, Nora and Le Corvoisier, Philippe and Delavest, Marine and Bellivier, Frank and Guevara, Pamela and Leboyer, Marion and Henry, Chantal and Houenou, Josselin}, - year = {2016}, - pmid = {27136413}, - keywords = {Humans, MRI, Adult, Female, Male, Young Adult, Middle Aged, Organ Size, Emotions, Surveys and Questionnaires, Hippocampus, Trauma, Amygdala, Limbic System, Tractography, Connectivity, Adult Survivors of Child Abuse}, - pages = {159--164}, -} - -@article{laidi_cerebellar_2015, - title = {Cerebellar volume in schizophrenia and bipolar {I} disorder with and without psychotic features}, - volume = {131}, - copyright = {All rights reserved}, - doi = {doi: 10.1111/acps.12363. Epub 2014 Nov 28.}, - abstract = {OBJECTIVE: -There is growing evidence that cerebellum plays a crucial role in cognition and emotional regulation. Cerebellum is likely to be involved in the physiopathology of both bipolar disorder and schizophrenia. The objective of our study was to compare cerebellar size between patients with bipolar disorder, patients with schizophrenia, and healthy controls in a multicenter sample. In addition, we studied the influence of psychotic features on cerebellar size in patients with bipolar disorder. -METHOD: -One hundred and fifteen patients with bipolar I disorder, 32 patients with schizophrenia, and 52 healthy controls underwent 3 Tesla MRI. Automated segmentation of cerebellum was performed using FreeSurfer software. Volumes of cerebellar cortex and white matter were extracted. Analyses of covariance were conducted, and age, sex, and intracranial volume were considered as covariates. -RESULTS: -Bilateral cerebellar cortical volumes were smaller in patients with schizophrenia compared with patients with bipolar I disorder and healthy controls. We found no significant difference of cerebellar volume between bipolar patients with and without psychotic features. No change was evidenced in white matter. -CONCLUSION: -Our results suggest that reduction in cerebellar cortical volume is specific to schizophrenia. Cerebellar dysfunction in bipolar disorder, if present, appears to be more subtle than a reduction in cerebellar volume.}, - journal = {Acta Psychiatr Scand}, - author = {Laidi, C. and d'Albis, M.-A. and Wessa, M. and Linke, J. and Phillips, M.-L. and Delavest, M. and Bellivier, F. and Versace, A. and Almeida, J. and Sarrazin, S. and Poupon, C. and Le Dudal, K. and Daban, C. and Hamdani, N. and Leboyer, M. and Houenou, J.}, - month = mar, - year = {2015}, - keywords = {Humans, Software, MRI, Adult, Adolescent, Female, Male, Young Adult, Bipolar Disorder, Middle Aged, Aged, Psychotic Disorders, psychosis, Case-Control Studies, cerebellum, Cross-Sectional Studies}, - pages = {223--33}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACL}, - annote = {UnirsPMID: 25430729 [PubMed - in process}, -} - -@article{guevara_automatic_2015, - title = {Automatic segmentation of short association bundles using a new multi-subject atlas of the left hemisphere fronto-parietal brain connections}, - volume = {2015}, - issn = {1557-170X}, - doi = {10.1109/EMBC.2015.7318390}, - abstract = {Human brain connection map is far from being complete. In particular the study of the superficial white matter (SWM) is an unachieved task. Its description is essential for the understanding of human brain function and the study of the pathogenesis associated to it. In this work we developed a method for the automatic creation of a SWM bundle multi-subject atlas. The atlas generation method is based on a cortical parcellation for the extraction of fibers connecting two different gyri. Then, an intra-subject fiber clustering is applied, in order to divide each bundle into sub-bundles with similar shape. After that, a two-step inter-subject fiber clustering is used in order to find the correspondence between the sub-bundles across the subjects, fuse similar clusters and discard the outliers. The method was applied to 40 subjects of a high quality HARDI database, focused on the left hemisphere fronto-parietal and insula brain regions. We obtained an atlas composed of 44 bundles connecting 22 pair of ROIs. Then the atlas was used to automatically segment 39 new subjects from the database.}, - language = {eng}, - journal = {Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, - author = {Guevara, M. and Seguel, D. and Roman, C. and Duclap, D. and Lebois, A. and Le Bihan, null and Mangin, J.-F. and Poupon, C. and Guevara, P.}, - year = {2015}, - pmid = {26736290}, - keywords = {Brain, Humans, Brain Mapping, Cluster Analysis}, - pages = {426--429}, -} - -@article{ewenczyk_antisaccades_2017, - title = {Antisaccades in {Parkinson} disease: {A} new marker of postural control?}, - volume = {88}, - issn = {1526-632X}, - shorttitle = {Antisaccades in {Parkinson} disease}, - doi = {10.1212/WNL.0000000000003658}, - abstract = {OBJECTIVE: To describe the relation between gaze and posture/gait control in Parkinson disease (PD) and to determine the role of the mesencephalic locomotor region (MLR) and cortex-MLR connection in saccadic behavior because this structure is a major area involved in both gait/postural control and gaze control networks. -METHODS: We recruited 30 patients with PD with or without altered postural control and 25 age-matched healthy controls (HCs). We assessed gait, balance, and neuropsychological status and separately recorded gait initiation and eye movements (visually guided saccades and volitional antisaccades). We identified correlations between the clinical and physiologic parameters that best characterized patients with postural instability. We measured resting-state functional connectivity in 2 pathways involving the frontal oculomotor cortices and the MLR and sought correlations with saccadic behavior. -RESULTS: Patients with PD with postural instability showed altered antisaccade latencies that correlated with the stand-walk-sit time (r = 0.78, p {\textless} 0.001) and the duration of anticipatory postural adjustments before gait initiation (r = 0.61, p = 0.001). Functional connectivity between the pedunculopontine nucleus (PPN) and the frontal eye field correlated with antisaccade latency in the HCs (r = -0.54, p = 0.02) but not in patients with PD. -CONCLUSIONS: In PD, impairment of antisaccade latencies, a simple and robust parameter, may be an indirect marker correlated with impaired release of anticipatory postural program. PPN alterations may account for both antisaccade and postural impairments.}, - language = {eng}, - number = {9}, - journal = {Neurology}, - author = {Ewenczyk, Claire and Mesmoudi, Salma and Gallea, Cécile and Welter, Marie-Laure and Gaymard, Bertrand and Demain, Adèle and Yahia Cherif, Lydia and Degos, Bertrand and Benali, Habib and Pouget, Pierre and Poupon, Cyril and Lehericy, Stéphane and Rivaud-Péchoux, Sophie and Vidailhet, Marie}, - month = feb, - year = {2017}, - pmid = {28130466}, - keywords = {Humans, Female, Male, Neuropsychological Tests, Middle Aged, Neural Pathways, Cognition, Eye Movement Measurements, GAIT, Parkinson Disease, Pedunculopontine Tegmental Nucleus, Postural Balance, STIMULATION, Gait, Saccades, Biomechanical Phenomena, GUIDED SACCADES, KeyWords Plus:FRONTAL EYE FIELD, MACAQUE MONKEY, MESENCEPHALIC RETICULAR-FORMATION, MOVEMENTS, PEDUNCULOPONTINE TEGMENTAL NUCLEUS, SUPERIOR COLLICULUS}, - pages = {853--861}, - annote = {The following values have no corresponding Zotero field:number: 9label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 9section: label: ACL}, - annote = {Unirs}, - annote = {UnirsPMID: 28130466 }, -} - -@article{bouhali_anatomical_2014, - title = {Anatomical connections of the visual word form area}, - volume = {34}, - issn = {1529-2401}, - doi = {10.1523/JNEUROSCI.4918-13.2014}, - abstract = {The visual word form area (VWFA), a region systematically involved in the identification of written words, occupies a reproducible location in the left occipitotemporal sulcus in expert readers of all cultures. Such a reproducible localization is paradoxical, given that reading is a recent invention that could not have influenced the genetic evolution of the cortex. Here, we test the hypothesis that the VWFA recycles a region of the ventral visual cortex that shows a high degree of anatomical connectivity to perisylvian language areas, thus providing an efficient circuit for both grapheme-phoneme conversion and lexical access. In two distinct experiments, using high-resolution diffusion-weighted data from 75 human subjects, we show that (1) the VWFA, compared with the fusiform face area, shows higher connectivity to left-hemispheric perisylvian superior temporal, anterior temporal and inferior frontal areas; (2) on a posterior-to-anterior axis, its localization within the left occipitotemporal sulcus maps onto a peak of connectivity with language areas, with slightly distinct subregions showing preferential projections to areas respectively involved in grapheme-phoneme conversion and lexical access. In agreement with functional data on the VWFA in blind subjects, the results suggest that connectivity to language areas, over and above visual factors, may be the primary determinant of VWFA localization.}, - language = {eng}, - number = {46}, - journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, - author = {Bouhali, Florence and Thiebaut de Schotten, Michel and Pinel, Philippe and Poupon, Cyril and Mangin, Jean-François and Dehaene, Stanislas and Cohen, Laurent}, - month = nov, - year = {2014}, - pmid = {25392507}, - keywords = {Humans, Brain Mapping, Adult, Female, Male, Young Adult, Temporal Lobe, Middle Aged, Visual Cortex, Neural Pathways, Functional Laterality, Frontal Lobe, Diffusion magnetic resonance imaging, reading, visual word form area}, - pages = {15402--15414}, - annote = {The following values have no corresponding Zotero field:number: 46label: ACL}, - annote = {Times Cited: 0}, - annote = {UnatiPMID: 25392507}, -} - -@article{kulikova_new_2016, - title = {A {New} {Strategy} for {Fast} {MRI}-{Based} {Quantification} of the {Myelin} {Water} {Fraction}: {Application} to {Brain} {Imaging} in {Infants}}, - volume = {11}, - issn = {1932-6203}, - shorttitle = {A {New} {Strategy} for {Fast} {MRI}-{Based} {Quantification} of the {Myelin} {Water} {Fraction}}, - doi = {10.1371/journal.pone.0163143}, - abstract = {The volume fraction of water related to myelin (fmy) is a promising MRI index for in vivo assessment of brain myelination, that can be derived from multi-component analysis of T1 and T2 relaxometry signals. However, existing quantification methods require rather long acquisition and/or post-processing times, making implementation difficult both in research studies on healthy unsedated children and in clinical examinations. The goal of this work was to propose a novel strategy for fmy quantification within acceptable acquisition and post-processing times. Our approach is based on a 3-compartment model (myelin-related water, intra/extra-cellular water and unrestricted water), and uses calibrated values of inherent relaxation times (T1c and T2c) for each compartment c. Calibration was first performed on adult relaxometry datasets (N = 3) acquired with large numbers of inversion times (TI) and echo times (TE), using an original combination of a region contraction approach and a non-negative least-square (NNLS) algorithm. This strategy was compared with voxel-wise fitting, and showed robust estimation of T1c and T2c. The accuracy of fmy calculations depending on multiple factors was investigated using simulated data. In the testing stage, our strategy enabled fast fmy mapping, based on relaxometry datasets acquired with reduced TI and TE numbers (acquisition {\textless}6 min), and analyzed with NNLS algorithm (post-processing {\textless}5min). In adults (N = 13, mean age 22.4±1.6 years), fmy maps showed variability across white matter regions, in agreement with previous studies. In healthy infants (N = 18, aged 3 to 34 weeks), asynchronous changes in fmy values were demonstrated across bundles, confirming the well-known progression of myelination.}, - language = {eng}, - number = {10}, - journal = {PloS One}, - author = {Kulikova, Sofya and Hertz-Pannier, Lucie and Dehaene-Lambertz, Ghislaine and Poupon, Cyril and Dubois, Jessica}, - year = {2016}, - pmid = {27736872}, - pmcid = {PMC5063462}, - keywords = {Algorithms, Brain, Humans, Brain Mapping, Adult, Infant, Myelin Sheath, Water}, - pages = {e0163143}, - annote = {The following values have no corresponding Zotero field:number: 10}, -} - -@article{worbe_altered_2015, - title = {Altered structural connectivity of cortico-striato-pallido-thalamic networks in {Gilles} de la {Tourette} syndrome}, - volume = {138}, - copyright = {All rights reserved}, - issn = {0006-8950}, - doi = {10.1093/brain/awu311}, - journal = {BRAIN}, - author = {Worbe, Yulia and Marrakchi-Kacem, Linda and Lecomte, Sophie and Valabregue, Romain and Poupon, Fabrice and Guevara, Pamela and Tucholka, Alan and Mangin, Jean-Francois and Vidailhet, Marie and Lehericy, Stephane and Hartmann, Andreas and Poupon, Cyril}, - month = feb, - year = {2015}, - keywords = {Humans, Image Processing, Computer-Assisted, Adult, Female, Male, Young Adult, Basal Ganglia, Anisotropy, Nerve Net, Thalamus, Tourette Syndrome, Globus Pallidus, Neostriatum, structural connectivity and tractography, Gilles de la Tourette syndrome, cortico-basal ganglia networks, Tics}, - pages = {472--482}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {Times Cited: 10}, - annote = {Unirs - UnatiPMID: 25392196}, -} - -@article{brion_noise_2013, - title = {Noise correction for {HARDI} and {HYDI} data obtained with multi-channel coils and sum of squares reconstruction: an anisotropic extension of the {LMMSE}}, - volume = {31}, - issn = {1873-5894}, - shorttitle = {Noise correction for {HARDI} and {HYDI} data obtained with multi-channel coils and sum of squares reconstruction}, - doi = {10.1016/j.mri.2013.04.002}, - abstract = {Parallel magnetic resonance imaging (MRI) yields noisy magnitude data, described in most cases as following a noncentral χ distribution when the signals received by the coils are combined as the sum of their squares. One well-known case of this noncentral χ noise model is the Rician model, but it is only valid in the case of single-channel acquisition. Although the use of parallel MRI is increasingly common, most of the correction methods still perform Rician noise removal, yielding an erroneous result due to an incorrect noise model. Moreover, the existence of noise correlations in phased array systems renders noise nonstationary and further modifies the noise description in parallel MRI. However, the noncentral χ model has been demonstrated to work as a good approximation as long as effective voxelwise parameters are used. A good correction step, adapted to the right noise model, is of paramount importance, especially when working with diffusion-weighted MR data, whose signal-to-noise ratio is low. In this paper, we present a noise removal technique designed to be fast enough for integration into a real-time reconstruction system, thus offering the convenience of obtaining corrected data almost instantaneously during the MRI scan. Our method employs the noncentral χ noise model and uses a simplified method to account for noise correlations; this leads to an efficient and rapid correction. The method consists of an anisotropic extension of the Linear Minimum Mean Square Error estimator (LMMSE) that is a far better edge-preserving method than the traditional LMMSE and addresses noncentral χ distributions along with empirically computed global effective parameters. The results on simulated and real data demonstrate that this anisotropic extended LMMSE outperforms the original LMMSE on images corrupted by noncentral χ noise. Moreover, in comparison with the existing LMMSE technique incorporating the estimation of voxelwise effective parameters, our method yields improved results.}, - language = {eng}, - number = {8}, - journal = {Magnetic Resonance Imaging}, - author = {Brion, Véronique and Poupon, Cyril and Riff, Olivier and Aja-Fernández, Santiago and Tristán-Vega, Antonio and Mangin, Jean-François and Le Bihan, Denis and Poupon, Fabrice}, - month = oct, - year = {2013}, - pmid = {23659768}, - keywords = {Algorithms, Brain, Humans, Image Enhancement, Reproducibility of Results, Sensitivity and Specificity, Data Interpretation, Statistical, Nerve Fibers, Myelinated, Diffusion Tensor Imaging, Least-Squares Analysis, Artifacts, Equipment Design, Equipment Failure Analysis, HARDI, Signal-To-Noise Ratio, HYDI, LMMSE, Noise correction, Noncentral χ, Parallel MRI, Real-time}, - pages = {1360--1371}, -} - -@article{mangin_toward_2013, - title = {Toward global tractography}, - volume = {80}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2013.04.009}, - abstract = {Diffusion-based tractography is an ill-posed problem, because the step-by-step reconstruction of a fibre bundle trajectory cannot afford any serious mistake in the evaluation of the local fibre orientations. Such evaluation is difficult, however, because the myriad fibres passing through a single voxel follow different directions. Modelling tractography as a global inverse problem is a simple framework which addresses the ill-posed nature of the problem. The key idea is that the results of tractography in the neighbourhood of an ambiguous local diffusion profile can help to infer the local fibre directions. This paper provides an overview of past achievements of global tractography and proposes guidelines for a future research programme in the hope that the potential of the technique will increase the interest of the community.}, - language = {eng}, - journal = {Neuroimage}, - author = {Mangin, J.-F. and Fillard, P. and Cointepas, Y. and Le Bihan, D. and Frouin, V. and Poupon, C.}, - month = oct, - year = {2013}, - pmid = {23587688}, - keywords = {Brain, Humans, Image Interpretation, Computer-Assisted, Models, Neurological, Nerve Fibers, Myelinated, Animals, Diffusion Tensor Imaging, Nerve Net, Models, Anatomic, Connectome, Global tractography, Diffusion MRI}, - pages = {290--296}, -} - -@article{lefranc_groupwise_2016, - title = {Groupwise connectivity-based parcellation of the whole human cortical surface using watershed-driven dimension reduction}, - volume = {30}, - issn = {1361-8423}, - doi = {10.1016/j.media.2016.01.003}, - abstract = {Segregating the human cortex into distinct areas based on structural connectivity criteria is of widespread interest in neuroscience. This paper presents a groupwise connectivity-based parcellation framework for the whole cortical surface using a new high quality diffusion dataset of 79 healthy subjects. Our approach performs gyrus by gyrus to parcellate the whole human cortex. The main originality of the method is to compress for each gyrus the connectivity profiles used for the clustering without any anatomical prior information. This step takes into account the interindividual cortical and connectivity variability. To this end, we consider intersubject high density connectivity areas extracted using a surface-based watershed algorithm. A wide validation study has led to a fully automatic pipeline which is robust to variations in data preprocessing (tracking type, cortical mesh characteristics and boundaries of initial gyri), data characteristics (including number of subjects), and the main algorithmic parameters. A remarkable reproducibility is achieved in parcellation results for the whole cortex, leading to clear and stable cortical patterns. This reproducibility has been tested across non-overlapping subgroups and the validation is presented mainly on the pre- and postcentral gyri.}, - language = {eng}, - journal = {Medical Image Analysis}, - author = {Lefranc, Sandrine and Roca, Pauline and Perrot, Matthieu and Poupon, Cyril and Le Bihan, Denis and Mangin, Jean-François and Rivière, Denis}, - month = may, - year = {2016}, - pmid = {26849421}, - keywords = {Algorithms, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Female, Male, Young Adult, Diffusion Tensor Imaging, Nerve Net, Connectome, Clustering, Connectome, Clustering, Structural connectivity, Diffusion tensor imaging, Structural connectivity}, - pages = {11--29}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati}, -} - -@article{yeh_diffusion_2013, - title = {Diffusion microscopist simulator: a general {Monte} {Carlo} simulation system for diffusion magnetic resonance imaging}, - volume = {8}, - issn = {1932-6203}, - shorttitle = {Diffusion microscopist simulator}, - doi = {10.1371/journal.pone.0076626}, - abstract = {This article describes the development and application of an integrated, generalized, and efficient Monte Carlo simulation system for diffusion magnetic resonance imaging (dMRI), named Diffusion Microscopist Simulator (DMS). DMS comprises a random walk Monte Carlo simulator and an MR image synthesizer. The former has the capacity to perform large-scale simulations of Brownian dynamics in the virtual environments of neural tissues at various levels of complexity, and the latter is flexible enough to synthesize dMRI datasets from a variety of simulated MRI pulse sequences. The aims of DMS are to give insights into the link between the fundamental diffusion process in biological tissues and the features observed in dMRI, as well as to provide appropriate ground-truth information for the development, optimization, and validation of dMRI acquisition schemes for different applications. The validity, efficiency, and potential applications of DMS are evaluated through four benchmark experiments, including the simulated dMRI of white matter fibers, the multiple scattering diffusion imaging, the biophysical modeling of polar cell membranes, and the high angular resolution diffusion imaging and fiber tractography of complex fiber configurations. We expect that this novel software tool would be substantially advantageous to clarify the interrelationship between dMRI and the microscopic characteristics of brain tissues, and to advance the biophysical modeling and the dMRI methodologies.}, - language = {eng}, - number = {10}, - journal = {PLoS One}, - author = {Yeh, Chun-Hung and Schmitt, Benoît and Le Bihan, Denis and Li-Schlittgen, Jing-Rebecca and Lin, Ching-Po and Poupon, Cyril}, - year = {2013}, - pmid = {24130783}, - pmcid = {PMC3794953}, - keywords = {Humans, Software, Neurons, Diffusion magnetic resonance imaging, Monte Carlo Method, Cell Membrane}, - pages = {e76626}, -} - -@article{assaf_connect_2013, - title = {The {CONNECT} project: {Combining} macro- and micro-structure}, - volume = {80}, - issn = {1095-9572}, - shorttitle = {The {CONNECT} project}, - doi = {10.1016/j.neuroimage.2013.05.055}, - abstract = {In recent years, diffusion MRI has become an extremely important tool for studying the morphology of living brain tissue, as it provides unique insights into both its macrostructure and microstructure. Recent applications of diffusion MRI aimed to characterize the structural connectome using tractography to infer connectivity between brain regions. In parallel to the development of tractography, additional diffusion MRI based frameworks (CHARMED, AxCaliber, ActiveAx) were developed enabling the extraction of a multitude of micro-structural parameters (axon diameter distribution, mean axonal diameter and axonal density). This unique insight into both tissue microstructure and connectivity has enormous potential value in understanding the structure and organization of the brain as well as providing unique insights to abnormalities that underpin disease states. The CONNECT (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements. This paper summarizes the project and describes the perspective of using micro-structural measures to study the connectome.}, - language = {eng}, - journal = {Neuroimage}, - author = {Assaf, Yaniv and Alexander, Daniel C. and Jones, Derek K. and Bizzi, Albero and Behrens, Tim E. J. and Clark, Chris A. and Cohen, Yoram and Dyrby, Tim B. and Huppi, Petra S. and Knoesche, Thomas R. and Lebihan, Denis and Parker, Geoff J. M. and Poupon, Cyril and {CONNECT consortium} and Anaby, Debbie and Anwander, Alfred and Bar, Leah and Barazany, Daniel and Blumenfeld-Katzir, Tamar and De-Santis, Silvia and Duclap, Delphine and Figini, Matteo and Fischi, Elda and Guevara, Pamela and Hubbard, Penny and Hofstetter, Shir and Jbabdi, Saad and Kunz, Nicolas and Lazeyras, Francois and Lebois, Alice and Liptrot, Matthew G. and Lundell, Henrik and Mangin, Jean-François and Dominguez, David Moreno and Morozov, Darya and Schreiber, Jan and Seunarine, Kiran and Nava, Simone and Poupon, Cyril and Riffert, Till and Sasson, Efrat and Schmitt, Benoit and Shemesh, Noam and Sotiropoulos, Stam N. and Tavor, Ido and Zhang, Hui Gary and Zhou, Feng-Lei}, - month = oct, - year = {2013}, - pmid = {23727318}, - keywords = {Brain, Humans, Image Enhancement, Models, Neurological, Diffusion Tensor Imaging, Nerve Net, Models, Anatomic, Connectome}, - pages = {273--282}, -} - -@article{li_numerical_2014, - title = {Numerical simulation of diffusion {MRI} signals using an adaptive time-stepping method}, - volume = {59}, - issn = {1361-6560}, - doi = {10.1088/0031-9155/59/2/441}, - abstract = {The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch-Torrey partial differential equation. We present a method for the numerical solution of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization. The time discretization is done using the explicit Runge-Kutta-Chebyshev method, which is more efficient than the forward Euler time discretization for diffusive-type problems. We use this approach to simulate the diffusion MRI signal from the extra-cylindrical compartment in a tissue model of the brain gray matter consisting of cylindrical and spherical cells and illustrate the effect of cell membrane permeability.}, - language = {eng}, - number = {2}, - journal = {Physics in Medicine and Biology}, - author = {Li, Jing-Rebecca and Calhoun, Donna and Poupon, Cyril and Le Bihan, Denis}, - month = jan, - year = {2014}, - pmid = {24351275}, - keywords = {Brain, Image Processing, Computer-Assisted, Models, Biological, Time Factors, Diffusion magnetic resonance imaging, Cell Membrane Permeability}, - pages = {441--454}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACL}, - annote = {Times Cited: 3}, - annote = {UnirsPMID: 24351275}, -} - -@article{pinel_genetic_2015, - title = {Genetic and {Environmental} {Influences} on the {Visual} {Word} {Form} and {Fusiform} {Face} {Areas}}, - volume = {25}, - issn = {1460-2199}, - doi = {10.1093/cercor/bhu048}, - abstract = {Two areas of the occipitotemporal cortex show a remarkable hemispheric lateralization: written words activate the visual word form area (VWFA) in the left fusiform gyrus and faces activate a symmetrical site in the right hemisphere, the fusiform face area (FFA). While the lateralization of the VWFA fits with the leftward asymmetry of the speech processing network, origin of the rightward asymmetry for faces is still unclear. Using fMRI data from 64 subjects (including 16 monozygotic (MZ) and 13 dizygotic (DZ) twin pairs), we investigated how activations evoked by written words, faces, and spoken language are co-lateralized in the temporal lobe, and whether this organization reflects genetic factors or individual reading expertise. We found that the lateralization of the left superior temporal activation for spoken language correlates with the lateralization of occipitotemporal activations for both written words and faces. Behavioral reading scores also modulate the responses to words and faces. Estimation of genetic and environmental contributions shows that activations of the VWFA, the occipital face area, and the temporal speech areas are partially under genetic control whereas activation of the FFA is primarily influenced by individual experience. Our results stress the importance of both genetic factors and acquired expertise in the occipitotemporal organization.}, - language = {eng}, - number = {9}, - journal = {Cerebral Cortex}, - author = {Pinel, Philippe and Lalanne, Christophe and Bourgeron, Thomas and Fauchereau, Fabien and Poupon, Cyril and Artiges, Eric and Le Bihan, Denis and Dehaene-Lambertz, Ghislaine and Dehaene, Stanislas}, - month = sep, - year = {2015}, - pmid = {24825786}, - keywords = {Humans, Brain Mapping, Image Processing, Computer-Assisted, Adult, Male, Young Adult, Temporal Lobe, Visual Perception, Functional Laterality, Photic Stimulation, Statistics as Topic, genetic, Pattern Recognition, Visual, Oxygen, VWFA, FFA, Gene-Environment Interaction, temporal, Twins, Dizygotic, Twins, Monozygotic}, - pages = {2478--2493}, - annote = {The following values have no corresponding Zotero field:number: 9label: ACL}, - annote = {Times Cited: 2}, - annote = {Unirs - MetricPMID: 24825786}, -} - -@article{nguyen_parameter_2015, - title = {Parameter estimation using macroscopic diffusion {MRI} signal models}, - volume = {60}, - issn = {1361-6560}, - doi = {10.1088/0031-9155/60/8/3389}, - abstract = {Macroscopic models of the diffusion MRI (dMRI) signal can be helpful to understanding the relationship between the tissue microstructure and the dMRI signal. We study the least squares problem associated with estimating tissue parameters such as the cellular volume fraction, the residence times and the effective diffusion coefficients using a recently developed macroscopic model of the dMRI signal called the Finite Pulse Kärger model that generalizes the original Kärger model to non-narrow gradient pulses. In order to analyze the quality of the estimation in a controlled way, we generated synthetic noisy dMRI signals by including the effect of noise on the exact signal produced by the Finite Pulse Kärger model. The noisy signals were then fitted using the macroscopic model. Minimizing the least squares, we estimated the model parameters. The bias and standard deviations of the estimated model parameters as a function of the signal to noise ratio (SNR) were obtained. We discuss the choice of the b-values, the least square weights, the extension to experimentally obtained dMRI data as well noise correction.}, - language = {eng}, - number = {8}, - journal = {Physics in Medicine and Biology}, - author = {Nguyen, Hang Tuan and Grebenkov, Denis and Van Nguyen, Dang and Poupon, Cyril and Le Bihan, Denis and Li, Jing-Rebecca}, - month = apr, - year = {2015}, - pmid = {25831194}, - keywords = {Algorithms, Reproducibility of Results, Image Processing, Computer-Assisted, Regression Analysis, Cerebral Cortex, Models, Theoretical, Animals, Rats, Least-Squares Analysis, Diffusion magnetic resonance imaging, Signal-To-Noise Ratio}, - pages = {3389--3413}, - annote = {The following values have no corresponding Zotero field:number: 8label: ACL}, - annote = {Times Cited: 0}, - annote = {Unirs - MetricPMID: 25831194}, -} - -@inproceedings{roman_short_2016, - title = {Short association bundle atlas based on inter-subject clustering from {HARDI} data}, - volume = {2016}, - doi = {10.1109/EMBC.2016.7591983}, - abstract = {This paper is focused on the study of short brain association fibers. We present an automatic method to identify short bundles of the superficial white matter based on inter-subject hierarchical clustering. Our method finds clusters of similar fibers, belonging to the different subjects, according to a distance measure between fibers. First, the algorithm obtains representative bundles and subsequently we perform an automatic labeling based on the anatomy, of the most stable connections. The analysis was applied to two independent groups of 37 subjects. Results between the two groups were compared, in order to keep reproducible connections for the atlas creation. The method was applied using linear and non-linear registration, where the non-linear registration showed significantly better results. A final atlas with 35 bundles in the left hemisphere and 27 in the right hemisphere from the whole brain was obtained. Finally results were validated using the atlas to segment 26 new subjects from another HARDI database.}, - language = {eng}, - booktitle = {Conference proceedings: ... {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society}. {IEEE} {Engineering} in {Medicine} and {Biology} {Society}. {Annual} {Conference}}, - author = {Roman, C. and Guevara, M. and Duclap, D. and Lebois, A. and Poupon, C. and Mangin, J.-F. and Guevara, P.}, - year = {2016}, - pmid = {28269513}, - keywords = {Algorithms, Brain, Humans, Reproducibility of Results, Image Processing, Computer-Assisted, Diffusion Magnetic Resonance Imaging, Databases, Factual, White Matter, Cluster Analysis, Connectome, Diffusion magnetic resonance imaging}, - pages = {5545--5549}, - annote = {The following values have no corresponding Zotero field:label: ACTI}, - annote = {UnirsPMID: 28269513}, -} - -@article{dalbis_local_2018, - title = {Local structural connectivity is associated with social cognition in autism spectrum disorder}, - volume = {141}, - issn = {1460-2156}, - doi = {10.1093/brain/awy275}, - abstract = {The current theory implying local, short-range overconnectivity in autism spectrum disorder, contrasting with long-range underconnectivity, is based on heterogeneous results, on limited data involving functional connectivity studies, on heterogeneous paediatric populations and non-specific methodologies. In this work, we studied short-distance structural connectivity in a homogeneous population of males with high-functioning autism spectrum disorder and used a novel methodology specifically suited for assessing U-shaped short-distance tracts, including a recently developed tractography-based atlas of the superficial white matter fibres. We acquired diffusion-weighted MRI for 58 males (27 subjects with high-functioning autism spectrum disorder and 31 control subjects) and extracted the mean generalized fractional anisotropy of 63 short-distance tracts. Neuropsychological evaluation included Wechsler Adult Intelligence Scale IV (WAIS-IV), Communication Checklist-Adult, Empathy Quotient, Social Responsiveness Scale and Behaviour Rating Inventory of Executive Function-Adult (BRIEF-A). In contradiction with the models of short-range over-connectivity in autism spectrum disorder, we found that patients with autism spectrum disorder had a significantly decreased anatomical connectivity in a component comprising 13 short tracts compared to controls. Specific short-tract atypicalities in temporal lobe and insula were significantly associated with clinical manifestations of autism spectrum disorder such as social awareness, language structure, pragmatic skills and empathy, emphasizing their importance in social dysfunction. Short-range decreased anatomical connectivity may thus be an important substrate of social deficits in autism spectrum disorder, in contrast with current models.}, - language = {eng}, - number = {12}, - journal = {Brain: A Journal of Neurology}, - author = {d'Albis, Marc-Antoine and Guevara, Pamela and Guevara, Miguel and Laidi, Charles and Boisgontier, Jennifer and Sarrazin, Samuel and Duclap, Delphine and Delorme, Richard and Bolognani, Federico and Czech, Christian and Bouquet, Céline and Ly-Le Moal, Myriam and Holiga, Stefan and Amestoy, Anouck and Scheid, Isabelle and Gaman, Alexandru and Leboyer, Marion and Poupon, Cyril and Mangin, Jean-François and Houenou, Josselin}, - month = dec, - year = {2018}, - pmid = {30423029}, - pages = {3472--3481}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/K95RIQ4J/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3PQZ935H/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8Z5Y4QS7/d’Albis et al. - 2018 - Local structural connectivity is associated with s.pdf:application/pdf}, -} - -@article{pyatigorskaya_comparative_2018, - title = {Comparative {Study} of {MRI} {Biomarkers} in the {Substantia} {Nigra} to {Discriminate} {Idiopathic} {Parkinson} {Disease}}, - volume = {39}, - issn = {1936-959X}, - doi = {10.3174/ajnr.A5702}, - abstract = {BACKGROUND AND PURPOSE: Several new MR imaging techniques have shown promising results in patients with Parkinson disease; however, the comparative diagnostic values of these measures at the individual level remain unclear. Our aim was to compare the diagnostic value of MR imaging biomarkers of substantia nigra damage for distinguishing patients with Parkinson disease from healthy volunteers. -MATERIALS AND METHODS: Thirty-six patients and 20 healthy volunteers were prospectively included. The MR imaging protocol at 3T included 3D T2-weighted and T1-weighted neuromelanin-sensitive images, diffusion tensor images, and R2* mapping. T2* high-resolution images were also acquired at 7T to evaluate the dorsal nigral hyperintensity sign. Quantitative analysis was performed using ROIs in the substantia nigra drawn manually around the area of high signal intensity on neuromelanin-sensitive images and T2-weighted images. Visual analysis of the substantia nigra neuromelanin-sensitive signal intensity and the dorsolateral nigral hyperintensity on T2* images was performed. -RESULTS: There was a significant decrease in the neuromelanin-sensitive volume and signal intensity in patients with Parkinson disease. There was also a significant decrease in fractional anisotropy and an increase in mean, axial, and radial diffusivity in the neuromelanin-sensitive substantia nigra at 3T and a decrease in substantia nigra volume on T2* images. The combination of substantia nigra volume, signal intensity, and fractional anisotropy in the neuromelanin-sensitive substantia nigra allowed excellent diagnostic accuracy (0.93). Visual assessment of both substantia nigra dorsolateral hyperintensity and neuromelanin-sensitive images had good diagnostic accuracy (0.91 and 0.86, respectively). -CONCLUSIONS: The combination of neuromelanin signal and volume changes with fractional anisotropy measurements in the substantia nigra showed excellent diagnostic accuracy. Moreover, the high diagnostic accuracy of visual assessment of substantia nigra changes using dorsolateral hyperintensity analysis or neuromelanin-sensitive signal changes indicates that these techniques are promising for clinical practice.}, - language = {eng}, - number = {8}, - journal = {AJNR. American journal of neuroradiology}, - author = {Pyatigorskaya, N. and Magnin, B. and Mongin, M. and Yahia-Cherif, L. and Valabregue, R. and Arnaldi, D. and Ewenczyk, C. and Poupon, C. and Vidailhet, M. and Lehéricy, S.}, - month = aug, - year = {2018}, - pmid = {29954816}, - pages = {1460--1467}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AJBI3E2T/Pyatigorskaya et al. - 2018 - Comparative Study of MRI Biomarkers in the Substan.pdf:application/pdf}, -} - -@article{gori_double_2018, - title = {Double {Diffeomorphism}: {Combining} {Morphometry} and {Structural} {Connectivity} {Analysis}}, - volume = {37}, - issn = {1558-254X}, - shorttitle = {Double {Diffeomorphism}}, - doi = {10.1109/TMI.2018.2813062}, - abstract = {The brain is composed of several neural circuits which may be seen as anatomical complexes composed of grey matter structures interconnected by white matter tracts. Grey and white matter components may be modeled as 3-D surfaces and curves, respectively. Neurodevelopmental disorders involve morphological and organizational alterations which cannot be jointly captured by usual shape analysis techniques based on single diffeomorphisms. We propose a new deformation scheme, called double diffeomorphism, which is a combination of two diffeomorphisms. The first one captures changes in structural connectivity, whereas the second one recovers the global morphological variations of both grey and white matter structures. This deformation model is integrated into a Bayesian framework for atlas construction. We evaluate it on a data-set of 3-D structures representing the neural circuits of patients with Gilles de la Tourette syndrome (GTS). We show that this approach makes it possible to localise, quantify, and easily visualise the pathological anomalies altering the morphology and organization of the neural circuits. Furthermore, results also indicate that the proposed deformation model better discriminates between controls and GTS patients than a single diffeomorphism.}, - language = {eng}, - number = {9}, - journal = {IEEE transactions on medical imaging}, - author = {Gori, Pietro and Colliot, Olivier and Kacem, Linda Marrakchi and Worbe, Yulia and Routier, Alexandre and Poupon, Cyril and Hartmann, Andreas and Ayache, Nicholas and Durrleman, Stanley}, - month = sep, - year = {2018}, - pmid = {29993599}, - pages = {2033--2043}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/PLV2TH2P/Gori et al. - 2018 - Double Diffeomorphism Combining Morphometry and S.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BHRD5MXQ/Gori et al. - 2018 - Double Diffeomorphism Combining Morphometry and S.pdf:application/pdf}, -} - -@article{leroi_simultaneous_2018, - title = {Simultaneous multi-parametric mapping of total sodium concentration, {T1}, {T2} and {ADC} at 7 {T} using a multi-contrast unbalanced {SSFP}}, - volume = {53}, - issn = {1873-5894}, - doi = {10.1016/j.mri.2018.07.012}, - abstract = {PURPOSE: Quantifying multiple NMR properties of sodium could be of benefit to assess changes in cellular viability in biological tissues. A proof of concept of Quantitative Imaging using Configuration States (QuICS) based on a SSFP sequence with multiple contrasts was implemented to extract simultaneously 3D maps of applied flip angle (FA), total sodium concentration, T1, T2, and Apparent Diffusion Coefficient (ADC). -METHODS: A 3D Cartesian Gradient Recalled Echo (GRE) sequence was used to acquire 11 non-balanced SSFP contrasts at a 6 × 6 × 6 mm3 isotropic resolution with carefully-chosen gradient spoiling area, RF amplitude and phase cycling, with TR/TE = 20/3.2 ms and 25 averages, leading to a total acquisition time of 1 h 18 min. A least-squares fit between the measured and the analytical complex signals was performed to extract quantitative maps from a mono-exponential model. Multiple sodium phantoms with different compositions were studied to validate the ability of the method to measure sodium NMR properties in various conditions. -RESULTS: Flip angle maps were retrieved. Relaxation times, ADC and sodium concentrations were estimated with controlled precision below 15\%, and were in accordance with measurements from established methods and literature. -CONCLUSION: The results illustrate the ability to retrieve sodium NMR properties maps, which is a first step toward the estimation of FA, T1, T2, concentration and ADC of 23Na for clinical research. With further optimization of the acquired QuICS contrasts, scan time could be reduced to be suitable with in vivo applications.}, - language = {eng}, - journal = {Magnetic Resonance Imaging}, - author = {Leroi, Lisa and Coste, Arthur and de Rochefort, Ludovic and Santin, Mathieu D. and Valabregue, Romain and Mauconduit, Franck and Giacomini, Eric and Luong, Michel and Chazel, Edouard and Valette, Julien and Le Bihan, Denis and Poupon, Cyril and Boumezbeur, Fawzi and Rabrait-Lerman, Cécile and Vignaud, Alexandre}, - month = nov, - year = {2018}, - pmid = {30055291}, - keywords = {Diffusion, Non proton MRI, Sodium, T(1) mapping, T(2) mapping}, - pages = {156--163}, - file = {Accepted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JK2BFGSL/Leroi et al. - 2018 - Simultaneous multi-parametric mapping of total sod.pdf:application/pdf;Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6CGPR2PS/Leroi et al. - 2018 - Simultaneous multi-parametric mapping of total sod.pdf:application/pdf}, -} - -@article{operto_cati:_2016, - title = {{CATI}: {A} {Large} {Distributed} {Infrastructure} for the {Neuroimaging} of {Cohorts}}, - volume = {14}, - issn = {1559-0089}, - shorttitle = {{CATI}}, - doi = {10.1007/s12021-016-9295-8}, - abstract = {This paper provides an overview of CATI, a platform dedicated to multicenter neuroimaging. Initiated by the French Alzheimer's plan (2008-2012), CATI is a research project called on to provide service to other projects like an industrial partner. Its core mission is to support the neuroimaging of large populations, providing concrete solutions to the increasing complexity involved in such projects by bringing together a service infrastructure, the know-how of its expert academic teams and a large-scale, harmonized network of imaging facilities. CATI aims to make data sharing across studies easier and promotes sharing as much as possible. In the last 4 years, CATI has assisted the clinical community by taking charge of 35 projects so far and has emerged as a recognized actor at the national and international levels.}, - language = {eng}, - number = {3}, - journal = {Neuroinformatics}, - author = {Operto, Grégory and Chupin, Marie and Batrancourt, Bénédicte and Habert, Marie-Odile and Colliot, Olivier and Benali, Habib and Poupon, Cyril and Champseix, Catherine and Delmaire, Christine and Marie, Sullivan and Rivière, Denis and Pélégrini-Issac, Mélanie and Perlbarg, Vincent and Trebossen, Régine and Bottlaender, Michel and Frouin, Vincent and Grigis, Antoine and Orfanos, Dimitri Papadopoulos and Dary, Hugo and Fillon, Ludovic and Azouani, Chabha and Bouyahia, Ali and Fischer, Clara and Edward, Lydie and Bouin, Mathilde and Thoprakarn, Urielle and Li, Jinpeng and Makkaoui, Leila and Poret, Sylvain and Dufouil, Carole and Bouteloup, Vincent and Chételat, Gaël and Dubois, Bruno and Lehéricy, Stéphane and Mangin, Jean-François and Cointepas, Yann and {CATI Consortium}}, - year = {2016}, - pmid = {27066973}, - keywords = {Humans, Neuroimaging, Information Dissemination, Data sharing, Computational Biology, Large-scale studies, Multicenter protocols, Multicenter Studies as Topic, Neuroimaging biomarkers, Workflow, Data Mining, Data mining}, - pages = {253--264}, - annote = {The following values have no corresponding Zotero field:number: 3}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QWHI6VJG/Operto et al. - 2016 - CATI A Large Distributed Infrastructure for the N.pdf:application/pdf}, -} - -@article{magalhaes_white_2017, - title = {White matter changes in microstructure associated with a maladaptive response to stress in rats}, - volume = {7}, - issn = {2158-3188}, - doi = {10.1038/tp.2016.283}, - abstract = {In today's society, every individual is subjected to stressful stimuli with different intensities and duration. This exposure can be a key trigger in several mental illnesses greatly affecting one's quality of life. Yet not all subjects respond equally to the same stimulus and some are able to better adapt to them delaying the onset of its negative consequences. The neural specificities of this adaptation can be essential to understand the true dynamics of stress as well as to design new approaches to reduce its consequences. In the current work, we employed ex vivo high field diffusion magnetic resonance imaging (MRI) to uncover the differences in white matter properties in the entire brain between Fisher 344 (F344) and Sprague-Dawley (SD) rats, known to present different responses to stress, and to examine the effects of a 2-week repeated inescapable stress paradigm. We applied a tract-based spatial statistics (TBSS) analysis approach to a total of 25 animals. After exposure to stress, SD rats were found to have lower values of corticosterone when compared with F344 rats. Overall, stress was found to lead to an overall increase in fractional anisotropy (FA), on top of a reduction in mean and radial diffusivity (MD and RD) in several white matter bundles of the brain. No effect of strain on the white matter diffusion properties was observed. The strain-by-stress interaction revealed an effect on SD rats in MD, RD and axial diffusivity (AD), with lower diffusion metric levels on stressed animals. These effects were localized on the left side of the brain on the external capsule, corpus callosum, deep cerebral white matter, anterior commissure, endopiriform nucleus, dorsal hippocampus and amygdala fibers. The results possibly reveal an adaptation of the SD strain to the stressful stimuli through synaptic and structural plasticity processes, possibly reflecting learning processes.}, - language = {eng}, - number = {1}, - journal = {Translational Psychiatry}, - author = {Magalhães, R. and Bourgin, J. and Boumezbeur, F. and Marques, P. and Bottlaender, M. and Poupon, C. and Djemaï, B. and Duchesnay, E. and Mériaux, S. and Sousa, N. and Jay, T. M. and Cachia, A.}, - year = {2017}, - pmid = {28117841}, - pmcid = {PMC5545740}, - keywords = {Brain, Male, Corpus Callosum, Anisotropy, Diffusion Magnetic Resonance Imaging, Animals, Rats, White Matter, Hippocampus, Corticosterone, Amygdala, Adaptation, Physiological, Anterior Cerebellar Commissure, External Capsule, Rats, Inbred F344, Rats, Sprague-Dawley, Stress, Psychological, Hippocampal layers, IN-VIVO, KeyWords Plus:PREFRONTAL CORTEX, LIFE EVENTS, OPTIC-NERVE, RADIAL DIFFUSIVITY, RETINAL ISCHEMIA}, - pages = {e1009}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 1}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unirs}, - annote = {UnirsPMID: 28117841 DOI: 10.1038/tp.2016.283}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BPAQNAWL/Magalhães et al. - 2017 - White matter changes in microstructure associated .pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/437MPGMD/tp2016283a.html:text/html;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/J5IQSBU2/tp2016283a.html:text/html}, -} - -@inproceedings{rolland_exploring_2019, - title = {Exploring {Microstructure} {Asymmetries} in the {Infant} {Brain} {Cortex}: {A} {Methodological} {Framework} {Combining} {Structural} and {Diffusion} {Mri}}, - shorttitle = {Exploring {Microstructure} {Asymmetries} in the {Infant} {Brain} {Cortex}}, - url = {https://ieeexplore.ieee.org/abstract/document/8759421}, - doi = {10.1109/ISBI.2019.8759421}, - abstract = {The development of the human brain is a complex process that starts during early pregnancy and extends until the end of adolescence. In parallel to morphological changes in brain size and gyrification, several microstructural changes occur in the cortex, such as the development of dendritic arborization, synaptogenesis and pruning, and fiber myelination. Magnetic Resonance Imaging (MRI) can provide indirect markers of these mechanisms through the mapping of quantitative parameters. Here, we used a dedicated methodological framework to perform reliable voxel-wise analyses over the infant cortex. The examination of hemispheric asymmetries in microstructure required careful alignment of morphological asymmetries through registration of native and flipped brains using a 2-step matching strategy of sulci (DISCO approach) and cortical ribbon (DAR℡ approach). We tested the potential of this approach in 1-to-5-month-old infants, with a focus on cortical longitudinal diffusivity from Diffusion Tensor Imaging (DTI). This enabled us to unravel different microstructural evolution patterns of specific sensorimotor and language regions in the left and right hemispheres.}, - urldate = {2024-02-28}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Rolland, C. and Lebenberg, J. and Leroy, F. and Moulton, E. and Adibpour, P. and Rivière, D. and Poupon, C. and Hertz-Pannier, L. and Mangin, J.-F. and Dehaene-Lambertz, G. and Dubois, J.}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {structural MRI, Reliability, Artificial intelligence, Diffusion tensor imaging, Microstructure, Pediatrics, diffusion tensor imaging DTI, cortical maturation, Developing brain, infants, Surface morphology}, - pages = {426--429}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UXMS7YIH/8759421.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/99P92Z8V/Rolland et al. - 2019 - Exploring Microstructure Asymmetries in the Infant.pdf:application/pdf}, -} - -@article{mohammadi_probastem_2023, - title = {{ProbaStem}, a pipeline towards the first high-resolution probabilistic atlas of the whole human brainstem}, - volume = {229}, - issn = {1863-2661}, - url = {https://link.springer.com/10.1007/s00429-023-02726-8}, - doi = {10.1007/s00429-023-02726-8}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {Brain Structure and Function}, - author = {Mohammadi, Mohammad Seyyed and Planty-Bonjour, Alexia and Poupon, Fabrice and Uszynski, Ivy and Poupon, Cyril and Destrieux, Christophe and Andersson, Frédéric}, - month = nov, - year = {2023}, - pages = {115--132}, -} - -@article{berre_effet_2023, - title = {Effet de l’électroconvulsivothérapie sur la microstructure hippocampique dans la dépression sévère: une étude en neurite orientation dispersion and density imaging ({NODDI})}, - volume = {50}, - issn = {01509861}, - shorttitle = {Effet de l’électroconvulsivothérapie sur la microstructure hippocampique dans la dépression sévère}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0150986123000482}, - doi = {10.1016/j.neurad.2023.01.041}, - language = {en}, - number = {2}, - urldate = {2024-02-27}, - journal = {Journal of Neuroradiology}, - author = {Berre, Alice Le and Attali, David and Uszinsky, Ivy and Debacker, Clément and Benzakoun, Joseph and Poupon, Cyril and Cachia, Arnaud and Oppenheim, Catherine and Plaze, Marion}, - month = mar, - year = {2023}, - pages = {126--127}, -} - -@article{herlin_cross-subject_2023, - title = {Cross-subject variability of the optic radiation anatomy in a cohort of 1065 healthy subjects}, - volume = {45}, - issn = {1279-8517}, - url = {https://link.springer.com/10.1007/s00276-023-03161-4}, - doi = {10.1007/s00276-023-03161-4}, - language = {en}, - number = {7}, - urldate = {2024-02-27}, - journal = {Surgical and Radiologic Anatomy}, - author = {Herlin, B. and Uszynski, I. and Chauvel, M. and Poupon, C. and Dupont, S.}, - month = may, - year = {2023}, - pages = {849--858}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/KM2TU9PL/Herlin et al. - 2023 - Cross-subject variability of the optic radiation a.pdf:application/pdf}, -} - -@techreport{chauvel_comparative_2023, - type = {preprint}, - title = {Comparative analysis of the chimpanzee and human brain superficial structural connectivities}, - url = {https://www.researchsquare.com/article/rs-3772776/v1}, - abstract = {Abstract - Diffusion MRI tractography (dMRI) has fundamentally transformed our ability to investigate white matter pathways in the human brain. While long-range connections have been extensively studied, short-range white matter bundles (SWMBs) have remained a relatively underexplored aspect of brain connectivity. This study undertakes a comprehensive examination of SWMB connectivity in both the human and chimpanzee brains, employing a novel combination of empirical and geometric methodologies to classify SWMB morphology in an objective manner. Leveraging two anatomical atlases, the Ginkgo Chauvel chimpanzee atlas and the Ginkgo Chauvel human atlas, comprising respectively 844 and 1375 superficial bundles, this research focuses on sparse representations of the morphology of SWMBs to explore the little-understood superficial connectivity of the chimpanzee brain and facilitate a deeper understanding of the variability in shape of these bundles. Ultimately, the analysis aims to uncover both commonalities and disparities in SWMBs between chimpanzees and humans, shedding light on the evolution and organization of these crucial neural structures.}, - urldate = {2024-02-27}, - institution = {In Review}, - author = {Chauvel, Maëlig and Pascucci, Marco and Uszynski, Ivy and Herlin, Bastien and Mangin, Jean-François and Hopkins, William and Poupon, Cyril}, - month = dec, - year = {2023}, - doi = {10.21203/rs.3.rs-3772776/v1}, -} - -@article{lechanoine_wikibrainstem_2021, - title = {{WIKIBrainStem}: {An} online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field {MRI}}, - volume = {236}, - issn = {10538119}, - shorttitle = {{WIKIBrainStem}}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811921003578}, - doi = {10.1016/j.neuroimage.2021.118080}, - language = {en}, - urldate = {2024-02-27}, - journal = {NeuroImage}, - author = {Lechanoine, François and Jacquesson, Timothée and Beaujoin, Justine and Serres, Barthélemy and Mohammadi, Mohammad and Planty-Bonjour, Alexia and Andersson, Frédéric and Poupon, Fabrice and Poupon, Cyril and Destrieux, Christophe}, - month = aug, - year = {2021}, - pages = {118080}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GDHPY56C/Lechanoine et al. - 2021 - WIKIBrainStem An online atlas to manually segment.pdf:application/pdf}, -} - -@inproceedings{uszynski_towards_nodate, - address = {London, England, UK}, - title = {Towards an ultra-high resolution structural connectivity atlas of the parrot brain using extreme high-field 17.{2T} diffusion {MRI}}, - url = {https://archive.ismrm.org/2022/0423.html}, - doi = {10.58530/2022/0423}, - abstract = {The cognitive abilities of parrots are known to be highly developed to the extent of matching those exhibited by crows and primates. However, little is known about the anatomy and structural connectivity of the parrot\’s brain. In this work, we propose to use the power of diffusion MRI along with the strong gradients of a unique 17.2T preclinical MRI system to deliver a first white matter atlas of the parrot brain.}, - language = {en}, - urldate = {2024-02-27}, - author = {Uszynski, Ivy and Ciobanu, Luisa and Bardin, Solène and Estienne, Pierre and Yamamoto, Kei and Poupon, Cyril}, - pages = {0423}, -} - -@article{pinel_functional_2019, - title = {The functional database of the {ARCHI} project: {Potential} and perspectives}, - volume = {197}, - issn = {10538119}, - shorttitle = {The functional database of the {ARCHI} project}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811919303428}, - doi = {10.1016/j.neuroimage.2019.04.056}, - language = {en}, - urldate = {2024-02-27}, - journal = {NeuroImage}, - author = {Pinel, Philippe and Forgeot d’Arc, Baudouin and Dehaene, Stanislas and Bourgeron, Thomas and Thirion, Bertrand and Le Bihan, Denis and Poupon, Cyril}, - month = aug, - year = {2019}, - pages = {527--543}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FQDCZ62Y/Pinel et al. - 2019 - The functional database of the ARCHI project Pote.pdf:application/pdf}, -} - -@inproceedings{roman_effect_2019, - address = {Berlin, Germany}, - title = {The effect of the number of fibers in tractography reconstruction of white matter bundles}, - isbn = {978-1-5386-1311-5}, - url = {https://ieeexplore.ieee.org/document/8856379/}, - doi = {10.1109/EMBC.2019.8856379}, - urldate = {2024-02-27}, - booktitle = {2019 41st {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society} ({EMBC})}, - publisher = {IEEE}, - author = {Roman, C. and Cardenas, N. and Poupon, C. and Mangin, J.-F. and Guevara, P.}, - month = jul, - year = {2019}, - pages = {2825--2829}, -} - -@article{ji_t240_2018, - title = {T240. {Relationship} {Between} {Cognitive} {Performance} and {Superficial} {White} {Matter} {Integrity} in the {Cingulate} {Cortex} in {Schizophrenia}: {A} {DWI} {Study} {Using} a {Novel} {Atlas}}, - volume = {83}, - issn = {00063223}, - shorttitle = {T240. {Relationship} {Between} {Cognitive} {Performance} and {Superficial} {White} {Matter} {Integrity} in the {Cingulate} {Cortex} in {Schizophrenia}}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0006322318306796}, - doi = {10.1016/j.biopsych.2018.02.577}, - language = {en}, - number = {9}, - urldate = {2024-02-27}, - journal = {Biological Psychiatry}, - author = {Ji, Ellen and Sarrazin, Samuel and Leboyer, Marion and Guevara, Miguel and Guevara, Pamela and Poupon, Cyril and Grigis, Antoine and Houenou, Josselin}, - month = may, - year = {2018}, - pages = {S222}, -} - -@inproceedings{mendoza_superficial_2023, - address = {Valparaíso, Chile}, - title = {Superficial white matter shape characterization using hierarchical clustering and a multi-subject bundle atlas}, - isbn = {978-1-5106-6254-4 978-1-5106-6255-1}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/2669738/Superficial-white-matter-shape-characterization-using-hierarchical-clustering-and-a/10.1117/12.2669738.full}, - doi = {10.1117/12.2669738}, - urldate = {2024-02-27}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Mendoza, Cristobal and Román, Claudio and Molina, Joaquín and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - editor = {Linguraru, Marius G. and Rittner, Letícia and Lepore, Natasha and Romero Castro, Eduardo and Brieva, Jorge and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {9}, -} - -@article{dalbis_study_2019, - title = {Study of corpus callosum cellular microstructure using diffusion microscopy {MRI} in subjects with autism spectrum disorders}, - volume = {29}, - issn = {0924977X}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0924977X18317309}, - doi = {10.1016/j.euroneuro.2018.11.883}, - language = {en}, - urldate = {2024-02-27}, - journal = {European Neuropsychopharmacology}, - author = {D'Albis, M.A. and Sarrazin, S. and Lebois, A. and Mangin, J.F. and Laidi, C. and Boisgontier, J. and Delorme, R. and Bolognani, F. and Holiga, S. and Dukart, J. and Bouquet, C. and Moal, M. Ly-Le and Amestoy, A. and Scheid, I. and Gaman, A. and Leboyer, M. and Poupon, C. and Houenou, J.}, - year = {2019}, - pages = {S598}, -} - -@article{berkovitch_perturbations_2018, - title = {Perturbations de l’accès conscient et de la connectivité cérébrale longue-distance dans la psychose}, - volume = {1}, - issn = {25902415}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S2590241519303824}, - doi = {10.1016/S2590-2415(19)30382-4}, - language = {fr}, - urldate = {2024-02-27}, - journal = {French Journal of Psychiatry}, - author = {Berkovitch, L. and Charles, L. and Del Cul, A. and Hamdani, N. and Delavest, M. and Sarrazin, S. and Mangin, J-F. and d’Albis, M-A. and Bellivier, F. and Poupon, C. and Leboyer, M. and Dehaene, S. and Houenou, J.}, - month = nov, - year = {2018}, - pages = {S146--S147}, -} - -@article{ji_alterations_2020, - title = {Alterations {In} {Short}-{Range} {Structural} {Connectivity} {Across} {The} {Psychosis} {Spectrum}: {Findings} {From} {The} {B}-{Snip} {Study}}, - volume = {46}, - issn = {0586-7614, 1745-1701}, - shorttitle = {Alterations {In} {Short}-{Range} {Structural} {Connectivity} {Across} {The} {Psychosis} {Spectrum}: {Findings} {From} {The} {B}-{Snip} {Study}}, - url = {https://academic.oup.com/schizophreniabulletin/article/46/Supplement_1/S97/5839281}, - doi = {10.1093/schbul/sbaa031.226}, - abstract = {Abstract - - Background - Schizophrenia (SZ) and bipolar disorder (BD) have been increasingly viewed as psychotic mood disorders along a shared spectrum. Long-range and short-range structural connectivity have been implicated in both disorders, conceptualising them as “disconnection syndromes”. There has been a rise in neuroimaging tools to understand the overlap and boundaries between the two disorders, which has shifted our focus towards appreciating traits in addition to diagnosis. Our recent pilot study examining short-range U-fibers found in superficial white matter (SWM) found shared and distinct traits among people with SZ and BD and we aimed to investigate SWM further using data from the Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) consortium. - - - Methods - Using diffusion weighted imaging (DWI), we performed whole brain tractography in 113 people with SZ, 69 people with SA disorder, 49 people with psychotic BD and 77 healthy controls using BrainVISA and Connectomist 2.0. Segmentation and labelling of SWM tracts were performed using a comprehensive U-fiber atlas. ComBat was applied to remove site effects and principle components analysis was performed to identity networks of bundles used for comparative analyses. - - - Results - Principle component analysis revealed a network comprised of 8 short tracts in frontal, parietal, and temporal regions that had decreased anatomical connectivity in patients, regardless of diagnosis, relative to healthy controls. This network overlaps, in part, regions that differed between patients (SZ and BD) and healthy controls in our recent pilot study. However, we were unable to detect differences between people with SZ, SA disorder and psychotic BD. - - - Discussion - We demonstrate that short U-fibers are likely vulnerable to pathological processes in psychotic illnesses, encouraging further understanding of their anatomy and function. Our lack of findings between patient groups may reflect a more homogeneous population (three subgroups of psychosis) and may suggest that abnormalities in SWM are less likely due to mood disturbances.}, - language = {en}, - number = {Supplement\_1}, - urldate = {2024-02-27}, - journal = {Schizophrenia Bulletin}, - author = {Ji, Ellen and Perus, Lisa and Grigis, Antoine and Poupon, Cyril and Sarrazin, Samuel and Guevara, Pamela and Guevara, Miguel and Mangin, Jean-François and Houenou, Josselin}, - month = may, - year = {2020}, - pages = {S97--S97}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LYB3RFE4/Ji et al. - 2020 - S160. ALTERATIONS IN SHORT-RANGE STRUCTURAL CONNEC.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8MTIP4QL/Ji et al. - 2018 - T145. ALTERATIONS IN SUPERFICIAL WHITE MATTER IN T.pdf:application/pdf}, -} - -@article{drobnjak_physical_2021, - title = {Physical and digital phantoms for validating tractography and assessing artifacts}, - volume = {245}, - issn = {10538119}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811921009769}, - doi = {10.1016/j.neuroimage.2021.118704}, - language = {en}, - urldate = {2024-02-27}, - journal = {NeuroImage}, - author = {Drobnjak, Ivana and Neher, Peter and Poupon, Cyril and Sarwar, Tabinda}, - month = dec, - year = {2021}, - pages = {118704}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YZTKQ43I/Drobnjak et al. - 2021 - Physical and digital phantoms for validating tract.pdf:application/pdf}, -} - -@article{dalbis_p806_2019, - title = {P.806 {Whole} brain long-range study of white matter cellular microstructure using diffusion microscopy {MRI} in subjects with autism spectrum disorders}, - volume = {29}, - issn = {0924977X}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0924977X19315469}, - doi = {10.1016/j.euroneuro.2019.09.672}, - language = {en}, - urldate = {2024-02-27}, - journal = {European Neuropsychopharmacology}, - author = {D'Albis, M.A. and Sarrazin, S. and Mangin, J.F. and Laidi, C. and Boisgontier, J. and Delorme, R. and Bolognani, F. and Holiga, S. and Bouquet, C. and Moal, M. Ly-Le and Amestoy, A. and Scheid, I. and Gaman, A. and Leboyer, M. and Poupon, C. and Houenou, J.}, - month = dec, - year = {2019}, - pages = {S537}, -} - -@inproceedings{vazquez_parallel_2019, - address = {Venice, Italy}, - title = {Parallel {Optimization} of {Fiber} {Bundle} {Segmentation} for {Massive} {Tractography} {Datasets}}, - isbn = {978-1-5386-3641-1}, - url = {https://ieeexplore.ieee.org/document/8759208/}, - doi = {10.1109/ISBI.2019.8759208}, - urldate = {2024-02-27}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - publisher = {IEEE}, - author = {Vazquez, Andrea and Lopez-Lopez, Narciso and Labra, Nicole and Figueroa, Miguel and Poupon, Cyril and Mangin, Jean-Francois and Hernandez, Cecilia and Guevara, Pamela}, - month = apr, - year = {2019}, - pages = {178--181}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Q5NFJLNY/Vazquez et al. - 2019 - Parallel Optimization of Fiber Bundle Segmentation.pdf:application/pdf}, -} - -@article{pyatigorskaya_multimodal_2020, - title = {Multimodal {Magnetic} {Resonance} {Imaging} {Quantification} of {Brain} {Changes} in {Progressive} {Supranuclear} {Palsy}}, - volume = {35}, - issn = {0885-3185, 1531-8257}, - url = {https://movementdisorders.onlinelibrary.wiley.com/doi/10.1002/mds.27877}, - doi = {10.1002/mds.27877}, - abstract = {Abstract - - Background - Progressive supranuclear palsy (PSP) is a neurodegenerative clinically heterogeneous disorder, formal diagnosis being based on postmortem histological brain examination. - - - Objective - We aimed to perform a precise in vivo staging of neurodegeneration in PSP using quantitative multimodal MRI. The ability of MRI biomarkers to differentiate PSP from PD was also evaluated. - - - Methods - - Eleven PSP patients were compared to 26 age‐matched healthy controls and 51 PD patients. Images were acquired at 3 Tesla (three‐dimensional T - 1 - ‐weighted, diffusion tensor, and neuromelanin‐sensitive images) and 7 Tesla (three‐dimensional‐T - 2 - * images). Regions of interest included the cortical areas, hippocampus, amygdala, basal ganglia, basal forebrain, brainstem nuclei, dentate nucleus, and cerebellum. Volumes, mean diffusivity, and fractional anisotropy were measured. In each region, a threshold value for group categorization was calculated, and four grades of change (0–3) were determined. - - - - Results - PSP patients showed extensive volume decreases and diffusion changes in the midbrain, SN, STN, globus pallidus, basal forebrain, locus coeruleus, pedunculopontine nucleus, and dentate nucleus, in close agreement with the degrees of impairment in histological analyses. The predictive factors for the separation of PSP and healthy controls were, in descending order, the neuromelanin‐based SN volume; midbrain fractional anisotropy; volumes of the midbrain, globus pallidus, and putamen; and fractional anisotropy in the locus coeruleus. The best predictors for separating PSP from PD were the neuromelanin‐based volume in the SN, fractional anisotropy in the pons, volumes of the midbrain and globus pallidus, and fractional anisotropy in the basal forebrain. - - - Conclusions - These results suggest that it is possible to evaluate brain neurodegeneration in PSP noninvasively, even in small brainstem nuclei, in close agreement with previously published histological data. © 2019 International Parkinson and Movement Disorder Society}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {Movement Disorders}, - author = {Pyatigorskaya, Nadya and Yahia‐Cherif, Lydia and Gaurav, Rahul and Ewenczyk, Claire and Gallea, Cecile and Valabregue, Romain and Gargouri, Fatma and Magnin, Benoit and Degos, Bertrand and Roze, Emmanuel and Bardinet, Eric and Poupon, Cyril and Arnulf, Isabelle and Vidailhet, Marie and Lehericy, Stéphane}, - month = jan, - year = {2020}, - pages = {161--170}, -} - -@inproceedings{popov_length-dependent_nodate, - address = {London, England, UK}, - title = {Length-dependent spatial distribution of short fiber bundles revealed with the mesoscopic {Chenonceau} dataset}, - url = {https://archive.ismrm.org/2022/0657.html}, - doi = {10.58530/2022/0657}, - abstract = {Mesoscopic diffusion datasets allow to study the superficial tracts of the human brain. We exploit the new Chenonceau Dataset, an ultra-high resolution diffusion-weighted dataset, to investigate the organization of short fibers ( between 10 and 60 mm ) in the whole brain. - To achieve this goal, we process the dense Chenonceau connectogram with a hierarchical clustering algorithm to obtain coherent fiber bundles, sorted over a centimetric range. It leads to the first density mapping of short fibers across the whole human brain. This mapping displays important inter-hemispheric variations, supporting the functional lateralization of various functional networks.}, - language = {en}, - urldate = {2024-02-27}, - author = {Popov, Alexandros and Uszynski, Ivy and Herlin, Bastien and Chauvel, Maelig and Maldonado, Igor and Destrieux, Christophe and Poupon, Cyril}, - pages = {0657}, -} - -@inproceedings{brulle_large-scale_nodate, - address = {London, England, UK}, - title = {Large-scale simulations to create large collections of realistic white matter samples using {MEDUSA}}, - url = {https://archive.ismrm.org/2022/2726.html}, - doi = {10.58530/2022/2726}, - abstract = {In this work, we demonstrate that the MEDUSA simulator can be used to create huge collections of brain white matter tissue microstructure samples in the frame of large-scale HPC simulation campaigns and how these Big Data could serve the design of novel computational models able to decode white matter microstructure.}, - language = {en}, - urldate = {2024-02-27}, - author = {Brullé, Alexis and Bachiri, Anas and Destrieux, Christophe and Wiber, Gilles and Delzescaux, Thierry and Uszynski, Ivy and Poupon, Cyril}, - pages = {2726}, -} - -@article{dubois_kerker_2018, - title = {Kerker {Effect} in {Ultrahigh}-{Field} {Magnetic} {Resonance} {Imaging}}, - volume = {8}, - issn = {2160-3308}, - url = {https://link.aps.org/doi/10.1103/PhysRevX.8.031083}, - doi = {10.1103/PhysRevX.8.031083}, - language = {en}, - number = {3}, - urldate = {2024-02-27}, - journal = {Physical Review X}, - author = {Dubois, Marc and Leroi, Lisa and Raolison, Zo and Abdeddaim, Redha and Antonakakis, Tryfon and De Rosny, Julien and Vignaud, Alexandre and Sabouroux, Pierre and Georget, Elodie and Larrat, Benoit and Tayeb, Gérard and Bonod, Nicolas and Amadon, Alexis and Mauconduit, Franck and Poupon, Cyril and Le Bihan, Denis and Enoch, Stefan}, - month = sep, - year = {2018}, - pages = {031083}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SCLVRZIB/Dubois et al. - 2018 - Kerker Effect in Ultrahigh-Field Magnetic Resonanc.pdf:application/pdf}, -} - -@inproceedings{chauvel_investigation_nodate, - address = {London, England, UK}, - title = {Investigation of the singularity of the chimpanzee brain superficial white matter bundles using diffusion {MRI} and clustering-based approaches}, - url = {https://archive.ismrm.org/2022/2107.html}, - doi = {10.58530/2022/2107}, - abstract = {A way to better appreciate the complex human brain evolution relies on comparative investigations with homologous species. We present here the superficial connectivity organization of the Chimpanzee brain using a combination of image processing and DBSCAN clustering analyzes obtained from 39 chimpanzees DTI scans. The results revealed the presence of U-fiber, V-fiber and Curved-fiber shapes already identified in Human superficial fiber connectivity studies. This non-negligeable short fibers organisation resemblance between Chimpanzees and Humans, brings out new perspectives on hominid brain singularity knowledge.}, - language = {en}, - urldate = {2024-02-27}, - author = {Chauvel, Maëlig and Uszynski, Ivy and Popov, Alexandros and Hopkins, William and Mangin, Jean-François and Poupon, Cyril}, - pages = {2107}, -} - -@inproceedings{chauvel_investigation_nodate-1, - address = {London, England, UK}, - title = {Investigation of the inferior fronto-occipital fasciculus in the macaque fascicularis brain using 11.7 {T} ultra-high field diffusion data}, - url = {https://archive.ismrm.org/2022/2102.html}, - doi = {10.58530/2022/2102}, - abstract = {In this study, we investigated the controversial presence of the inferior fronto-occipital fasciculus (IFOF) in the macaque species ( - Macaca fascicularis - ) using ultra-high field MRI (11.7 T) diffusion data. Thanks to a fiber clustering approach, we were able to reconstruct the IFOF in both hemispheres. We observed thin frontal connections and a more developed fasciculus on the right hemisphere compared to the left. The presence of this special fasciculus, known in Humans as being part of the ventral pathways for multi-modal language processing, is a new step forward concerning the comprehension of the macaque brain, and the primate brain in general.}, - language = {en}, - urldate = {2024-02-27}, - author = {Chauvel, Maëlig and Uszynski, Ivy and Fischer, Clara and Poupon, Fabrice and Destrieux, Christophe and Maldonado, Igor and Poupon, Cyril}, - pages = {2102}, -} - -@article{haeger_imaging_2020, - title = {Imaging the aging brain: study design and baseline findings of the {SENIOR} cohort}, - volume = {12}, - issn = {1758-9193}, - shorttitle = {Imaging the aging brain}, - url = {https://alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1}, - doi = {10.1186/s13195-020-00642-1}, - abstract = {Abstract - - Background - Current demographic trends point towards an aging society entailing increasing occurrence and burden of neurodegenerative diseases. In this context, understanding physiological aging and its turning point into neurodegeneration is essential for the development of possible biomarkers and future therapeutics of brain disease. - - - Methods - The SENIOR study represents a longitudinal, observational study including cognitively healthy elderlies aged between 50 and 70 years old at the time of inclusion, being followed annually over 10 years. Our multimodal protocol includes structural, diffusion, functional, and sodium magnetic resonance imaging (MRI) at 3 T and 7 T, positron emission tomography (PET), blood samples, genetics, audiometry, and neuropsychological and neurological examinations as well as assessment of neuronal risk factors. - - - Results - One hundred forty-two participants (50\% females) were enrolled in the SENIOR cohort with a mean age of 60 (SD 6.3) years at baseline. Baseline results with multiple regression analyses reveal that cerebral white matter lesions can be predicted by cardiovascular and cognitive risk factors and age. Cardiovascular risk factors were strongly associated with juxtacortical and periventricular lesions. Intra-subject across-test variability as a measure of neuropsychological test performance and possible cognitive marker predicts white matter volume and is significantly associated with risk profile. Division of the cohort into subjects with a higher and lower risk profile shows significant differences in intra-subject across-test variability and volumes as well as cortical thickness of brain regions of the temporal lobe. There is no difference between the lower- and higher-risk groups in amyloid load using PET data from a subset of 81 subjects. - - - Conclusions - We here describe the study protocol and baseline findings of the SENIOR observational study which aim is the establishment of integrated, multiparametric maps of normal aging and the identification of early biomarkers for neurodegeneration. We show that intra-subject across-test variability as a marker of neuropsychological test performance as well as age, gender, and combined risk factors influence neuronal decline as represented by decrease in brain volume, cortical thickness, and increase in white matter lesions. Baseline findings will be used as underlying basis for the further implications of aging and neuronal degeneration as well as examination of brain aging under different aspects of brain pathology versus physiological aging.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {Alzheimer's Research \& Therapy}, - author = {Haeger, Alexa and Mangin, Jean-François and Vignaud, Alexandre and Poupon, Cyril and Grigis, Antoine and Boumezbeur, Fawzi and Frouin, Vincent and Deverre, Jean-Robert and Sarazin, Marie and Hertz-Pannier, Lucie and Bottlaender, Michel and {the SENIOR team} and Baron, Christine and Berland, Valérie and Blancho, Nathalie and Desmidt, Séverine and Doublé, Christine and Ginisty, Chantal and Joly-Testault, Véronique and Laurier, Laurence and Lecomte, Yann and Leroy, Claire and Manciot, Christine and Marchand, Stephanie and Mediouni, Gaelle and Millot, Xavier and Monassier, Ludivine and Roger, Séverine and Vuillemard, Catherine}, - month = dec, - year = {2020}, - keywords = {Imaging, Aging, Biomarker, Prevention, Dementia, Neurodegenerative disease, Alzheimer’s disease, Cognitive decline, Intra-person across-test variability}, - pages = {77}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AMRXRWZU/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf;PubMed Central Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/STJTPBIP/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf}, -} - -@incollection{lepore_identification_2019, - address = {Cham}, - title = {Identification of {U}-{Bundles} {Based} on {Sulcus} {Morphology}}, - volume = {11379}, - isbn = {978-3-030-13834-9 978-3-030-13835-6}, - url = {http://link.springer.com/10.1007/978-3-030-13835-6_1}, - language = {en}, - urldate = {2024-02-27}, - booktitle = {Processing and {Analysis} of {Biomedical} {Information}}, - publisher = {Springer International Publishing}, - author = {Guevara, M. and Sun, Z. Y. and Guevara, P. and Rivière, D. and Poupon, C. and Mangin, J.-F.}, - editor = {Lepore, Natasha and Brieva, Jorge and Romero, Eduardo and Racoceanu, Daniel and Joskowicz, Leo}, - year = {2019}, - doi = {10.1007/978-3-030-13835-6_1}, - note = {Series Title: Lecture Notes in Computer Science}, - pages = {3--7}, -} - -@inproceedings{artiges_ginkgo_nodate, - address = {London, England, UK}, - title = {Ginkgo: a novel modular and and {Open} {Source} {MRI} pulse sequence development framework dedicated to {MRI} systems}, - shorttitle = {Ginkgo}, - url = {https://archive.ismrm.org/2022/2778.html}, - doi = {10.58530/2022/2778}, - abstract = {We created a new object-oriented environment for MR pulse-sequence development based on IDEA VE11C and above versions using an Open Science philosophy. This Ginkgo toolkit uses a modular structure to facilitate the design of pulse sequences using the aggregation of basic open-source sequence blocks available from the toolkit. Proofs of concept of the productivity gain reached using Ginkgo are provided through the implementation of a series of sequence models including a diffusion-weighted PGSE 3D EPI sequence.}, - language = {en}, - urldate = {2024-02-27}, - author = {Artiges, Anaïs and Mauconduit, Franck and Uszynski, Ivy and Mulot, Baptiste and Chaillou, Elodie and Ciuciu, Philippe and Poupon, Cyril}, - pages = {2778}, -} - -@article{reuter_faconstructor_2019, - title = {{FAConstructor}: an interactive tool for geometric modeling of nerve fiber architectures in the brain}, - volume = {14}, - issn = {1861-6410, 1861-6429}, - shorttitle = {{FAConstructor}}, - url = {http://link.springer.com/10.1007/s11548-019-02053-6}, - doi = {10.1007/s11548-019-02053-6}, - language = {en}, - number = {11}, - urldate = {2024-02-27}, - journal = {International Journal of Computer Assisted Radiology and Surgery}, - author = {Reuter, Jan André and Matuschke, Felix and Menzel, Miriam and Schubert, Nicole and Ginsburger, Kévin and Poupon, Cyril and Amunts, Katrin and Axer, Markus}, - month = nov, - year = {2019}, - pages = {1881--1889}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FDER4HUH/Reuter et al. - 2019 - FAConstructor an interactive tool for geometric m.pdf:application/pdf}, -} - -@article{yang_diffusion_2021, - title = {Diffusion {MRI} tractography for neurosurgery: the basics, current state, technical reliability and challenges}, - volume = {66}, - issn = {0031-9155, 1361-6560}, - shorttitle = {Diffusion {MRI} tractography for neurosurgery}, - url = {https://iopscience.iop.org/article/10.1088/1361-6560/ac0d90}, - doi = {10.1088/1361-6560/ac0d90}, - abstract = {Abstract - - Diffusion magnetic resonance imaging (dMRI) tractography is currently the only imaging technique that allows for non-invasive delineation and visualisation of white matter (WM) tracts - in vivo, - prompting rapid advances in related fields of brain MRI research in recent years. One of its major clinical applications is for pre-surgical planning and intraoperative image guidance in neurosurgery, where knowledge about the location of WM tracts nearby the surgical target can be helpful to guide surgical resection and optimise post-surgical outcomes. Surgical injuries to these WM tracts can lead to permanent neurological and functional deficits, making the accuracy of tractography reconstructions paramount. The quality of dMRI tractography is influenced by many modifiable factors, ranging from MRI data acquisition through to the post-processing of tractography output, with the potential of error propagation based on decisions made at each and subsequent processing steps. Research over the last 25 years has significantly improved the anatomical accuracy of tractography. An updated review about tractography methodology in the context of neurosurgery is now timely given the thriving research activities in dMRI, to ensure more appropriate applications in the clinical neurosurgical realm. This article aims to review the dMRI physics, and tractography methodologies, highlighting recent advances to provide the key concepts of tractography-informed neurosurgery, with a focus on the general considerations, the current state of practice, technical challenges, potential advances, and future demands to this field.}, - number = {15}, - urldate = {2024-02-27}, - journal = {Physics in Medicine \& Biology}, - author = {Yang, Joseph Yuan-Mou and Yeh, Chun-Hung and Poupon, Cyril and Calamante, Fernando}, - month = aug, - year = {2021}, - pages = {15TR01}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HXDHM6MU/Yang et al. - 2021 - Diffusion MRI tractography for neurosurgery the b.pdf:application/pdf}, -} - -@incollection{kaden_diffeomorphic_2018, - address = {Cham}, - title = {Diffeomorphic {Registration} of {Diffusion} {Mean} {Apparent} {Propagator} {Fields} {Using} {Dynamic} {Programming} on a {Minimum} {Spanning} {Tree}}, - isbn = {978-3-319-73838-3 978-3-319-73839-0}, - url = {http://link.springer.com/10.1007/978-3-319-73839-0_6}, - urldate = {2024-02-27}, - booktitle = {Computational {Diffusion} {MRI}}, - publisher = {Springer International Publishing}, - author = {Ginsburger, Kévin and Poupon, Fabrice and Teillac, Achille and Mangin, Jean-Francois and Poupon, Cyril}, - editor = {Kaden, Enrico and Grussu, Francesco and Ning, Lipeng and Tax, Chantal M. W. and Veraart, Jelle}, - year = {2018}, - doi = {10.1007/978-3-319-73839-0_6}, - note = {Series Title: Mathematics and Visualization}, - pages = {81--90}, -} - -@article{pagnamenta_defective_2019, - title = {Defective tubulin detyrosination causes structural brain abnormalities with cognitive deficiency in humans and mice}, - volume = {28}, - issn = {0964-6906, 1460-2083}, - url = {https://academic.oup.com/hmg/article/28/20/3391/5540982}, - doi = {10.1093/hmg/ddz186}, - abstract = {Abstract - Reversible detyrosination of tubulin, the building block of microtubules, is crucial for neuronal physiology. Enzymes responsible for detyrosination were recently identified as complexes of vasohibins (VASHs) one or two with small VASH-binding protein (SVBP). Here we report three consanguineous families, each containing multiple individuals with biallelic inactivation of SVBP caused by truncating variants (p.Q28* and p.K13Nfs*18). Affected individuals show brain abnormalities with microcephaly, intellectual disability and delayed gross motor and speech development. Immunoblot testing in cells with pathogenic SVBP variants demonstrated that the encoded proteins were unstable and non-functional, resulting in a complete loss of VASH detyrosination activity. Svbp knockout mice exhibit drastic accumulation of tyrosinated tubulin and a reduction of detyrosinated tubulin in brain tissue. Similar alterations in tubulin tyrosination levels were observed in cultured neurons and associated with defects in axonal differentiation and architecture. Morphological analysis of the Svbp knockout mouse brains by anatomical magnetic resonance imaging showed a broad impact of SVBP loss, with a 7\% brain volume decrease, numerous structural defects and a 30\% reduction of some white matter tracts. Svbp knockout mice display behavioural defects, including mild hyperactivity, lower anxiety and impaired social behaviour. They do not, however, show prominent memory defects. Thus, SVBP-deficient mice recapitulate several features observed in human patients. Altogether, our data demonstrate that deleterious variants in SVBP cause this neurodevelopmental pathology, by leading to a major change in brain tubulin tyrosination and alteration of microtubule dynamics and neuron physiology.}, - language = {en}, - number = {20}, - urldate = {2024-02-27}, - journal = {Human Molecular Genetics}, - author = {Pagnamenta, Alistair T and Heemeryck, Pierre and Martin, Hilary C and Bosc, Christophe and Peris, Leticia and Uszynski, Ivy and Gory-Fauré, Sylvie and Couly, Simon and Deshpande, Charu and Siddiqui, Ata and Elmonairy, Alaa A and {WGS500 Consortium} and {Genomics England Research Consortium} and Jayawant, Sandeep and Murthy, Sarada and Walker, Ian and Loong, Lucy and Bauer, Peter and Vossier, Frédérique and Denarier, Eric and Maurice, Tangui and Barbier, Emmanuel L and Deloulme, Jean-Christophe and Taylor, Jenny C and Blair, Edward M and Andrieux, Annie and Moutin, Marie-Jo}, - month = oct, - year = {2019}, - pages = {3391--3405}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/H7V6TGWU/Pagnamenta et al. - 2019 - Defective tubulin detyrosination causes structural.pdf:application/pdf}, -} - -@inproceedings{lopez-lopez_cortical_2019, - address = {Valparaiso, Chile}, - title = {Cortical surface parcellation based on intra-subject white matter fiber clustering}, - isbn = {978-1-72813-185-6}, - url = {https://ieeexplore.ieee.org/document/8988066/}, - doi = {10.1109/CHILECON47746.2019.8988066}, - urldate = {2024-02-27}, - booktitle = {2019 {IEEE} {CHILEAN} {Conference} on {Electrical}, {Electronics} {Engineering}, {Information} and {Communication} {Technologies} ({CHILECON})}, - publisher = {IEEE}, - author = {Lopez-Lopez, Narciso and Vazquez, Andrea and Poupon, Cyril and Mangin, Jean-Francois and Guevara, Pamela}, - month = nov, - year = {2019}, - pages = {1--6}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YBRHYPYT/Lopez-Lopez et al. - 2019 - Cortical surface parcellation based on intra-subje.pdf:application/pdf}, -} - -@inproceedings{silva_cortical_2019, - address = {Venice, Italy}, - title = {Cortical {Surface} {Parcellation} {Based} on {Graph} {Representation} of {Short} {Fiber} {Bundle} {Connections}}, - isbn = {978-1-5386-3641-1}, - url = {https://ieeexplore.ieee.org/document/8759580/}, - doi = {10.1109/ISBI.2019.8759580}, - urldate = {2024-02-27}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - publisher = {IEEE}, - author = {Silva, Felipe and Guevara, Miguel and Poupon, Cyril and Mangin, Jean-Francois and Hernandez, Cecilia and Guevara, Pamela}, - month = apr, - year = {2019}, - pages = {1479--1482}, -} - -@article{moulton_connectivity_2019, - title = {Connectivity between the visual word form area and the parietal lobe improves after the first year of reading instruction: a longitudinal {MRI} study in children}, - issn = {1863-2653, 1863-2661}, - shorttitle = {Connectivity between the visual word form area and the parietal lobe improves after the first year of reading instruction}, - url = {http://link.springer.com/10.1007/s00429-019-01855-3}, - doi = {10.1007/s00429-019-01855-3}, - language = {en}, - urldate = {2024-02-27}, - journal = {Brain Structure and Function}, - author = {Moulton, Eric and Bouhali, Florence and Monzalvo, Karla and Poupon, Cyril and Zhang, Hui and Dehaene, Stanislas and Dehaene-Lambertz, Ghislaine and Dubois, Jessica}, - month = mar, - year = {2019}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WEAN33B8/Moulton et al. - 2019 - Connectivity between the visual word form area and.pdf:application/pdf}, -} - -@article{schilling_challenges_2019, - title = {Challenges in diffusion {MRI} tractography – {Lessons} learned from international benchmark competitions}, - volume = {57}, - issn = {0730725X}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0730725X18305162}, - doi = {10.1016/j.mri.2018.11.014}, - language = {en}, - urldate = {2024-02-27}, - journal = {Magnetic Resonance Imaging}, - author = {Schilling, Kurt G. and Daducci, Alessandro and Maier-Hein, Klaus and Poupon, Cyril and Houde, Jean-Christophe and Nath, Vishwesh and Anderson, Adam W. and Landman, Bennett A. and Descoteaux, Maxime}, - month = apr, - year = {2019}, - pages = {194--209}, - file = {Accepted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LT5HQHJW/Schilling et al. - 2019 - Challenges in diffusion MRI tractography – Lessons.pdf:application/pdf}, -} - -@article{r_daudin_bin1_2021, - title = {{BIN1} genetic risk factor for {Alzheimer} is sufficient to induce early structural tract alterations in entorhinal-hippocampal area and memory-related hippocampal multi-scale impairments}, - url = {http://biorxiv.org/content/early/2021/03/09/437228.abstract}, - doi = {10.1101/437228}, - abstract = {Genetic factors are known to contribute to Late Onset Alzheimer’s disease (LOAD) but their contribution to pathophysiology, specially to prodomic phases accessible to therapeutic approaches are far to be understood.To translate genetic risk of Alzheimer’s disease (AD) into mechanistic insight, we generated transgenic mouse lines that express a ∼195 kbp human BAC that includes only BIN1, a gene associated to LOAD. This model gives a modest BIN1 overexpression, dependent of the number of BAC copies. At 6 months of age, we detected impaired entorhinal cortex (EC)-hippocampal pathways with specific impairments in EC-dentate gyrus synaptic long-term potentiation, dendritic spines of granular cells and recognition episodic memory. Structural changes were quantified using MRI. Their whole-brain functional impact were analyzed using resting state fMRI with a hypoconnectivity centered on entorhinal cortex.These early phenotype defects independent of any changes in A-beta can be instrumental in the search for new AD drug targets.Competing Interest StatementThe authors have declared no competing interest.}, - journal = {bioRxiv}, - author = {{R Daudin} and {D Marechal} and {R Golgolab} and {Q Wang} and {Y Abe} and {T. Tsurugizawa} and {N Bourg} and {M Sartori} and {Y Loe-Mie} and {J Lipecka} and {C Guerrera} and {A McKenzie} and {B Potier} and {P Dutar} and {J Viard} and {A.M Lepagnol-Bestel} and {A Winkeler} and {I. Uszynski} and {V Hindié} and {MC Birling} and {L Lindner} and {C Chevalier} and {G Pavlovic} and {M Reis} and {H Kranz} and {G Dupuis} and {S Lévêque-Fort} and {J Diaz} and {E Davenas} and {D Dembele} and {H. Atas-Ozcan} and {J Laporte} and {C Thibault-Carpentier} and {B Malissen} and {J.C Rain} and {C. Poupon} and {D Le Bihan} and {B Zhang} and {Y Herault} and {L. Ciobanu} and {M Simonneau}}, - month = jan, - year = {2021}, - pages = {437228}, -} - -@article{nabulsi_aberrant_2022, - title = {Aberrant {Subnetwork} and {Hub} {Dysconnectivity} in {Adult} {Bipolar} {Disorder}: {A} {Multicenter} {Graph} {Theory} {Analysis}}, - volume = {32}, - issn = {1047-3211, 1460-2199}, - shorttitle = {Aberrant {Subnetwork} and {Hub} {Dysconnectivity} in {Adult} {Bipolar} {Disorder}}, - url = {https://academic.oup.com/cercor/article/32/10/2254/6380064}, - doi = {10.1093/cercor/bhab356}, - abstract = {Abstract - Neuroimaging evidence implicates structural network-level abnormalities in bipolar disorder (BD); however, there remain conflicting results in the current literature hampered by sample size limitations and clinical heterogeneity. Here, we set out to perform a multisite graph theory analysis to assess the extent of neuroanatomical dysconnectivity in a large representative study of individuals with BD. - This cross-sectional multicenter international study assessed structural and diffusion-weighted magnetic resonance imaging data obtained from 109 subjects with BD type 1 and 103 psychiatrically healthy volunteers. - Whole-brain metrics, permutation-based statistics, and connectivity of highly connected nodes were used to compare network-level connectivity patterns in individuals with BD compared with controls. - The BD group displayed longer characteristic path length, a weakly connected left frontotemporal network, and increased rich-club dysconnectivity compared with healthy controls. - Our multisite findings implicate emotion and reward networks dysconnectivity in bipolar illness and may guide larger scale global efforts in understanding how human brain architecture impacts mood regulation in BD.}, - language = {en}, - number = {10}, - urldate = {2024-02-27}, - journal = {Cerebral Cortex}, - author = {Nabulsi, Leila and McPhilemy, Genevieve and O’Donoghue, Stefani and Cannon, Dara M and Kilmartin, Liam and O’Hora, Denis and Sarrazin, Samuel and Poupon, Cyril and D’Albis, Marc-Antoine and Versace, Amelia and Delavest, Marine and Linke, Julia and Wessa, Michèle and Phillips, Mary L and Houenou, Josselin and McDonald, Colm}, - month = may, - year = {2022}, - pages = {2254--2264}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/X6SXUXYL/Nabulsi et al. - 2022 - Aberrant Subnetwork and Hub Dysconnectivity in Adu.pdf:application/pdf}, -} - -@inproceedings{pinto_stringent_2018, - address = {Honolulu, HI, USA}, - title = {A stringent fiber distance measure for {dMRI} tractography clustering and segmentation}, - isbn = {978-1-5386-3646-6}, - url = {https://ieeexplore.ieee.org/document/8512333/}, - doi = {10.1109/EMBC.2018.8512333}, - urldate = {2024-02-27}, - booktitle = {2018 40th {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} and {Biology} {Society} ({EMBC})}, - publisher = {IEEE}, - author = {Pinto, Daniela and Roman, Claudio and Guevara, Miguel and Poupon, Cyril and Mangin, Jean-Francaois and Guevara, Pamela}, - month = jul, - year = {2018}, - pages = {1--4}, -} - -@techreport{daudin_bin1_2018, - type = {preprint}, - title = {{BIN1} genetic risk factor for {Alzheimer} is sufficient to induce early structural tract alterations in entorhinal-hippocampal area and memory-related hippocampal multi-scale impairments}, - url = {http://biorxiv.org/lookup/doi/10.1101/437228}, - abstract = {Abstract - Genetic factors are known to contribute to Late Onset Alzheimer’s disease (LOAD) but their contribution to pathophysiology, specially to prodomic phases accessible to therapeutic approaches are far to be understood. - - To translate genetic risk of Alzheimer’s disease (AD) into mechanistic insight, we generated transgenic mouse lines that express a ∼195 kbp human BAC that includes only - BIN1 - , a gene associated to LOAD. This model gives a modest BIN1 overexpression, dependent of the number of BAC copies. At 6 months of age, we detected impaired entorhinal cortex (EC)-hippocampal pathways with specific impairments in EC-dentate gyrus synaptic long-term potentiation, dendritic spines of granular cells and recognition episodic memory. Structural changes were quantified using MRI. Their whole-brain functional impact were analyzed using resting state fMRI with a hypoconnectivity centered on entorhinal cortex. - - These early phenotype defects independent of any changes in A-beta can be instrumental in the search for new AD drug targets.}, - language = {en}, - urldate = {2024-02-27}, - institution = {Neuroscience}, - author = {Daudin, R and Marechal, D and Golgolab, R and Wang, Q and Abe, Y and Tsurugizawa, T. and Bourg, N and Sartori, M and Loe-Mie, Y and Lipecka, J and Guerrera, C and McKenzie, A and Potier, B and Dutar, P and Viard, J and Lepagnol-Bestel, A.M and Winkeler, A and Uszynski, I. and Hindié, V and Birling, Mc and Lindner, L and Chevalier, C and Pavlovic, G and Reiss, M and Kranz, H and Dupuis, G and Lévêque-Fort, S and Diaz, J and Davenas, E and Dembele, D and Atas-Ozcan, H. and Laporte, J and Thibault-Carpentier, C and Malissen, B and Rain, J.C and Poupon, C. and Le Bihan, D and Zhang, B and Herault, Y and Ciobanu, L. and Simonneau, M}, - month = oct, - year = {2018}, - doi = {10.1101/437228}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/62I93ZP2/Daudin et al. - 2018 - BIN1 genetic risk factor for Alzheimer is sufficie.pdf:application/pdf}, -} - -@article{vazquez_automatic_2020, - title = {Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information}, - volume = {19}, - issn = {1475-925X}, - url = {https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-020-00786-z}, - doi = {10.1186/s12938-020-00786-z}, - abstract = {Abstract - - Background - Diffusion MRI is the preferred non-invasive in vivo modality for the study of brain white matter connections. Tractography datasets contain 3D streamlines that can be analyzed to study the main brain white matter tracts. Fiber clustering methods have been used to automatically group similar fibers into clusters. However, due to inter-subject variability and artifacts, the resulting clusters are difficult to process for finding common connections across subjects, specially for superficial white matter. - - - Methods - We present an automatic method for labeling of short association bundles on a group of subjects. The method is based on an intra-subject fiber clustering that generates compact fiber clusters. Posteriorly, the clusters are labeled based on the cortical connectivity of the fibers, taking as reference the Desikan–Killiany atlas, and named according to their relative position along one axis. Finally, two different strategies were applied and compared for the labeling of inter-subject bundles: a matching with the Hungarian algorithm, and a well-known fiber clustering algorithm, called QuickBundles. - - - Results - Individual labeling was executed over four subjects, with an execution time of 3.6 min. An inspection of individual labeling based on a distance measure showed good correspondence among the four tested subjects. Two inter-subject labeling were successfully implemented and applied to 20 subjects and compared using a set of distance thresholds, ranging from a conservative value of 10 mm to a moderate value of 21 mm. Hungarian algorithm led to a high correspondence, but low reproducibility for all the thresholds, with 96 s of execution time. QuickBundles led to better correspondence, reproducibility and short execution time of 9 s. Hence, the whole processing for the inter-subject labeling over 20 subjects takes 1.17 h. - - - Conclusion - We implemented a method for the automatic labeling of short bundles in individuals, based on an intra-subject clustering and the connectivity of the clusters with the cortex. The labels provide useful information for the visualization and analysis of individual connections, which is very difficult without any additional information. Furthermore, we provide two fast inter-subject bundle labeling methods. The obtained clusters could be used for performing manual or automatic connectivity analysis in individuals or across subjects.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {BioMedical Engineering OnLine}, - author = {Vázquez, Andrea and López-López, Narciso and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Ladra, Susana and Guevara, Pamela}, - month = dec, - year = {2020}, - keywords = {Clustering, Tractography, Fiber bundle, Superficial white matter, Fiber labeling}, - pages = {42}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/89DX6DK5/Vázquez et al. - 2020 - Automatic group-wise whole-brain short association.pdf:application/pdf}, -} - -@article{osorio_abrainvis_2021, - title = {{ABrainVis}: an android brain image visualization tool}, - volume = {20}, - issn = {1475-925X}, - shorttitle = {{ABrainVis}}, - url = {https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/s12938-021-00909-0}, - doi = {10.1186/s12938-021-00909-0}, - abstract = {Abstract - - Background - The visualization and analysis of brain data such as white matter diffusion tractography and magnetic resonance imaging (MRI) volumes is commonly used by neuro-specialist and researchers to help the understanding of brain structure, functionality and connectivity. As mobile devices are widely used among users and their technology shows a continuous improvement in performance, different types of applications have been designed to help users in different work areas. - - - Results - We present, ABrainVis, an Android mobile tool that allows users to visualize different types of brain images, such as white matter diffusion tractographies, represented as fibers in 3D, segmented fiber bundles, MRI 3D images as rendered volumes and slices, and meshes. The tool enables users to choose and combine different types of brain imaging data to provide visual anatomical context for specific visualization needs. ABrainVis provides high performance over a wide range of Android devices, including tablets and cell phones using medium and large tractography datasets. Interesting visualizations including brain tumors and arteries, along with fiber, are given as examples of case studies using ABrainVis. - - - Conclusions - The functionality, flexibility and performance of ABrainVis tool introduce an improvement in user experience enabling neurophysicians and neuroscientists fast visualization of large tractography datasets, as well as the ability to incorporate other brain imaging data such as MRI volumes and meshes, adding anatomical contextual information.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {BioMedical Engineering OnLine}, - author = {Osorio, Ignacio and Guevara, Miguel and Bonometti, Danilo and Carrasco, Diego and Descoteaux, Maxime and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = dec, - year = {2021}, - keywords = {Brain imaging, 3D rendering, Mobile visualization}, - pages = {72}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UGZD27KA/Osorio et al. - 2021 - ABrainVis an android brain image visualization to.pdf:application/pdf}, -} - -@article{sarrazin_multicentric_2022, - title = {A multicentric multimodal in vivo microscopy {MRI} study of bipolar disorder reveals axonal loss and demyelination}, - volume = {65}, - issn = {0924-9338, 1778-3585}, - url = {https://www.cambridge.org/core/product/identifier/S0924933822004291/type/journal_article}, - doi = {10.1192/j.eurpsy.2022.429}, - abstract = {Introduction - Bipolar disorder has been repeatedly associated with abnormalities of white matter. However, DTI is intrinsically limited and the precise cellular mechanisms that underlie these alterations remains unknown. - - - Objectives - Our aim was to investigate microscopical characteristics of white matter using MRI in patients with bipolar and healthy controls. - - - Methods - 77 patients and 71 controls from 3 sites had a T1 structural MRI, a multi-shell HARDI MRI and at one site with a T1-weighted VFA-SPGR acquisition, and a T2 MSME acquisition. The volume fraction and the orientation dispersion was extracted using NODDI from DW images in each site. Myelin Water Fraction was extracted in 33 patients and 36 controls to probe myelin characteristics. White matter bundles were reconstructed using deterministic tractography. Statistical analyses were performed after harmonization by the ComBat algorithm and controlled for age, gender and handedness. - - - Results - We found significant lower axonal density in patients along the short fibers of the left cingulum, the left anterior arcuate and the left inferior fronto-occipital fasciculus. We found lower mean MWF in patients along the short fibers of the right cingulum, the left inferior fronto-occipital fasciculus, the left anterior arcuate and the splenium of the corpus callosum. We found higher mean orientation dispersion in patients only along the left uncinate fasciculus. - - - Conclusions - We report alterations of limbic and inter-hemispheric white matter tracts in patients with bipolar disorder reflecting axonal loss, demyelination and architecture alterations. These results contribute to better capture the plurality of the mechanisms involved in bipolar disorder that cannot be deciphered with classical diffusion MRI. - - - Disclosure - No significant relationships.}, - language = {en}, - number = {S1}, - urldate = {2024-02-27}, - journal = {European Psychiatry}, - author = {Sarrazin, S. and Poupon, C. and Uszynski, I. and Mangin, J.-F. and Polosan, M. and Favre, P. and Laidi, C. and D’Albis, M.-A. and Leboyer, M. and Lledo, P.-M. and Henry, C. and Emsell, L. and Shakeel, M. and Goghari, V. and Houenou, J.}, - month = jun, - year = {2022}, - pages = {S160--S160}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HPPXX4L4/Sarrazin et al. - 2022 - A multicentric multimodal in vivo microscopy MRI s.pdf:application/pdf}, -} - -@article{yebga_hot_novel_2022, - title = {A novel male {Japanese} quail structural connectivity atlas using ultra-high field diffusion {MRI} at 11.7 {T}}, - volume = {227}, - issn = {1863-2653, 1863-2661}, - url = {https://link.springer.com/10.1007/s00429-022-02457-2}, - doi = {10.1007/s00429-022-02457-2}, - abstract = {Abstract - - The structural connectivity of animal brains can be revealed using post-mortem diffusion-weighted magnetic resonance imaging (MRI). Despite the existence of several structural atlases of avian brains, few of them address the bird’s structural connectivity. In this study, a novel atlas of the structural connectivity is proposed for the male Japanese quail ( - Coturnix japonica - ), aiming at investigating two lines divergent on their emotionality trait: the short tonic immobility (STI) and the long tonic immobility (LTI) lines. The STI line presents a low emotionality trait, while the LTI line expresses a high emotionality trait. 21 male Japanese quail brains from both lines were scanned post-mortem for this study, using a preclinical Bruker 11.7 T MRI scanner. Diffusion-weighted MRI was performed using a 3D segmented echo planar imaging (EPI) pulsed gradient spin-echo (PGSE) sequence with a 200  - - - \$\${\textbackslash}upmu\$\$ - - μ - - - - m isotropic resolution, 75 diffusion-encoding directions and a b-value fixed at 4500 s/mm - 2 - . Anatomical MRI was likewise performed using a 2D anatomical T - 2 - -weighted spin-echo (SE) sequence with a 150  - - - \$\${\textbackslash}upmu\$\$ - - μ - - - - m isotropic resolution. This very first anatomical connectivity atlas of the male Japanese quail reveals 34 labeled fiber tracts and the existence of structural differences between the connectivity patterns characterizing the two lines. Thus, the link between the male Japanese quail’s connectivity and its underlying anatomical structures has reached a better understanding.}, - language = {en}, - number = {5}, - urldate = {2023-01-12}, - journal = {Brain Structure and Function}, - author = {Yebga Hot, Raïssa and Siwiaszczyk, Marine and Love, Scott A. and Andersson, Frédéric and Calandreau, Ludovic and Poupon, Fabrice and Beaujoin, Justine and Herlin, Bastien and Boumezbeur, Fawzi and Mulot, Baptiste and Chaillou, Elodie and Uszynski, Ivy and Poupon, Cyril}, - month = jun, - year = {2022}, - pages = {1577--1597}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/PT6EFX3J/Yebga Hot et al. - 2022 - A novel male Japanese quail structural connectivit.pdf:application/pdf;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8JNWUP96/Yebga Hot et al. - 2022 - A novel male Japanese quail structural connectivit.pdf:application/pdf}, -} - -@article{guevara_disentangling_2022, - title = {Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification}, - volume = {255}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922003214}, - doi = {10.1016/j.neuroimage.2022.119197}, - abstract = {Each variation of the cortical folding pattern implies a particular rearrangement of the geometry of the fibers of the underlying white matter. While this rearrangement only impacts the ends of the long pathways, it may affect most of the trajectory of the short bundles. Therefore, mapping the short fibers of the human brain using diffusion-based tractography requires a dedicated strategy to overcome the variability of the folding patterns. In this paper, we propose a fiber-based stratification strategy splitting the population into homogeneous groups for disentangling the superficial white matter bundle organization. This strategy introduces a new refined fiber distance which includes angular considerations for inferring fine-grained atlases of the short bundles surrounding a specific sulcus and a subtractogram distance that quantifies the similitude between fiber sets of two different subjects. The stratification splits the population into groups with similar regional fiber organization using manifold learning. We first successfully test the hypothesis that the main source of variability of the regional fiber organization is the variability of the regional folding pattern. Then, in each group, we proceed with the automatic identification of the most stable bundles, at a higher granularity level than what can be achieved with the non-stratified whole population, enabling the disentanglement of the very variable configuration of the short fibers. Finally, the method searches for bundle correspondence across groups to build a population level atlas. As a proof of concept, the atlas refinement achieved by this strategy is illustrated for the fibers that surround the central sulcus and the superior temporal sulcus using the HCP dataset.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Sun, Zhong-Yi and Guevara, Pamela and Rivière, Denis and Grigis, Antoine and Poupon, Cyril and Mangin, Jean-François}, - month = jul, - year = {2022}, - keywords = {Tractography, Short association fibers, Diffusion-weighted imaging, Cortical variability, Superficial white matter, U-fibers, White matter bundle}, - pages = {119197}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EWUQUNGE/S1053811922003214.html:text/html}, -} - -@article{roman_superficial_2022, - title = {Superficial white matter bundle atlas based on hierarchical fiber clustering over probabilistic tractography data}, - volume = {262}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922006656}, - doi = {10.1016/j.neuroimage.2022.119550}, - abstract = {The study of short association fibers is still an incomplete task due to their higher inter-subject variability and the smaller size of this kind of fibers in comparison to known long association bundles. However, their description is essential to understand human brain dysfunction and better characterize the human brain connectome. In this work, we present a multi-subject atlas of short association fibers, which was computed using a superficial white matter bundle identification method based on fiber clustering. To create the atlas, we used probabilistic tractography from one hundred subjects from the HCP database, aligned with non-linear registration. The method starts with an intra-subject clustering of short fibers (30-85 mm). Based on a cortical atlas, the intra-subject cluster centroids from all subjects are segmented to identify the centroids connecting each region of interest (ROI) of the atlas. To reduce computational load, the centroids from each ROI group are randomly separated into ten subgroups. Then, an inter-subject hierarchical clustering is applied to each centroid subgroup, followed by a second level of clustering to select the most-reproducible clusters across subjects for each ROI group. Finally, the clusters are labeled according to the regions that they connect, and clustered to create the final bundle atlas. The resulting atlas is composed of 525 bundles of superficial short association fibers along the whole brain, with 384 bundles connecting pairs of different ROIs and 141 bundles connecting portions of the same ROI. The reproducibility of the bundles was verified using automatic segmentation on three different tractogram databases. Results for deterministic and probabilistic tractography data show high reproducibility, especially for probabilistic tractography in HCP data. In comparison to previous work, our atlas features a higher number of bundles and greater cortical surface coverage.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Román, Claudio and Hernández, Cecilia and Figueroa, Miguel and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela}, - month = nov, - year = {2022}, - keywords = {dMRI, Hierarchical clustering, Superficial white matter, Human Connectome Project, Short association bundles}, - pages = {119550}, -} - -@inproceedings{molina_group-wise_2023, - title = {Group-wise cortical parcellation based on structural connectivity and hierarchical clustering}, - volume = {12567}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670L/Group-wise-cortical-parcellation-based-on-structural-connectivity-and-hierarchical/10.1117/12.2670138.full}, - doi = {10.1117/12.2670138}, - abstract = {This paper presents a new cortical parcellation method based on group-wise connectivity and hierarchical clustering. A preliminary sub-parcellation is performed using intra-subject and inter-subject fiber clustering to obtain representative bundles among subjects with similar shapes and trajectories. The sub-parcellation is obtained by intersecting fiber clusters with cortical meshes. Next, mean connectivity and mean overlap matrices are computed over the sub-parcels to obtain spatial and connectivity information. To hierarchize the information, we propose to weight both matrices, to obtain an affinity graph, and then a dendrogram to merge or divide parcels by their hierarchy. Finally, to obtain homogeneous parcels, the method computes morphological operations. By selecting a different number of clusters over the dendrogram, the method obtains a different number of parcels and a variation in the resulting parcel sizes, depending on the parameters used. We computed the coefficient of variation (CV ) of the parcel size to evaluate the homogeneity of the parcels. Preliminary results suggest that the use of representative clusters and the integration of sub-parcel overlap and connectivity strength provide useful information to generate cortical parcellations at different levels of granularity. Even results are preliminary, this novel method allows researchers to add group-wise connectivity strength and spatial information for the construction of diffusion-based parcellations. Future work will include a detailed analysis of parameters, such as the matrix weights and the number of sub-parcel clusters, and the generation of hierarchical parcellations to improve the insight into the cortex subdivision and hierarchy among parcels.}, - urldate = {2024-03-12}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Molina, Joaquín and Mendoza, Cristóbal and Román, Claudio and Houenou, Josselin and Poupon, Cyril and Mangin, Jean François and El-Deredy, Wael and Hernández, Cecilia and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {172--181}, -} - -@inproceedings{poo_fiber_2023, - title = {Fiber bundles simulator using exponential curves to validate fiber clustering algorithms}, - volume = {12567}, - url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12567/125670J/Fiber-bundles-simulator-using-exponential-curves-to-validate-fiber-clustering/10.1117/12.2669811.full}, - doi = {10.1117/12.2669811}, - abstract = {Currently, there are many methods for processing diffusion MRI (dMRI) tractography data, with the aim to identify the main white matter connections. However, methods like fiber clustering lack ground truth, making the evaluation of the effectiveness of different clustering algorithms problematic. An alternative to evaluate the performance and test the efficacy of these algorithms is to use simulated fiber datasets. Nevertheless, the simulation of this data is not trivial due to brain fibers’ irregular and complex shape. Although many fiber bundle simulators exist, they have been developed for other purposes, such as validating tractography algorithms or local diffusion models. In addition, these simulators usually use simple fiber bundle configurations without considering complex bundle shapes. With this in mind, the main goal of this work is to implement a simulator of brain fiber bundles based on exponential curves for validating fiber clustering methods. This representation uses bundle centroids and shape parameters to obtain a more realistic appearance of the fascicles. The simulator was validated using a deep white matter fiber bundle atlas, obtaining a good percentage of intersection between the original and simulated bundles, of up to 82\%. Furthermore, we used groups of simulated bundles for the whole brain to evaluate the performance of a fiber clustering algorithm (QuickBundles) when using different distance thresholds, showing the utility of the proposed simulator.}, - urldate = {2024-03-12}, - booktitle = {18th {International} {Symposium} on {Medical} {Information} {Processing} and {Analysis}}, - publisher = {SPIE}, - author = {Poo, Elida and Kublik, Carlos and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = mar, - year = {2023}, - pages = {154--163}, -} - -@article{ginsburger_improving_2018, - title = {Improving the {Realism} of {White} {Matter} {Numerical} {Phantoms}: {A} {Step} toward a {Better} {Understanding} of the {Influence} of {Structural} {Disorders} in {Diffusion} {MRI}}, - volume = {6}, - issn = {2296-424X}, - shorttitle = {Improving the {Realism} of {White} {Matter} {Numerical} {Phantoms}}, - url = {https://www.frontiersin.org/articles/10.3389/fphy.2018.00012}, - doi = {10.3389/fphy.2018.00012}, - abstract = {White matter is composed of irregularly packed axons leading to a structural disorder in the extra-axonal space. Diffusion MRI experiments using oscillating gradient spin echo sequences have shown that the diffusivity transverse to axons in this extra-axonal space is dependent on the frequency of the employed sequence. In this study, we observe the same frequency-dependence using 3D simulations of the diffusion process in disordered media. We design a novel white matter numerical phantom generation algorithm which constructs biomimicking geometric configurations with few design parameters, and enables to control the level of disorder of the generated phantoms. The influence of various geometrical parameters present in white matter, such as global angular dispersion, tortuosity, presence of Ranvier nodes, beading, on the extra-cellular perpendicular diffusivity frequency dependence was investigated by simulating the diffusion process in numerical phantoms of increasing complexity and fitting the resulting simulated diffusion MR signal attenuation with an adequate analytical model designed for trapezoidal OGSE sequences. This work suggests that angular dispersion and especially beading have non-negligible effects on this extracellular diffusion metrics that may be measured using standard OGSE DW-MRI clinical protocols.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Physics}, - author = {Ginsburger, Kévin and Poupon, Fabrice and Beaujoin, Justine and Estournet, Delphine and Matuschke, Felix and Mangin, Jean-François and Axer, Markus and Poupon, Cyril}, - month = feb, - year = {2018}, - note = {Publisher: Frontiers}, - keywords = {Axonal Diameter, Biomimicking numerical phantoms, diffusion time-dependence, Monte-Carlo Simulations, Trapezoidal OGSE sequences, white matter microstructure}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TWWXMXTJ/Ginsburger et al. - 2018 - Improving the Realism of White Matter Numerical Ph.pdf:application/pdf}, -} - -@article{beaujoin_post-mortem_2018, - title = {Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion {MRI} at 11.7 {T}}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-018-1617-1}, - doi = {10.1007/s00429-018-1617-1}, - abstract = {The human hippocampus plays a key role in memory management and is one of the first structures affected by Alzheimer’s disease. Ultra-high magnetic resonance imaging provides access to its inner structure in vivo. However, gradient limitations on clinical systems hinder access to its inner connectivity and microstructure. A major target of this paper is the demonstration of diffusion MRI potential, using ultra-high field (11.7 T) and strong gradients (750 mT/m), to reveal the extra- and intra-hippocampal connectivity in addition to its microstructure. To this purpose, a multiple-shell diffusion-weighted acquisition protocol was developed to reach an ultra-high spatio-angular resolution with a good signal-to-noise ratio. The MRI data set was analyzed using analytical Q-Ball Imaging, Diffusion Tensor Imaging (DTI), and Neurite Orientation Dispersion and Density Imaging models. High Angular Resolution Diffusion Imaging estimates allowed us to obtain an accurate tractography resolving more complex fiber architecture than DTI models, and subsequently provided a map of the cross-regional connectivity. The neurite density was akin to that found in the histological literature, revealing the three hippocampal layers. Moreover, a gradient of connectivity and neurite density was observed between the anterior and the posterior part of the hippocampus. These results demonstrate that ex vivo ultra-high field/ultra-high gradients diffusion-weighted MRI allows the mapping of the inner connectivity of the human hippocampus, its microstructure, and to accurately reconstruct elements of the polysynaptic intra-hippocampal pathway using fiber tractography techniques at very high spatial/angular resolutions.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Beaujoin, Justine and Palomero-Gallagher, Nicola and Boumezbeur, Fawzi and Axer, Markus and Bernard, Jeremy and Poupon, Fabrice and Schmitz, Daniel and Mangin, Jean-François and Poupon, Cyril}, - month = jun, - year = {2018}, - keywords = {Human hippocampus, Structural connectivity, Microstructure imaging, Neurite density, Diffusion MRI}, - pages = {2157--2179}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/D7RW9LR5/Beaujoin et al. - 2018 - Post-mortem inference of the human hippocampal con.pdf:application/pdf}, -} - -@article{lebenberg_framework_2018, - title = {A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-018-1735-9}, - doi = {10.1007/s00429-018-1735-9}, - abstract = {Robust spatial alignment of post mortem data and in vivo MRI acquisitions from different ages, especially from the early developmental stages, into standard spaces is still a bottleneck hampering easy comparison with the mainstream neuroimaging results. In this paper, we test a landmark-based spatial normalization strategy as a framework for the seamless integration of any macroscopic dataset in the context of the Human Brain Project (HBP). This strategy stems from an approach called DISCO embedding sulcal constraints in a registration framework used to initialize DARTEL, the widely used spatial normalization approach proposed in the SPM software. We show that this strategy is efficient with a heterogeneous dataset including challenging data as preterm newborns, infants, post mortem histological data and a synthetic atlas computed from averaging the ICBM database, as well as more commonly studied data acquired in vivo in adults. We then describe some perspectives for a research program aiming at improving folding pattern matching for atlas inference in the context of the future HBP’s portal.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Lebenberg, J. and Labit, M. and Auzias, G. and Mohlberg, H. and Fischer, C. and Rivière, D. and Duchesnay, E. and Kabdebon, C. and Leroy, F. and Labra, N. and Poupon, F. and Dickscheid, T. and Hertz-Pannier, L. and Poupon, C. and Dehaene-Lambertz, G. and Hüppi, P. and Amunts, K. and Dubois, J. and Mangin, J.-F.}, - month = dec, - year = {2018}, - keywords = {Algorithms, Brain, Humans, Magnetic Resonance Imaging, Software, MRI, Image Processing, Computer-Assisted, Adult, Middle Aged, Databases, Factual, Aged, Aged, 80 and over, Atlases as Topic, Cytoarchitecture, Diffeomorphism, Folding pattern, HBP, Infant, Newborn, Infant, Premature, Spatial normalization}, - pages = {4153--4168}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UTZ99AGC/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8F53LJM9/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QM4UDBZI/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf}, -} - -@article{lebenberg_mapping_2019, - title = {Mapping the asynchrony of cortical maturation in the infant brain: {A} {MRI} multi-parametric clustering approach}, - volume = {185}, - issn = {1053-8119}, - shorttitle = {Mapping the asynchrony of cortical maturation in the infant brain}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918306372}, - doi = {10.1016/j.neuroimage.2018.07.022}, - abstract = {While the main neural networks are in place at term birth, intense changes in cortical microstructure occur during early infancy with the development of dendritic arborization, synaptogenesis and fiber myelination. These maturational processes are thought to relate to behavioral acquisitions and the development of cognitive abilities. Nevertheless, in vivo investigations of such relationships are still lacking in healthy infants. To bridge this gap, we aimed to study the cortical maturation using non-invasive Magnetic Resonance Imaging, over a largely unexplored period (1–5 post-natal months). In a first univariate step, we focused on different quantitative parameters: longitudinal relaxation time (T1), transverse relaxation time (T2), and axial diffusivity from diffusion tensor imaging (λ//) These individual maps, acquired with echo-planar imaging to limit the acquisition time, showed spatial distortions that were first corrected to reliably match the thin cortical ribbon identified on high-resolution T2-weighted images. Averaged maps were also computed over the infants group to summarize the parameter characteristics during early infancy. In a second step, we considered a multi-parametric approach that leverages parameters complementarity, avoids reliance on pre-defined regions of interest, and does not require spatial constraints. Our clustering strategy allowed us to group cortical voxels over all infants in 5 clusters with distinct microstructural T1 and λ// properties The cluster maps over individual cortical surfaces and over the group were in sound agreement with benchmark post mortem studies of sub-cortical white matter myelination, showing a progressive maturation of 1) primary sensori-motor areas, 2) adjacent unimodal associative cortices, and 3) higher-order associative regions. This study thus opens a consistent approach to study cortical maturation in vivo.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Lebenberg, J. and Mangin, J. -F. and Thirion, B. and Poupon, C. and Hertz-Pannier, L. and Leroy, F. and Adibpour, P. and Dehaene-Lambertz, G. and Dubois, J.}, - month = jan, - year = {2019}, - keywords = {Clustering, Cortical maturation, Diffusion tensor imaging DTI, Human brain project (HBP), Infancy, Magnetic resonance imaging MRI, Quantitative T1 and T2 mapping}, - pages = {641--653}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8N52EF8U/Lebenberg et al. - 2019 - Mapping the asynchrony of cortical maturation in t.pdf:application/pdf}, -} - -@inproceedings{avila_inference_2019, - address = {Cham}, - series = {Mathematics and {Visualization}}, - title = {Inference of an {Extended} {Short} {Fiber} {Bundle} {Atlas} {Using} {Sulcus}-{Based} {Constraints} for a {Diffeomorphic} {Inter}-subject {Alignment}}, - isbn = {978-3-030-05831-9}, - doi = {10.1007/978-3-030-05831-9_25}, - abstract = {We present a new framework for the creation of an extended atlas of short fiber bundlesShort fiber bundles between 20 and 80 mm length. This method uses a Diffeomorphic inter-subject alignmentDiffeomorphic inter-subject alignment procedure including information of cortical foldings and forces the accurate match of the sulci that have to be circumvented by the U-bundlesU-bundle. Then, a clustering is performed to extract the most reproducible bundles across subjects. First results show an increased number of U-bundlesU-bundle consistently mapped in the general population compared with previous atlases created from the same database. Future analysis over this new extended Brain atlasBrain atlas may improve our understanding of the relationship between the folding pattern and the U-bundleU-bundle variability. The ultimate aim will be the possibility to detect abnormal configurations induced by developmental issues.}, - language = {en}, - booktitle = {Computational {Diffusion} {MRI}}, - publisher = {Springer International Publishing}, - author = {Avila, Nicole Labra and Lebenberg, Jessica and Rivière, Denis and Auzias, Guillaume and Fischer, Clara and Poupon, Fabrice and Guevara, Pamela and Poupon, Cyril and Mangin, Jean-François}, - editor = {Bonet-Carne, Elisenda and Grussu, Francesco and Ning, Lipeng and Sepehrband, Farshid and Tax, Chantal M. W.}, - year = {2019}, - keywords = {Sulci, Cortical folding pattern, Bundle atlas, dMRI, Diffusion MRI, White matter, Brain atlas, Diffeomorphic alignment, Short fiber bundles, Sulcus base alignment, U-bundles, U-fiber}, - pages = {323--333}, -} - -@article{ginsburger_medusa_2019, - title = {{MEDUSA}: {A} {GPU}-based tool to create realistic phantoms of the brain microstructure using tiny spheres}, - volume = {193}, - issn = {1053-8119}, - shorttitle = {{MEDUSA}}, - url = {https://www.sciencedirect.com/science/article/pii/S105381191930151X}, - doi = {10.1016/j.neuroimage.2019.02.055}, - abstract = {A GPU-based tool to generate realistic phantoms of the brain microstructure is presented. Using a spherical meshing technique which decomposes each microstructural item into a set of overlapping spheres, the phantom construction is made very fast while reliably avoiding the collisions between items in the scene. This novel method is applied to the construction of human brain white matter microstructural components, namely axonal fibers, oligodendrocytes and astrocytes. The algorithm reaches high values of packing density and angular dispersion for the axonal fibers, even in the case of multiple white matter fiber populations and enables the construction of complex biomimicking geometries including myelinated axons, beaded axons, and glial cells. The method can be readily adapted to model gray matter microstructure.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Ginsburger, Kévin and Matuschke, Felix and Poupon, Fabrice and Mangin, Jean-François and Axer, Markus and Poupon, Cyril}, - month = jun, - year = {2019}, - keywords = {Diffusion MRI, White matter, GPU, Phantom generation}, - pages = {10--24}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FLUUQRUL/Ginsburger et al. - 2019 - MEDUSA A GPU-based tool to create realistic phant.pdf:application/pdf}, -} - -@article{ji_increased_2019, - title = {Increased and {Decreased} {Superficial} {White} {Matter} {Structural} {Connectivity} in {Schizophrenia} and {Bipolar} {Disorder}}, - volume = {45}, - issn = {0586-7614}, - url = {https://doi.org/10.1093/schbul/sbz015}, - doi = {10.1093/schbul/sbz015}, - abstract = {Schizophrenia (SZ) and bipolar disorder (BD) are often conceptualized as “disconnection syndromes,” with substantial evidence of abnormalities in deep white matter tracts, forming the substrates of long-range connectivity, seen in both disorders. However, the study of superficial white matter (SWM) U-shaped short-range tracts remained challenging until recently, although findings from postmortem studies suggest they are likely integral components of SZ and BD neuropathology. This diffusion weighted imaging (DWI) study aimed to investigate SWM microstructure in vivo in both SZ and BD for the first time. We performed whole brain tractography in 31 people with SZ, 32 people with BD and 54 controls using BrainVISA and Connectomist 2.0. Segmentation and labeling of SWM tracts were performed using a novel, comprehensive U-fiber atlas. Analysis of covariances yielded significant generalized fractional anisotropy (gFA) differences for 17 SWM bundles in frontal, parietal, and temporal cortices. Post hoc analyses showed gFA reductions in both patient groups as compared with controls in bundles connecting regions involved in language processing, mood regulation, working memory, and motor function (pars opercularis, insula, anterior cingulate, precentral gyrus). We also found increased gFA in SZ patients in areas overlapping the default mode network (inferior parietal, middle temporal, precuneus), supporting functional hyperconnectivity of this network evidenced in SZ. We thus illustrate that short U-fibers are vulnerable to the pathological processes in major psychiatric illnesses, encouraging improved understanding of their anatomy and function.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Schizophrenia Bulletin}, - author = {Ji, Ellen and Guevara, Pamela and Guevara, Miguel and Grigis, Antoine and Labra, Nicole and Sarrazin, Samuel and Hamdani, Nora and Bellivier, Frank and Delavest, Marine and Leboyer, Marion and Tamouza, Ryad and Poupon, Cyril and Mangin, Jean-François and Houenou, Josselin}, - month = oct, - year = {2019}, - pages = {1367--1378}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Y7YQ6NHY/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A6NRGXW3/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf}, -} - -@article{gilson_network_2019, - title = {Network analysis of whole-brain {fMRI} dynamics: {A} new framework based on dynamic communicability}, - volume = {201}, - issn = {1053-8119}, - shorttitle = {Network analysis of whole-brain {fMRI} dynamics}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811919305889}, - doi = {10.1016/j.neuroimage.2019.116007}, - abstract = {Neuroimaging techniques such as MRI have been widely used to explore the associations between brain areas. Structural connectivity (SC) captures the anatomical pathways across the brain and functional connectivity (FC) measures the correlation between the activity of brain regions. These connectivity measures have been much studied using network theory in order to uncover the distributed organization of brain structures, in particular FC for task-specific brain communication. However, the application of network theory to study FC matrices is often “static” despite the dynamic nature of time series obtained from fMRI. The present study aims to overcome this limitation by introducing a network-oriented analysis applied to whole-brain effective connectivity (EC) useful to interpret the brain dynamics. Technically, we tune a multivariate Ornstein-Uhlenbeck (MOU) process to reproduce the statistics of the whole-brain resting-state fMRI signals, which provides estimates for MOU-EC as well as input properties (similar to local excitabilities). The network analysis is then based on the Green function (or network impulse response) that describes the interactions between nodes across time for the estimated dynamics. This model-based approach provides time-dependent graph-like descriptor, named communicability, that characterize the roles that either nodes or connections play in the propagation of activity within the network. They can be used at both global and local levels, and also enables the comparison of estimates from real data with surrogates (e.g. random network or ring lattice). In contrast to classical graph approaches to study SC or FC, our framework stresses the importance of taking the temporal aspect of fMRI signals into account. Our results show a merging of functional communities over time, moving from segregated to global integration of the network activity. Our formalism sets a solid ground for the analysis and interpretation of fMRI data, including task-evoked activity.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Gilson, Matthieu and Kouvaris, Nikos E. and Deco, Gustavo and Mangin, Jean-François and Poupon, Cyril and Lefranc, Sandrine and Rivière, Denis and Zamora-López, Gorka}, - month = nov, - year = {2019}, - pages = {116007}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/D8EJIZX8/S1053811919305889.html:text/html;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3AR2H57H/Gilson et al. - 2019 - Network analysis of whole-brain fMRI dynamics A n.pdf:application/pdf}, -} - -@inproceedings{lopez-lopez_geosp_2020, - address = {Montreal, QC, Canada}, - title = {{GeoSP}: {A} parallel method for a cortical surface parcellation based on geodesic distance}, - isbn = {978-1-72811-990-8}, - shorttitle = {{GeoSP}}, - url = {https://ieeexplore.ieee.org/document/9175779/}, - doi = {10.1109/EMBC44109.2020.9175779}, - urldate = {2024-03-12}, - booktitle = {2020 42nd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - publisher = {IEEE}, - author = {Lopez-Lopez, Narciso and Vazquez, Andrea and Poupon, Cyril and Mangin, Jean-Francois and Ladra, Susana and Guevara, Pamela}, - month = jul, - year = {2020}, - pages = {1696--1700}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EZEUZVBT/Lopez-Lopez et al. - 2020 - GeoSP A parallel method for a cortical surface pa.pdf:application/pdf}, -} - -@inproceedings{huerta_inter-subject_2020, - title = {Inter-{Subject} {Clustering} of {Brain} {Fibers} from {Whole}-{Brain} {Tractography}}, - url = {https://ieeexplore.ieee.org/abstract/document/9175342}, - doi = {10.1109/EMBC44109.2020.9175342}, - abstract = {This work presents an effective multiple subject clustering method using whole-brain tractography datasets. The method is able to obtain fiber clusters that are representative of the population. The proposed approach first applies a fast intra-subject clustering algorithm on each subject obtaining the cluster centroids for all subjects. Second, it compresses the collection of centroids to a latent space through the encoder of a trained autoencoder. Finally, it uses a modified HDBSCAN with adjusted parameters on the encoded centroids of all subjects to obtain the final inter-subject clusters. The results shows that the proposed method outperforms other clustering strategies, and it is able to retrieve known fascicles in a reasonable execution time, achieving a precision over 87\% and F1 score above 86\% on a collection of 20 simulated subjects.}, - urldate = {2024-03-12}, - booktitle = {2020 42nd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Huerta, Isaías and Vázquez, Andrea and López-López, Narciso and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela and Hernández, Cecilia}, - month = jul, - year = {2020}, - note = {ISSN: 2694-0604}, - keywords = {Sociology, Statistics, Clustering algorithms, Measurement, Image reconstruction, White matter, Optical fiber networks}, - pages = {1687--1691}, -} - -@article{lopez-lopez_coarse_2020, - title = {From {Coarse} to {Fine}-{Grained} {Parcellation} of the {Cortical} {Surface} {Using} a {Fiber}-{Bundle} {Atlas}}, - volume = {14}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2020.00032}, - doi = {10.3389/fninf.2020.00032}, - abstract = {We present a hybrid method to create fine-grained parcellations of the cortical surface, from a coarse-grained parcellation according to an anatomical atlas, based on cortico-cortical connectivity. The connectivity information is obtained from segmented superficial and deep white matter bundles, according to bundle atlases, instead of the whole tractography. Thus, a direct matching between the fiber bundles and the cortical regions is obtained, avoiding the problem of finding the correspondence of the cortical parcels among subjects. Generating parcels from segmented fiber bundles can give a good representation of the human brain connectome since they are based on bundle atlases that contain the most reproducible short and long connections found on a population of subjects. The method first processes the tractography of each subject and extracts the bundles of the atlas, based on a segmentation algorithm. Next, the intersection between the fiber bundles and the cortical mesh is calculated, to define the initial and final intersection points of each fiber. A fiber filtering is then applied to eliminate misclassified fibers, based on the anatomical definition of each bundle and the labels of Desikan-Killiany anatomical parcellation. Then, a parcellation algorithm is performed to create a subdivision of the anatomical regions of the cortex, reproducible across subjects. This step resolves the overlapping of the fiber bundle extremities over the cortical mesh within each anatomical region. For the analysis, it considers the density of the connections and the degree of overlapping, represented with a graph. One of our parcellations, an atlas composed of 160 parcels, achieves a reproducibility across subjects of ≈ 0.74, based on the average Dice's coefficient between subject's connectivity matrices, rather than ≈ 0.73 obtained for a macro anatomical parcellation of 150 parcels. Moreover, we compared two of our parcellations with state-of-the-art atlases, finding a degree of similarity with dMRI, functional, anatomical, and multi-modal atlases. The higher similarity was found for our parcellation composed of 185 sub-parcels with another parcellation based on dMRI data from the same database, but created with a different approach, leading to 130 parcels in common based on a Dice's coefficient ≥ 0.5.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {López-López, Narciso and Vázquez, Andrea and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Ladra, Susana and Guevara, Pamela}, - month = sep, - year = {2020}, - note = {Publisher: Frontiers}, - keywords = {tractography, parcellation, connectivity, Cortex, white matter, fiber bundle}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7YR7NN5G/López-López et al. - 2020 - From Coarse to Fine-Grained Parcellation of the Co.pdf:application/pdf}, -} - -@article{vazquez_ffclust_2020, - title = {{FFClust}: {Fast} fiber clustering for large tractography datasets for a detailed study of brain connectivity}, - volume = {220}, - issn = {1053-8119}, - shorttitle = {{FFClust}}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811920305565}, - doi = {10.1016/j.neuroimage.2020.117070}, - abstract = {Automated methods that can identify white matter bundles from large tractography datasets have several applications in neuroscience research. In these applications, clustering algorithms have shown to play an important role in the analysis and visualization of white matter structure, generating useful data which can be the basis for further studies. This work proposes FFClust, an efficient fiber clustering method for large tractography datasets containing millions of fibers. Resulting clusters describe the whole set of main white matter fascicles present on an individual brain. The method aims to identify compact and homogeneous clusters, which enables several applications. In individuals, the clusters can be used to study the local connectivity in pathological brains, while at population level, the processing and analysis of reproducible bundles, and other post-processing algorithms can be carried out to study the brain connectivity and create new white matter bundle atlases. The proposed method was evaluated in terms of quality and execution time performance versus the state-of-the-art clustering techniques used in the area. Results show that FFClust is effective in the creation of compact clusters, with a low intra-cluster distance, while keeping a good quality Davies–Bouldin index, which is a metric that quantifies the quality of clustering approaches. Furthermore, it is about 8.6 times faster than the most efficient state-of-the-art method for one million fibers dataset. In addition, we show that FFClust is able to correctly identify atlas bundles connecting different brain regions, as an example of application and the utility of compact clusters.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Vázquez, Andrea and López-López, Narciso and Sánchez, Alexis and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = oct, - year = {2020}, - keywords = {Tractography, Fiber clustering, White matter bundle}, - pages = {117070}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BQ4YZUH6/Vázquez et al. - 2020 - FFClust Fast fiber clustering for large tractogra.pdf:application/pdf}, -} - -@article{sarrazin_neuroimaging_2020, - title = {Neuroimaging {Evidence} for {Increased} {Neurite} {Density} in {Patients} {Taking} {Lithium}: {A} {Replication} {Study}}, - volume = {90}, - issn = {0033-3190}, - shorttitle = {Neuroimaging {Evidence} for {Increased} {Neurite} {Density} in {Patients} {Taking} {Lithium}}, - url = {https://doi.org/10.1159/000507556}, - doi = {10.1159/000507556}, - abstract = {Dear Editor,The biological mechanisms underlying the efficacy of lithium therapy remain largely unknown. In Psychotherapy and Psychosomatics [1], we have recently published the first study showing increased neurite density in patients taking lithium with Neurite Orientation Dispersion and Density Imaging (NODDI), an advanced model of MRI diffusion [2]. Albeit confirming previous results associating lithium with changes of grey matter volume [3], replication remains a priority in the field of neuroscience [4].Here, we report a replication of our previous results – higher neurite density within the left frontal cortex – in patients under lithium therapy compared with patients without lithium therapy, in a completely independent sample. Data were collected in Calgary (AB, Canada) from 23 controls and 26 patients with bipolar disorder upon which only 7 (26.9\%) were prescribed with lithium at the time of scan. MRI data were acquired with a General Electric MR750 3T device and included T1 structural MRI (MPRAGE, voxel size: 1 × 1 × 1 mm), and multi-shell, high angular resolution diffusion MRI (EPI, 96 × 96 × 60, voxel size: 2.5 × 2.5 × 2.5 mm), 98 gradient directions, 3 b-shells: b = 300, 700, and 2,000 mm2/s (8, 30, and 60 directions, respectively) and 10 b = 0 mm2/s images (1, 3, and 6 per shell, respectively). Both the MRI manufacturer and the diffusion weighted acquisition (number of directions, b values) were different from the original publication [1]. The sole measure of interest was the mean intracellular fraction within the left frontal cortex as defined by the Desikan-Killiany atlas [1].}, - number = {1}, - urldate = {2024-03-12}, - journal = {Psychotherapy and Psychosomatics}, - author = {Sarrazin, Samuel and Poupon, Cyril and Uszynski, Ivy and Teillac, Achille and Mangin, Jean-François and Polosan, Mircea and Favre, Pauline and Laidi, Charles and D'Albis, Marc-Antoine and Leboyer, Marion and Lledo, Pierre-Marie and Henry, Chantal and Emsell, Louise and Shakeel, Mohammed K. and Goghari, Vina M. and Houenou, Josselin}, - month = may, - year = {2020}, - pages = {71--72}, -} - -@inproceedings{roman_study_2021, - title = {Study {Of} {Precentral}-{Postcentral} {Connections} {On} {Hcp} {Data} {Using} {Probabilistic} {Tractography} {And} {Fiber} {Clustering}}, - url = {https://ieeexplore.ieee.org/abstract/document/9434093}, - doi = {10.1109/ISBI48211.2021.9434093}, - abstract = {The study of the superficial white matter and its description is essential for the understanding of human brain function and the study of pathogenesis. However, the study of these fibers is still an incomplete task due to the high inter-subject variability and the size of this kind of fibers. In this work, a superficial white matter bundle identification based on fiber clustering was performed using probabilistic tractography on 100 subjects from the The Human Connectome Project (HCP) data, aligned with a non-linear registration. The method starts with an intra-subject clustering, followed by a segmentation of fibers connecting the precentral (PrC) and postcentral (PoC) regions, based on a ROI atlas. Due to the high amount of fibers, they were randomly separated into groups. An inter-subject clustering was applied on the fibers of each group, and then two clustering levels were applied to select the most reproducible bundles. Seven bundles per hemisphere were obtained, connecting the PrC and PoC regions. These were compared with bundles from previous atlases, showing in general more coverage and some bundles not found in previous atlases.}, - urldate = {2024-03-12}, - booktitle = {2021 {IEEE} 18th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Román, C. and López-López, N. and Houenou, J. and Poupon, C. and Mangin, J.-F. and Hernández, C. and Guevara, P.}, - month = apr, - year = {2021}, - note = {ISSN: 1945-8452}, - keywords = {Probabilistic logic, Tractography, Short association fibers, Diffusion-weighted imaging, Task analysis, Biomedical imaging, White matter, Superficial white matter, White matter bundle}, - pages = {55--59}, -} - -@article{goicovich_fiber_2021, - title = {Fiber {Clustering} {Acceleration} {With} a {Modified} {Kmeans}++ {Algorithm} {Using} {Data} {Parallelism}}, - volume = {15}, - issn = {1662-5196}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2021.727859}, - doi = {10.3389/fninf.2021.727859}, - abstract = {Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets. These methods enable exploratory bundle inspection using visualization and other methods that require identifying brain white matter structures in individuals or a population. Some applications, such as real-time visualization and inter-subject clustering, need fast and high-quality intra-subject clustering algorithms. This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm. The proposed GPGPU implementation exploits data parallelism using both multicore and GPU fine-grained parallelism present in commodity architectures, including current laptops and desktop computers. Our approach implements all FFClust steps in parallel, improving execution times in all of them. In addition, our parallel approach includes a parallel Kmeans++ algorithm implementation and defines a new variant of Kmeans++ to reduce the impact of choosing outliers as initial centroids. The results show that our approach provides clustering quality results very similar to FFClust, and it requires an execution time of 3.5 seconds for processing about a million fibers, achieving a speedup of 11.5 times compared to FFClust.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Neuroinformatics}, - author = {Goicovich, Isaac and Olivares, Paulo and Román, Claudio and Vázquez, Andrea and Poupon, Cyril and Mangin, Jean-François and Guevara, Pamela and Hernández, Cecilia}, - month = sep, - year = {2021}, - note = {Publisher: Frontiers}, - keywords = {Fiber clustering, White matter bundle, Data parallelism, GPGPU - CUDA, Parallel Computing}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5NEWXUYM/Goicovich et al. - 2021 - Fiber Clustering Acceleration With a Modified Kmea.pdf:application/pdf}, -} - -@article{schilling_tractography_2021, - title = {Tractography dissection variability: {What} happens when 42 groups dissect 14 white matter bundles on the same dataset?}, - volume = {243}, - issn = {1053-8119}, - shorttitle = {Tractography dissection variability}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921007758}, - doi = {10.1016/j.neuroimage.2021.118502}, - abstract = {White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same intended white matter pathways, which directly affects tractography results, quantification, and interpretation. In this study, we aim to evaluate and quantify the variability that arises from different protocols for bundle segmentation. Through an open call to users of fiber tractography, including anatomists, clinicians, and algorithm developers, 42 independent teams were given processed sets of human whole-brain streamlines and asked to segment 14 white matter fascicles on six subjects. In total, we received 57 different bundle segmentation protocols, which enabled detailed volume-based and streamline-based analyses of agreement and disagreement among protocols for each fiber pathway. Results show that even when given the exact same sets of underlying streamlines, the variability across protocols for bundle segmentation is greater than all other sources of variability in the virtual dissection process, including variability within protocols and variability across subjects. In order to foster the use of tractography bundle dissection in routine clinical settings, and as a fundamental analytical tool, future endeavors must aim to resolve and reduce this heterogeneity. Although external validation is needed to verify the anatomical accuracy of bundle dissections, reducing heterogeneity is a step towards reproducible research and may be achieved through the use of standard nomenclature and definitions of white matter bundles and well-chosen constraints and decisions in the dissection process.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Schilling, Kurt G. and Rheault, François and Petit, Laurent and Hansen, Colin B. and Nath, Vishwesh and Yeh, Fang-Cheng and Girard, Gabriel and Barakovic, Muhamed and Rafael-Patino, Jonathan and Yu, Thomas and Fischi-Gomez, Elda and Pizzolato, Marco and Ocampo-Pineda, Mario and Schiavi, Simona and Canales-Rodríguez, Erick J. and Daducci, Alessandro and Granziera, Cristina and Innocenti, Giorgio and Thiran, Jean-Philippe and Mancini, Laura and Wastling, Stephen and Cocozza, Sirio and Petracca, Maria and Pontillo, Giuseppe and Mancini, Matteo and Vos, Sjoerd B. and Vakharia, Vejay N. and Duncan, John S. and Melero, Helena and Manzanedo, Lidia and Sanz-Morales, Emilio and Peña-Melián, Ángel and Calamante, Fernando and Attyé, Arnaud and Cabeen, Ryan P. and Korobova, Laura and Toga, Arthur W. and Vijayakumari, Anupa Ambili and Parker, Drew and Verma, Ragini and Radwan, Ahmed and Sunaert, Stefan and Emsell, Louise and De Luca, Alberto and Leemans, Alexander and Bajada, Claude J. and Haroon, Hamied and Azadbakht, Hojjatollah and Chamberland, Maxime and Genc, Sila and Tax, Chantal M. W. and Yeh, Ping-Hong and Srikanchana, Rujirutana and Mcknight, Colin D. and Yang, Joseph Yuan-Mou and Chen, Jian and Kelly, Claire E. and Yeh, Chun-Hung and Cochereau, Jerome and Maller, Jerome J. and Welton, Thomas and Almairac, Fabien and Seunarine, Kiran K and Clark, Chris A. and Zhang, Fan and Makris, Nikos and Golby, Alexandra and Rathi, Yogesh and O'Donnell, Lauren J. and Xia, Yihao and Aydogan, Dogu Baran and Shi, Yonggang and Fernandes, Francisco Guerreiro and Raemaekers, Mathijs and Warrington, Shaun and Michielse, Stijn and Ramírez-Manzanares, Alonso and Concha, Luis and Aranda, Ramón and Meraz, Mariano Rivera and Lerma-Usabiaga, Garikoitz and Roitman, Lucas and Fekonja, Lucius S. and Calarco, Navona and Joseph, Michael and Nakua, Hajer and Voineskos, Aristotle N. and Karan, Philippe and Grenier, Gabrielle and Legarreta, Jon Haitz and Adluru, Nagesh and Nair, Veena A. and Prabhakaran, Vivek and Alexander, Andrew L. and Kamagata, Koji and Saito, Yuya and Uchida, Wataru and Andica, Christina and Abe, Masahiro and Bayrak, Roza G. and Wheeler-Kingshott, Claudia A. M. Gandini and D'Angelo, Egidio and Palesi, Fulvia and Savini, Giovanni and Rolandi, Nicolò and Guevara, Pamela and Houenou, Josselin and López-López, Narciso and Mangin, Jean-François and Poupon, Cyril and Román, Claudio and Vázquez, Andrea and Maffei, Chiara and Arantes, Mavilde and Andrade, José Paulo and Silva, Susana Maria and Calhoun, Vince D. and Caverzasi, Eduardo and Sacco, Simone and Lauricella, Michael and Pestilli, Franco and Bullock, Daniel and Zhan, Yang and Brignoni-Perez, Edith and Lebel, Catherine and Reynolds, Jess E and Nestrasil, Igor and Labounek, René and Lenglet, Christophe and Paulson, Amy and Aulicka, Stefania and Heilbronner, Sarah R. and Heuer, Katja and Chandio, Bramsh Qamar and Guaje, Javier and Tang, Wei and Garyfallidis, Eleftherios and Raja, Rajikha and Anderson, Adam W. and Landman, Bennett A. and Descoteaux, Maxime}, - month = nov, - year = {2021}, - keywords = {Tractography, White matter, Bundle segmentation, Dissection, Fiber pathways}, - pages = {118502}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BW5AD93V/Schilling et al. - 2021 - Tractography dissection variability What happens .pdf:application/pdf}, -} - -@inproceedings{vergara_group-wise_2021, - title = {Group-{Wise} {Cortical} {Surface} {Parcellation} {Based} on {Inter}-{Subject} {Fiber} {Clustering}}, - url = {https://ieeexplore.ieee.org/abstract/document/9631099}, - doi = {10.1109/EMBC46164.2021.9631099}, - abstract = {We present an automatic algorithm for the group-wise parcellation of the cortical surface. The method is based on the structural connectivity obtained from representative brain fiber clusters, calculated via an inter-subject clustering scheme. Preliminary regions were defined from cluster-cortical mesh intersection points. The final parcellation was obtained using parcel probability maps to model and integrate the connectivity information of all subjects, and graphs to represent the overlap between parcels. Two inter-subject clustering schemes were tested, generating a total of 171 and 109 parcels, respectively. The resulting parcels were quantitatively compared with three state-of-the-art atlases. The best parcellation returned 69 parcels with a Dice similarity coefficient greater than 0.5. To the best of our knowledge, this is the first diffusion-based cortex parcellation method based on whole-brain inter-subject fiber clustering.}, - urldate = {2024-03-12}, - booktitle = {2021 43rd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Vergara, Christopher and Silva, Felipe and Huerta, Isaías and López-López, Narciso and Vázquez, Andrea and Houenou, Josselin and Poupon, Cyril and Mangin, Jean-François and Hernández, Cecilia and Guevara, Pamela}, - month = nov, - year = {2021}, - note = {ISSN: 2694-0604}, - keywords = {Brain modeling, Clustering algorithms, Biology, Optical fiber testing}, - pages = {2655--2659}, -} - -@inproceedings{mendoza_enhanced_2021, - title = {Enhanced {Automatic} {Segmentation} for {Superficial} {White} {Matter} {Fiber} {Bundles} for {Probabilistic} {Tractography} {Datasets}}, - url = {https://ieeexplore.ieee.org/abstract/document/9630529}, - doi = {10.1109/EMBC46164.2021.9630529}, - abstract = {This paper presents an enhanced algorithm for automatic segmentation of superficial white matter (SWM) bundles from probabilistic dMRI tractography datasets, based on a multi-subject bundle atlas. Previous segmentation methods use the maximum Euclidean distance between corresponding points of the subject fibers and the atlas centroids. However, this scheme might include noisy fibers. Here, we propose a three step approach to discard noisy fibers improving the identification of fibers. The first step applies a fiber clustering and the segmentation is performed between the centroids of the clusters and the atlas centroids. This step removes outliers and enables a better identification of fibers with similar shapes. The second step applies a fiber filter based on two different fiber similarities. One is the Symmetrized Segment-Path Distance (SSPD) over 2D ISOMAP and the other is an adapted version of SSPD for 3D space. The last step eliminates noisy fibers by removing those that connect regions that are far from the main atlas bundle connections. We perform an experimental evaluation using ten subjects of the Human Connectome (HCP) database. The evaluation only considers the bundles connecting precentral and postcentral gyri, with a total of seven bundles per hemisphere. For comparison, the bundles of the ten subjects were manually segmented. Bundles segmented with our method were evaluated in terms of similarity to manually segmented bundles and the final number of fibers. The results show that our approach obtains bundles with a higher similarity score than the state-of-the-art method and maintains a similar number of fibers.Clinical relevance—Many brain pathologies or disorders can occur in specific regions of the SWM automatic segmentation of reliable SWM bundles would help applications to clinical research.}, - urldate = {2024-03-12}, - booktitle = {2021 43rd {Annual} {International} {Conference} of the {IEEE} {Engineering} in {Medicine} \& {Biology} {Society} ({EMBC})}, - author = {Mendoza, C. and Román, C. and Vázquez, A. and Poupon, C. and Mangin, J.-F. and Hernández, C. and Guevara, P.}, - month = nov, - year = {2021}, - note = {ISSN: 2694-0604}, - keywords = {Sociology, Probabilistic logic, Reliability, Shape, Three-dimensional displays, Trajectory, Noise measurement}, - pages = {3654--3658}, -} - -@article{sarrazin_higher_2019, - title = {Higher in vivo {Cortical} {Intracellular} {Volume} {Fraction} {Associated} with {Lithium} {Therapy} in {Bipolar} {Disorder}: {A} {Multicenter} {NODDI} {Study}}, - volume = {88}, - issn = {0033-3190}, - shorttitle = {Higher in vivo {Cortical} {Intracellular} {Volume} {Fraction} {Associated} with {Lithium} {Therapy} in {Bipolar} {Disorder}}, - url = {https://doi.org/10.1159/000498854}, - doi = {10.1159/000498854}, - abstract = {Background: MRI studies in patients with bipolar disorder have suggested that lithium is associated with grey matter increases that may underlie its therapeutic effects. However, the relationship between grey matter volume and cellular microstructural changes is not straightforward, as modifications of different cellular compartments of grey matter may be involved. Objectives: Our aim was to test the hypothesis that dendritic density is higher in patients undergoing lithium therapy than in patients without lithium, using advanced modelling of water diffusion investigated with MRI. Method: We included 41 patients and 40 controls matched for age and gender from two sites. All subjects underwent 3T MRI with 3 shells of diffusion. We used neurite orientation dispersion and density imaging to compare the grey matter neurite density between patients undergoing lithium therapy or not and control subjects. Results: We found a significant group effect in the left prefrontal region (p = 0.001, Bonferroni corrected): patients without lithium had a lower frontal neurite density than controls (p = 0.009), while those on lithium had a higher mean neurite density than those without (p \< 0.001). Patients on lithium were not different from controls (p = 0.08). Conclusions: This is the first study to report in vivo evidence of preserved neurite density of the prefrontal cortex in humans associated with lithium intake. Changes of intracellular volume fraction are thought to reflect changes of grey matter microstructural organization. This reinforces the hypothesis of lithium having a positive effect on the neuronal compartment in humans.}, - number = {3}, - urldate = {2024-03-12}, - journal = {Psychotherapy and Psychosomatics}, - author = {Sarrazin, Samuel and Poupon, Cyril and Teillac, Achille and Mangin, Jean-François and Polosan, Mircea and Favre, Pauline and Laidi, Charles and D'Albis, Marc-Antoine and Leboyer, Marion and Lledo, Pierre-Marie and Henry, Chantal and Houenou, Josselin}, - month = apr, - year = {2019}, - pages = {171--176}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5BWMSZNZ/Higher-in-vivo-Cortical-Intracellular-Volume.html:text/html}, -} - -@article{chauvel_vivo_2023, - title = {In vivo mapping of the deep and superficial white matter connectivity in the chimpanzee brain}, - volume = {282}, - issn = {10538119}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S105381192300513X}, - doi = {10.1016/j.neuroimage.2023.120362}, - language = {en}, - urldate = {2024-03-18}, - journal = {NeuroImage}, - author = {Chauvel, Maëlig and Uszynski, Ivy and Herlin, Bastien and Popov, Alexandros and Leprince, Yann and Mangin, Jean-François and Hopkins, William D. and Poupon, Cyril}, - month = nov, - year = {2023}, - keywords = {Diffusion MRI, Chimpanzee brain connectivity, Deep white matter atlas, Superficial white matter atlas}, - pages = {120362}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HW259AB3/Chauvel et al. - 2023 - In vivo mapping of the deep and superficial white .pdf:application/pdf;Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RJ7ZUGRJ/Chauvel et al. - 2023 - In vivo mapping of the deep and superficial.pdf:application/pdf}, -} diff --git a/bibutils/data/platform_v-20240621.bib b/bibutils/data/platform_v-20240621.bib deleted file mode 100644 index 58cd9c2..0000000 --- a/bibutils/data/platform_v-20240621.bib +++ /dev/null @@ -1,2474 +0,0 @@ - -@article{spechler_cannabis_2015, - title = {Cannabis use in early adolescence: {Evidence} of amygdala hypersensitivity to signals of threat}, - volume = {16}, - copyright = {All rights reserved}, - issn = {1878-9293}, - doi = {10.1016/j.dcn.2015.08.007}, - abstract = {Cannabis use in adolescence may be characterized by differences in the neural basis of affective processing. In this study, we used an fMRI affective face processing task to compare a large group (n = 70) of 14-year olds with a history of cannabis use to a group (n = 70) of never-using controls matched on numerous characteristics including IQ, SES, alcohol and cigarette use. The task contained short movies displaying angry and neutral faces. Results indicated that cannabis users had greater reactivity in the bilateral amygdalae to angry faces than neutral faces, an effect that was not observed in their abstinent peers. In contrast, activity levels in the cannabis users in cortical areas including the right temporal-parietal junction and bilateral dorsolateral prefrontal cortex did not discriminate between the two face conditions, but did differ in controls. Results did not change after excluding subjects with any psychiatric symptomology. Given the high density of cannabinoid receptors in the amygdala, our findings suggest cannabis use in early adolescence is associated with hypersensitivity to signals of threat. Hypersensitivity to negative affect in adolescence may place the subject at-risk for mood disorders in adulthood. (C) 2015 Published by Elsevier Ltd.}, - journal = {DEVELOPMENTAL COGNITIVE NEUROSCIENCE}, - author = {Spechler, Philip A. and Orr, Catherine A. and Chaarani, Bader and Kan, Kees-Jan and Mackey, Scott and Morton, Aaron and Snowe, Mitchell P. and Hudson, Kelsey E. and Althoff, Robert R. and Higgins, Stephen T. and Cattrell, Anna and Flor, Herta and Nees, Frauke and Banaschewski, Tobias and Bokde, Arun L. W. and Whelan, Robert and Buechel, Christian and Bromberg, Uli and Conrod, Patricia and Frouin, Vincent and Papadopoulos, Dimitri and Gallinat, Jurgen and Heinz, Andreas and Walter, Henrik and Ittermann, Bernd and Gowland, Penny and Paus, Tomas and Poustka, Luise and Martinot, Jean-Luc and Artiges, Eric and Smolka, Michael N. and Schumann, Gunter and Garavan, Hugh}, - month = dec, - year = {2015}, - keywords = {fMRI, Amygdala, Adolescence, Cannabis, Face processing, Faces}, - pages = {63--70}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {UnatiPMID: 26347227}, -} - -@inproceedings{laroche_drum_2017, - title = {Drum extraction in single channel audio signals using multi-layer non negative matrix factor deconvolution}, - copyright = {All rights reserved}, - abstract = {In this paper, we propose a supervised multilayer factorization method designed for harmonic/percussive source separation and drum extraction. Our method decomposes the audio signals in sparse orthogonal components which capture the harmonic content, while the drum is represented by an extension of non negative matrix factorization which is able to exploit time-frequency dictionaries to take into account non stationary drum sounds. The drum dictionaries represent various real drum hits and the decomposition has more physical sense and allows for a better interpretation of the results. Experiments on real music data for a harmonic/percussive source separation task show that our method outperforms other state of the art algorithms. Finally, our method is very robust to non stationary harmonic sources that are usually poorly decomposed by existing methods.}, - author = {Laroche, C. and Papadopoulos, H. and Kowalski, M. and Richard, G.}, - month = mar, - year = {2017}, - keywords = {Index Terms - Drum extraction, Source separation, Non-negative matrix factorization}, - annote = {The following values have no corresponding Zotero field:pub-location: Nouvelle Orleans, United Stateslabel: ACTI}, - annote = {Unati - Parietal}, -} - -@inproceedings{laroche_methode_2015, - title = {Méthode {Structurée} de décomposition en matrices non- négatives appliquéè a la séparation de sources audio}, - copyright = {All rights reserved}, - abstract = {Dans cet article, nous proposons une méthode structurée de décomposition en matrices non-négatives visant a utiliser la structure multi-couche des signaux audio. Les signaux audio peuvent etre vus comme une superposition de deux couches : la couche tonale (modélisée par des sommes de sinuso¨des evoluant lentement en fréquence et en temps) et la couche transitoire (les sons percussifs, ´ ev enements de courtes durées etalés en fréquence). Notre méthode décompose une partie du signal en composantes orthogonales parcimonieuses, bien adaptées pour l'extraction tonale tandis que la partie transitoire est représentée par des bases de décomposition classiques. Les résultats de séparation de sources obtenus sur des signaux réels de musique ont montré que notre approche obtient des résultats similaires a ceux de l'´ etat de l'art. Abstract – In this paper, we propose a new unconstrained nonnegative matrix factorization method designed to utilize the multilayer structure of audio signals to improve the quality of the source separation. The tonal layer is sparse in frequency and temporally stable, while the transient layer is composed of short term broadband sounds. Our method has a part well suited for tonal extraction which decomposes the signals in sparse orthogonal components, while the transient part is represented by a regular nonnegative matrix factorization decomposition. Experiments on real music data in a source separation context show that such decomposition is suitable for audio signal. Compared with three state-of-the-art harmonic/percussive decomposition algorithms, the proposed method shows competitive performances.}, - author = {Laroche, C. and Kowalski, M. and Papadopoulos, H. and Richard, G.}, - month = sep, - year = {2015}, - annote = {The following values have no corresponding Zotero field:pub-location: Lyon, Francelabel: ACTI}, - annote = {Unati - Parietal}, -} - -@inproceedings{laroche_structured_2015, - title = {A structured nonnegative matrix factorization for source separation}, - copyright = {All rights reserved}, - abstract = {In this paper, we propose a new unconstrained nonnegative matrix factorization method designed to utilize the multilayer structure of audio signals to improve the quality of the source separation. The tonal layer is sparse in frequency and temporally stable, while the transient layer is composed of short term broadband sounds. Our method has a part well suited for tonal extraction which decomposes the signals in sparse orthogonal components, while the transient part is represented by a regular nonnegative matrix factorization decomposition. Experiments on synthetic and real music data in a source separation context show that such decomposition is suitable for audio signal. Compared with three state-of-the-art har-monic/percussive decomposition algorithms, the proposed method shows competitive performances. Index Terms— nonnegative matrix factorization, projec-tive nonnegative matrix factorization, audio source separation , harmonic/percussive decomposition.}, - author = {Laroche, C. and Kowalski, M. and Papadopoulos, H. and Richard, G.}, - month = aug, - year = {2015}, - annote = {The following values have no corresponding Zotero field:pub-location: Nice, Francelabel: ACTI}, - annote = {Unati - Parietal}, -} - -@article{ortuno-sierra_new_2015, - title = {New evidence of factor structure and measurement invariance of the {SDQ} across five {European} nations}, - volume = {24}, - copyright = {All rights reserved}, - issn = {1018-8827}, - doi = {10.1007/s00787-015-0729-x}, - abstract = {The main purpose of the present study was to analyse the internal structure and to test the measurement invariance of the Strengths and Difficulties Questionnaire (SDQ), self-reported version, in five European countries. The sample consisted of 3012 adolescents aged between 12 and 17 years (M = 14.20; SD = 0.83). The five-factor model (with correlated errors added), and the five-factor model (with correlated errors added) with the reverse-worded items allowed to cross-load on the Prosocial subscale, displayed adequate goodness of-fit indices. Multi-group confirmatory factor analysis showed that the five-factor model (with correlated errors added) had partial strong measurement invariance by countries. A total of 11 of the 25 items were non-invariant across samples. The level of internal consistency of the Total difficulties score was 0.84, ranging between 0.69 and 0.78 for the SDQ subscales. The findings indicate that the SDQ's subscales need to be modified in various ways for screening emotional and behavioural problems in the five European countries that were analysed.}, - number = {12}, - journal = {EUROPEAN CHILD \& ADOLESCENT PSYCHIATRY}, - author = {Ortuno-Sierra, Javier and Fonseca-Pedrero, Eduardo and Aritio-Solana, Rebeca and Moreno Velasco, Alvaro and Chocarro de Luis, Edurne and Schumann, Gunter and Cattrell, Anna and Flor, Herta and Nees, Frauke and Banaschewski, Tobias and Bokde, Arun and Whelan, Rob and Buechel, Christian and Bromberg, Uli and Conrod, Patricia and Frouin, Vincent and Papadopoulos, Dimitri and Gallinat, Juergen and Garavan, Hugh and Heinz, Andreas and Walter, Henrik and Struve, Maren and Gowland, Penny and Paus, Tomas and Poustka, Luise and Martinot, Jean-Luc and Paillere-Martinot, Marie-Laure and Vetter, Nora C. and Smolka, Michael N. and Lawrence, Claire}, - month = dec, - year = {2015}, - keywords = {Behavioural problems, Factorial structure, Measurement invariance, SDQ, Self-report}, - pages = {1523--1534}, - annote = {The following values have no corresponding Zotero field:number: 12label: ACL}, - annote = {UnatiPMID: 26036862}, -} - -@article{stringaris_brains_2015, - title = {The {Brain}'s {Response} to {Reward} {Anticipation} and {Depression} in {Adolescence}: {Dimensionality}, {Specificity}, and {Longitudinal} {Predictions} in a {Community}-{Based} {Sample}}, - volume = {172}, - copyright = {All rights reserved}, - issn = {0002-953X}, - doi = {10.1176/appi.ajp.2015.14101298}, - abstract = {Objective: The authors examined whether alterations in the brain's reward network operate as a mechanism across the spectrum of risk for depression. They then tested whether these alterations are specific to anhedonia as compared with low mood and whether they are predictive of depressive outcomes. Method: Functional MRI was used to collect blood-oxygen-level-dependent (BOLD) responses to anticipation of reward in the monetary incentive task in 1,576 adolescents in a community-based sample. Adolescents with current subthreshold depression and clinical depression were compared with matched healthy subjects. In addition, BOLD responses were compared across adolescents with anhedonia, low mood, or both symptoms, cross-sectionally and longitudinally. Results: Activity in the ventral striatum was reduced in participants with subthreshold and clinical depression relative to healthy comparison subjects. Low ventral striatum activation predicted transition to subthreshold or clinical depression in previously healthy adolescents at 2-year follow-up. Brain responses during reward anticipation decreased in a graded manner between healthy adolescents, adolescents with current or future subthreshold depression, and adolescents with current or future clinical depression. Low ventral striatum activity was associated with anhedonia but not low mood; however, the combined presence of both symptoms showed the strongest reductions in the ventral striatum in all analyses. Conclusions: The findings suggest that reduced striatal activation operates as a mechanism across the risk spectrum for depression. It is associated with anhedonia in healthy adolescents and is a behavioral indicator of positive valence systems, consistent with predictions based on the Research Domain Criteria.}, - number = {12}, - journal = {AMERICAN JOURNAL OF PSYCHIATRY}, - author = {Stringaris, Argyris and Belil, Pablo Vidal-Ribas and Artiges, Eric and Lemaitre, Herve and Gollier-Briant, Fanny and Wotke, Selina and Vulser, Helene and Miranda, Ruben and Penttilae, Jani and Struve, Maren and Fadai, Tahmine and Kappel, Viola and Grimmer, Yvonne and Goodman, Robert and Poustka, Luise and Conrod, Patricia and Cattrell, Anna and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Buechel, Christian and Flor, Herta and Frouin, Vincent and Gattinat, Juergen and Garavan, Hugh and Gowtand, Penny and Heinz, Andreas and Ittermann, Bernd and Nees, Frauke and Papadopoulos, Dimitri and Paus, Tomas and Smolka, Michael N. and Walter, Henrik and Whelan, Rob and Martinot, Jean-Luc and Schumann, Gunter and Paillere-Martinot, Marie-Laure}, - month = dec, - year = {2015}, - pages = {1215--1223}, - annote = {The following values have no corresponding Zotero field:number: 12label: ACL}, - annote = {UnatiPMID: 26085042}, -} - -@article{peres_longitudinal_2018, - title = {Longitudinal {Study} of {Irradiation}-{Induced} {Brain} {Microstructural} {Alterations} {With} {S}-{Index}, a {Diffusion} {MRI} {Biomarker}, and {MR} {Spectroscopy}}, - issn = {1879-355X}, - doi = {10.1016/j.ijrobp.2018.01.070}, - abstract = {PURPOSE: Radiation therapy is widely used for the treatment of brain tumors, but it may lead to severe cognitive impairments. Previous studies have shown that ionizing irradiation induces demyelination, blood-brain barrier alterations, and impaired neurogenesis in animal models. Hence, noninvasive and sensitive biomarkers of irradiation injury are needed to investigate these effects in patients and improve radiation therapy protocols. -METHODS AND MATERIALS: The heads of 3-month-old male C57BL/6RJ mice (15 control mice and 15 irradiated mice) were exposed to radiation doses of 3 fractions of 5 Gy from a 60Co source with a medical irradiator. A longitudinal study was performed to investigate cranial irradiation-induced (3 fractions of 5 Gy) microstructural tissue alterations using water diffusion magnetic resonance imaging and magnetic resonance spectroscopy in different areas of the mouse brain (cortex, thalamus, striatum, olfactory bulbs [OBs], hippocampus, and subventricular zone [SVZ]). In addition to the quantification of standard non-Gaussian diffusion parameters, apparent diffusion coefficient (ADC0) and kurtosis (K), we evaluated a new composite diffusion metric, designated the S-index (ie, "signature index"). -RESULTS: We observed a significant decrease in the S-index in the SVZ from 1 month to 8 months after brain irradiation (P {\textless} .05). An interesting finding was that, along with a decrease in taurine levels (up to -15\% at 2 months, P {\textless} .01), a delayed S-index drop was observed in the OBs from 4 months after irradiation and maintained until the end of our experiment (P {\textless} .0001). These observations suggest that S-index variations revealed the irradiation-induced decline of neurogenesis that was further confirmed by a decrease in neural stem cells in the SVZ and in newborn neurons in the OBs of irradiated animals. -CONCLUSIONS: This study demonstrates that diffusion magnetic resonance imaging, especially through the S-index approach, is a relevant imaging modality to monitor brain irradiation injury and probe microstructural changes underlying irradiation-induced cognitive deficits.}, - language = {eng}, - journal = {International Journal of Radiation Oncology, Biology, Physics}, - author = {Pérès, Elodie Anne and Etienne, Olivier and Grigis, Antoine and Boumezbeur, Fawzi and Boussin, François Dominique and Le Bihan, Denis}, - month = feb, - year = {2018}, - pmid = {29680253}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/M9UD3CRR/Pérès et al. - 2018 - Longitudinal Study of Irradiation-Induced Brain Mi.pdf:application/pdf}, -} - -@article{operto_cati:_2016, - title = {{CATI}: {A} {Large} {Distributed} {Infrastructure} for the {Neuroimaging} of {Cohorts}}, - volume = {14}, - issn = {1559-0089}, - shorttitle = {{CATI}}, - doi = {10.1007/s12021-016-9295-8}, - abstract = {This paper provides an overview of CATI, a platform dedicated to multicenter neuroimaging. Initiated by the French Alzheimer's plan (2008-2012), CATI is a research project called on to provide service to other projects like an industrial partner. Its core mission is to support the neuroimaging of large populations, providing concrete solutions to the increasing complexity involved in such projects by bringing together a service infrastructure, the know-how of its expert academic teams and a large-scale, harmonized network of imaging facilities. CATI aims to make data sharing across studies easier and promotes sharing as much as possible. In the last 4 years, CATI has assisted the clinical community by taking charge of 35 projects so far and has emerged as a recognized actor at the national and international levels.}, - language = {eng}, - number = {3}, - journal = {Neuroinformatics}, - author = {Operto, Grégory and Chupin, Marie and Batrancourt, Bénédicte and Habert, Marie-Odile and Colliot, Olivier and Benali, Habib and Poupon, Cyril and Champseix, Catherine and Delmaire, Christine and Marie, Sullivan and Rivière, Denis and Pélégrini-Issac, Mélanie and Perlbarg, Vincent and Trebossen, Régine and Bottlaender, Michel and Frouin, Vincent and Grigis, Antoine and Orfanos, Dimitri Papadopoulos and Dary, Hugo and Fillon, Ludovic and Azouani, Chabha and Bouyahia, Ali and Fischer, Clara and Edward, Lydie and Bouin, Mathilde and Thoprakarn, Urielle and Li, Jinpeng and Makkaoui, Leila and Poret, Sylvain and Dufouil, Carole and Bouteloup, Vincent and Chételat, Gaël and Dubois, Bruno and Lehéricy, Stéphane and Mangin, Jean-François and Cointepas, Yann and {CATI Consortium}}, - year = {2016}, - pmid = {27066973}, - keywords = {Humans, Neuroimaging, Information Dissemination, Data sharing, Computational Biology, Large-scale studies, Multicenter protocols, Multicenter Studies as Topic, Neuroimaging biomarkers, Workflow, Data Mining, Data mining}, - pages = {253--264}, - annote = {The following values have no corresponding Zotero field:number: 3}, - file = {Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QWHI6VJG/Operto et al. - 2016 - CATI A Large Distributed Infrastructure for the N.pdf:application/pdf}, -} - -@article{grigis_neuroimaging_2017, - title = {Neuroimaging, {Genetics}, and {Clinical} {Data} {Sharing} in {Python} {Using} the {CubicWeb} {Framework}}, - volume = {11}, - issn = {1662-5196}, - doi = {10.3389/fninf.2017.00018}, - abstract = {In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts.}, - language = {eng}, - journal = {Frontiers in Neuroinformatics}, - author = {Grigis, Antoine and Goyard, David and Cherbonnier, Robin and Gareau, Thomas and Papadopoulos Orfanos, Dimitri and Chauvat, Nicolas and Di Mascio, Adrien and Schumann, Gunter and Spooren, Will and Murphy, Declan and Frouin, Vincent}, - year = {2017}, - pmid = {28360851}, - pmcid = {PMC5352661}, - keywords = {data sharing, database, neuroimaging, genetics, Python, medical informatics, web service}, - pages = {18}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/P9KL2KYM/Grigis et al. - 2017 - Neuroimaging, Genetics, and Clinical Data Sharing .pdf:application/pdf}, -} - -@article{ji_t240_2018, - title = {T240. {Relationship} {Between} {Cognitive} {Performance} and {Superficial} {White} {Matter} {Integrity} in the {Cingulate} {Cortex} in {Schizophrenia}: {A} {DWI} {Study} {Using} a {Novel} {Atlas}}, - volume = {83}, - issn = {00063223}, - shorttitle = {T240. {Relationship} {Between} {Cognitive} {Performance} and {Superficial} {White} {Matter} {Integrity} in the {Cingulate} {Cortex} in {Schizophrenia}}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0006322318306796}, - doi = {10.1016/j.biopsych.2018.02.577}, - language = {en}, - number = {9}, - urldate = {2024-02-27}, - journal = {Biological Psychiatry}, - author = {Ji, Ellen and Sarrazin, Samuel and Leboyer, Marion and Guevara, Miguel and Guevara, Pamela and Poupon, Cyril and Grigis, Antoine and Houenou, Josselin}, - month = may, - year = {2018}, - pages = {S222}, -} - -@article{ji_alterations_2020, - title = {Alterations {In} {Short}-{Range} {Structural} {Connectivity} {Across} {The} {Psychosis} {Spectrum}: {Findings} {From} {The} {B}-{Snip} {Study}}, - volume = {46}, - issn = {0586-7614, 1745-1701}, - shorttitle = {Alterations {In} {Short}-{Range} {Structural} {Connectivity} {Across} {The} {Psychosis} {Spectrum}: {Findings} {From} {The} {B}-{Snip} {Study}}, - url = {https://academic.oup.com/schizophreniabulletin/article/46/Supplement_1/S97/5839281}, - doi = {10.1093/schbul/sbaa031.226}, - abstract = {Abstract - - Background - Schizophrenia (SZ) and bipolar disorder (BD) have been increasingly viewed as psychotic mood disorders along a shared spectrum. Long-range and short-range structural connectivity have been implicated in both disorders, conceptualising them as “disconnection syndromes”. There has been a rise in neuroimaging tools to understand the overlap and boundaries between the two disorders, which has shifted our focus towards appreciating traits in addition to diagnosis. Our recent pilot study examining short-range U-fibers found in superficial white matter (SWM) found shared and distinct traits among people with SZ and BD and we aimed to investigate SWM further using data from the Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) consortium. - - - Methods - Using diffusion weighted imaging (DWI), we performed whole brain tractography in 113 people with SZ, 69 people with SA disorder, 49 people with psychotic BD and 77 healthy controls using BrainVISA and Connectomist 2.0. Segmentation and labelling of SWM tracts were performed using a comprehensive U-fiber atlas. ComBat was applied to remove site effects and principle components analysis was performed to identity networks of bundles used for comparative analyses. - - - Results - Principle component analysis revealed a network comprised of 8 short tracts in frontal, parietal, and temporal regions that had decreased anatomical connectivity in patients, regardless of diagnosis, relative to healthy controls. This network overlaps, in part, regions that differed between patients (SZ and BD) and healthy controls in our recent pilot study. However, we were unable to detect differences between people with SZ, SA disorder and psychotic BD. - - - Discussion - We demonstrate that short U-fibers are likely vulnerable to pathological processes in psychotic illnesses, encouraging further understanding of their anatomy and function. Our lack of findings between patient groups may reflect a more homogeneous population (three subgroups of psychosis) and may suggest that abnormalities in SWM are less likely due to mood disturbances.}, - language = {en}, - number = {Supplement\_1}, - urldate = {2024-02-27}, - journal = {Schizophrenia Bulletin}, - author = {Ji, Ellen and Perus, Lisa and Grigis, Antoine and Poupon, Cyril and Sarrazin, Samuel and Guevara, Pamela and Guevara, Miguel and Mangin, Jean-François and Houenou, Josselin}, - month = may, - year = {2020}, - pages = {S97--S97}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LYB3RFE4/Ji et al. - 2020 - S160. ALTERATIONS IN SHORT-RANGE STRUCTURAL CONNEC.pdf:application/pdf;Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8MTIP4QL/Ji et al. - 2018 - T145. ALTERATIONS IN SUPERFICIAL WHITE MATTER IN T.pdf:application/pdf}, -} - -@article{haeger_imaging_2020, - title = {Imaging the aging brain: study design and baseline findings of the {SENIOR} cohort}, - volume = {12}, - issn = {1758-9193}, - shorttitle = {Imaging the aging brain}, - url = {https://alzres.biomedcentral.com/articles/10.1186/s13195-020-00642-1}, - doi = {10.1186/s13195-020-00642-1}, - abstract = {Abstract - - Background - Current demographic trends point towards an aging society entailing increasing occurrence and burden of neurodegenerative diseases. In this context, understanding physiological aging and its turning point into neurodegeneration is essential for the development of possible biomarkers and future therapeutics of brain disease. - - - Methods - The SENIOR study represents a longitudinal, observational study including cognitively healthy elderlies aged between 50 and 70 years old at the time of inclusion, being followed annually over 10 years. Our multimodal protocol includes structural, diffusion, functional, and sodium magnetic resonance imaging (MRI) at 3 T and 7 T, positron emission tomography (PET), blood samples, genetics, audiometry, and neuropsychological and neurological examinations as well as assessment of neuronal risk factors. - - - Results - One hundred forty-two participants (50\% females) were enrolled in the SENIOR cohort with a mean age of 60 (SD 6.3) years at baseline. Baseline results with multiple regression analyses reveal that cerebral white matter lesions can be predicted by cardiovascular and cognitive risk factors and age. Cardiovascular risk factors were strongly associated with juxtacortical and periventricular lesions. Intra-subject across-test variability as a measure of neuropsychological test performance and possible cognitive marker predicts white matter volume and is significantly associated with risk profile. Division of the cohort into subjects with a higher and lower risk profile shows significant differences in intra-subject across-test variability and volumes as well as cortical thickness of brain regions of the temporal lobe. There is no difference between the lower- and higher-risk groups in amyloid load using PET data from a subset of 81 subjects. - - - Conclusions - We here describe the study protocol and baseline findings of the SENIOR observational study which aim is the establishment of integrated, multiparametric maps of normal aging and the identification of early biomarkers for neurodegeneration. We show that intra-subject across-test variability as a marker of neuropsychological test performance as well as age, gender, and combined risk factors influence neuronal decline as represented by decrease in brain volume, cortical thickness, and increase in white matter lesions. Baseline findings will be used as underlying basis for the further implications of aging and neuronal degeneration as well as examination of brain aging under different aspects of brain pathology versus physiological aging.}, - language = {en}, - number = {1}, - urldate = {2024-02-27}, - journal = {Alzheimer's Research \& Therapy}, - author = {Haeger, Alexa and Mangin, Jean-François and Vignaud, Alexandre and Poupon, Cyril and Grigis, Antoine and Boumezbeur, Fawzi and Frouin, Vincent and Deverre, Jean-Robert and Sarazin, Marie and Hertz-Pannier, Lucie and Bottlaender, Michel and {the SENIOR team} and Baron, Christine and Berland, Valérie and Blancho, Nathalie and Desmidt, Séverine and Doublé, Christine and Ginisty, Chantal and Joly-Testault, Véronique and Laurier, Laurence and Lecomte, Yann and Leroy, Claire and Manciot, Christine and Marchand, Stephanie and Mediouni, Gaelle and Millot, Xavier and Monassier, Ludivine and Roger, Séverine and Vuillemard, Catherine}, - month = dec, - year = {2020}, - keywords = {Imaging, Aging, Biomarker, Prevention, Dementia, Neurodegenerative disease, Alzheimer’s disease, Cognitive decline, Intra-person across-test variability}, - pages = {77}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AMRXRWZU/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf;PubMed Central Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/STJTPBIP/Haeger et al. - 2020 - Imaging the aging brain study design and baseline.pdf:application/pdf}, -} - -@article{backhausen_interplay_2023, - title = {Interplay of early negative life events, development of orbitofrontal cortical thickness and depression in young adulthood}, - journal = {JCPP Advances}, - author = {Backhausen, Lea L and Granzow, Jonas and Fröhner, Juliane H and Artiges, Eric and Paillère-Martinot, Marie-Laure and Lemaître, Hervé and Sticca, Fabio and Banaschewski, Tobias and Desrivières, Sylvane and Grigis, Antoine and {others}}, - year = {2023}, - note = {Publisher: Wiley Online Library}, - pages = {e12210}, -} - -@article{roser_188_2023, - title = {188. {Cerebellar} {Vermis} and {Depressive} {Symptoms} in {Bipolar} {Disorder}}, - volume = {93}, - number = {9}, - journal = {Biological Psychiatry}, - author = {Roser, Mathilde and Macone, Alexandre and Piguet, Camille and D'Albis, Marc-Antoine and Grigis, Antoine and Duchesnay, Edouard and Victor, Julie and Leprince, Yann and Krystal, Sidney and Leboyer, Marion and {others}}, - year = {2023}, - note = {Publisher: Elsevier}, - pages = {S169--S170}, -} - -@inproceedings{hemforth_interpretable_2023, - title = {Interpretable automatic detection of incomplete hippocampal inversions using anatomical criteria}, - volume = {12464}, - booktitle = {Medical {Imaging} 2023: {Image} {Processing}}, - publisher = {SPIE}, - author = {Hemforth, Lisa and Cury, Claire and Frouin, Vincent and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and {others}}, - year = {2023}, - pages = {137--143}, -} - -@article{lotter_human_2023, - title = {Human cortex development is shaped by molecular and cellular brain systems}, - journal = {bioRxiv}, - author = {Lotter, Leon D and Saberi, Amin and Hansen, Justine Y and Misic, Bratislav and Paquola, Casey and Barker, Gareth J and Bokde, Arun LW and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and {others}}, - year = {2023}, - note = {Publisher: Cold Spring Harbor Laboratory Preprints}, -} - -@article{freichel_drinking_2023, - title = {Drinking {Motives}, {Personality} {Traits}, {Life} {Stressors}-{Identifying} {Pathways} to {Harmful} {Alcohol} {Use} in {Adolescence} {Using} a {Panel} {Network} {Approach}}, - journal = {Addiction}, - author = {Freichel, René and Pfirrmann, Janine and Cousjin, Janna and de Jong, Peter and Franken, Ingmar and Banaschewski, Tobias and Bokde, Arun LW and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and {others}}, - year = {2023}, - note = {Publisher: Wiley Online Library}, -} - -@inproceedings{farrens_pysap_2022, - title = {{PySAP}: {From} {Galaxies} to {Brains} and {Beyond}}, - volume = {532}, - booktitle = {Astronomical {Society} of the {Pacific} {Conference} {Series}}, - author = {Farrens, Samuel and Grigis, A and El Gueddari, L and Ramzi, Z and Chaithya, GR and Ciuciu, P and Starck, J-L}, - year = {2022}, - pages = {77}, -} - -@inproceedings{gomez_characterization_2022, - title = {Characterization of {Brain} {Activity} {Patterns} {Across} {States} of {Consciousness} {Based} on {Variational} {Auto}-{Encoders}}, - booktitle = {International {Conference} on {Medical} {Image} {Computing} and {Computer}-{Assisted} {Intervention}}, - publisher = {Springer Nature Switzerland Cham}, - author = {Gomez, Chloé and Grigis, Antoine and Uhrig, Lynn and Jarraya, Béchir}, - year = {2022}, - pages = {419--429}, -} - -@article{maitra_psychotic_2023, - title = {Psychotic {Like} {Experiences} in {Healthy} {Adolescents} are {Underpinned} by {Lower} {Fronto}-{Temporal} {Cortical} {Gyrification}: a {Study} from the {IMAGEN} {Consortium}}, - volume = {49}, - number = {2}, - journal = {Schizophrenia Bulletin}, - author = {Maitra, Raka and Horne, Charlotte M and O’Daly, Owen and Papanastasiou, Evangelos and Gaser, Christian and IMAGEN Consortium Shergill Sukhi Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, UK Kent and Medway Medical School, Canterbury, UK}, - year = {2023}, - note = {Publisher: Oxford University Press US}, - pages = {309--318}, -} - -@inproceedings{grigis_interpretable_2022, - title = {Interpretable {Signature} of {Consciousness} in {Resting}-{State} {Functional} {Network} {Brain} {Activity}}, - booktitle = {International {Conference} on {Medical} {Image} {Computing} and {Computer}-{Assisted} {Intervention}}, - publisher = {Springer Nature Switzerland Cham}, - author = {Grigis, Antoine and Gomez, Chloé and Frouin, Vincent and Uhrig, Lynn and Jarraya, Béchir}, - year = {2022}, - pages = {261--270}, -} - -@inproceedings{ambroise_multi-modal_2021, - title = {Multi-modal {Latent} {Variable} {Model} could help individuals stratification: application to {HBN} cohort}, - author = {Ambroise, C and Mihailov, A and Frouin, V and Grigis, A}, - year = {2021}, -} - -@misc{dufumier_benchmarking_2021, - title = {Benchmarking {CNN} on {3D} {Anatomical} {Brain} {MRI}: {Architectures}, {Data} {Augmentation} and {Deep} {Ensemble} {Learning}}, - author = {Dufumier, Benoit and Gori, Pietro and Battaglia, Ilaria and Victor, Julie and Grigis, Antoine and Duchesnay, Edouard}, - year = {2021}, -} - -@misc{schumann_satellite_2021, - title = {Satellite {Imaging} of {Global} {Urbanicity} relates to {Brain} and {Behavior} in {Young} {People}}, - author = {Schumann, Gunter and XU, JIAYUAN and Liu, Xiaoxuan and Ing, Alex and LI, QIAOJUN and Qin, Wen and Guo, Lining and Huang, Conghong and Chen, Jingliang and Wang, Meiyun and {others}}, - year = {2021}, -} - -@inproceedings{peres_diffusion-weighted_2016, - title = {Diffusion-weighted {MR} {Imaging} and {Spectroscopy} reveal brain tissue alterations induced by ionizing radiation in the mouse brain}, - author = {Pérès, Elodie A and Boumezbeur, Fawzi and Etienne, Olivier and Grigis, Antoine and Boussin, François D and Le Bihan, Denis}, - year = {2016}, -} - -@article{farrens_pysap_2020, - title = {{PySAP}: {Python} {Sparse} data {Analysis} {Package}}, - journal = {Astrophysics Source Code Library}, - author = {Farrens, S and Grigis, A and El Gueddari, L and Ramzi, Z and Chaithya, GR and Starck, S and Sarthou, B and Cherkaoui, H and Ciuciu, P and Starck, J-L}, - year = {2020}, - pages = {ascl--2008}, -} - -@inproceedings{sun_manifold-based_2020, - title = {Manifold-based exploration of the links between precentral sulcus interruptions and language-associated area 55b}, - author = {Sun, ZY and Fischer, C and Grigis, A and Rivière, D and Mangin, Jean-François}, - year = {2020}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/ADRFLNLB/Sun et al. - 2020 - Manifold-based exploration of the links between pr.pdf:application/pdf}, -} - -@inproceedings{sun_manifold-based_2019, - title = {Manifold-based exploration of the links between cortical morphology and functional architecture}, - author = {Sun, Zhong Yi and Rivière, Denis and Fischer, Clara and Grigis, Antoine and Poupon, Cyril and Mangin, Jean-François}, - year = {2019}, - file = {Available Version (via Google Scholar):/home/ed203246/snap/zotero-snap/common/Zotero/storage/69TL6MRQ/Sun et al. - 2019 - Manifold-based exploration of the links between co.pdf:application/pdf}, -} - -@inproceedings{gay_cartographie_2015, - title = {Cartographie {T2}* sur cerveau entier pour les études multicentriques de recherche clinique}, - booktitle = {2. {SFRMBM}}, - author = {Gay, David and Chupin, Marie and Poupon, Cyril and Mangin, Jean-François and Dary, Hugo and Kaaouana, Takoua and Grigis, Antoine and de Sousa, Paulo Loureiro and Delmaire, Christine and de Rochefort, Ludovic and {others}}, - year = {2015}, - pages = {1--p}, -} - -@article{grigis_predicting_2020, - title = {Predicting cortical signatures of consciousness using dynamic functional connectivity graph-convolutional neural networks}, - journal = {bioRxiv}, - author = {Grigis, Antoine and Gomez, Chloé and Tasserie, Jordy and Ambroise, Corentin and Frouin, Vincent and Jarraya, Béchir and Uhrig, Lynn}, - year = {2020}, - note = {Publisher: Cold Spring Harbor Laboratory}, - pages = {2020--05}, -} - -@article{artiges_quantifying_2019, - title = {Quantifying performance of machine learning methods for neuroimaging data}, - volume = {199}, - number = {1}, - journal = {NeuroImage}, - author = {Artiges, Eric and Martinot, Jean-Luc and Smolka, Michael N and Henrik, Walter}, - year = {2019}, - pages = {351--365}, -} - -@article{judd_independent_2019, - title = {Independent effects of socioeconomic status and genetics on adolescent cognition and brain development}, - journal = {bioRxiv}, - author = {Judd, Nicholas and Sauce, Bruno and Wiedenhoeft, John and Tromp, Jeshua and Chaarani, Bader and Schliep, Alexander and Stringaris, Argyris and Noort, Betteke van and Penttilä, Jani and Grimmer, Yvonne and Insensee, Corinna and Becker, Andreas and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and {others}}, - year = {2019}, - note = {Publisher: Cold Spring Harbor Laboratory}, - pages = {866624}, -} - -@article{milham_accelerating_2020, - title = {Accelerating the {Evolution} of {Nonhuman} {Primate} {Neuroimaging}}, - volume = {105}, - number = {4}, - journal = {Neuron}, - author = {Milham, Michael and Petkov, Christopher I. and Margulies, Daniel S. and Schroeder, Charles E. and Basso, Michele A. and Belin, Pascal and Fair, Damien A. and Fox, Andrew and Kastner, Sabine and Mars, Rogier B. and Messinger, Adam and Poirier, Colline and Vanduffel, Wim and Essen, David C. Van and Alvand, Ashkan and Becker, Yannick and Hamed, Suliann Ben and Benn, Austin and Bodin, Clementine and Boretius, Susann and Cagna, Bastien and Coulon, Olivier and El-Gohary, Sherif Hamdy and Evrard, Henry and Forkel, Stephanie J. and Friedrich, Patrick and Froudist-Walsh, Sean and Garza-Villarreal, Eduardo A. and Yang Gao and, Alessandro Gozzi and Grigis, Antoine and Hartig, Renee and {others}}, - year = {2020}, - note = {Publisher: Elsevier}, - pages = {600--603}, -} - -@article{farrens_pysap_2020-1, - title = {{PySAP}: {Python} {Sparse} {Data} {Analysis} {Package} for multidisciplinary image processing}, - volume = {32}, - journal = {Astronomy and Computing}, - author = {Farrens, S and Grigis, A and El Gueddari, L and Ramzi, Z and Chaithya, GR and Starck, S and Sarthou, B and Cherkaoui, H and Ciuciu, P and Starck, J-L}, - year = {2020}, - note = {Publisher: Elsevier}, - pages = {100402}, -} - -@article{lett_f51_2019, - title = {F51. {Putative} {Causal} {Relationship} {Among} {Polygenic} {Scores}, {Cortical} {Surfaces}, and {General} {Intelligence}}, - volume = {85}, - number = {10}, - journal = {Biological Psychiatry}, - author = {Lett, Tristram and Vogel, Bob and Ripke, Stephan and Wackerhagen, Carolin and Erk, Susanne and Brandl, Eva J. and Nöthen, Markus and Rietschel, Marcella and Degenhardt, Franziska and Romanczuk-Seiferth, Nina and Witt, Stephanie and Banaschewski, Tobias and Barker, Gareth and Bokde, Arun and Bromberg, Uli and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Frouin, Vincent and {others}}, - year = {2019}, - note = {Publisher: Elsevier}, - pages = {S232}, -} - -@article{doger_de_speville_relationships_2017, - title = {Relationships between regional radiation doses and cognitive decline in children treated with cranio-spinal irradiation for posterior fossa tumors}, - volume = {7}, - journal = {Frontiers in oncology}, - author = {Doger de Speville, Elodie and Robert, Charlotte and Perez-Guevara, Martin and Grigis, Antoine and Bolle, Stephanie and Pinaud, Clemence and Dufour, Christelle and Beaudré, Anne and Kieffer, Virginie and Longaud, Audrey and {others}}, - year = {2017}, - note = {Publisher: Frontiers}, - pages = {166}, -} - -@article{grigis_longitudinal_2012, - title = {Longitudinal change detection in diffusion {MRI} using multivariate statistical testing on tensors}, - volume = {60}, - number = {4}, - journal = {Neuroimage}, - author = {Grigis, Antoine and Noblet, Vincent and Heitz, Fabrice and Blanc, Frederic and de Seze, Jerome and Kremer, Stephane and Rumbach, Lucien and Armspach, Jean-Paul}, - year = {2012}, - note = {Publisher: Elsevier}, - pages = {2206--2221}, -} - -@article{grigis_learning_2020, - title = {Learning to leverage salient regions in neuro-oncology using {Deap} {Learning}}, - journal = {bioRxiv}, - author = {Grigis, A and Alentorn, A and Frouin, V}, - year = {2020}, - note = {Publisher: Cold Spring Harbor Laboratory}, - pages = {2020--10}, -} - -@article{grigis_longitudinal_2013, - title = {Longitudinal change detection: inference on the diffusion tensor along white matter pathways}, - volume = {17}, - number = {3}, - journal = {Medical image analysis}, - author = {Grigis, Antoine and Noblet, Vincent and Blanc, Fréderic and Heitz, Fabrice and de Seze, Jérome and Kremer, Stéphane and Armspach, Jean-Paul}, - year = {2013}, - note = {Publisher: Elsevier}, - pages = {375--386}, -} - -@inproceedings{rosenthal_relationship_2020, - title = {{THE} {RELATIONSHIP} {BETWEEN} {AMYGDALA} {NEURAL} {ACTIVATION} {IN} {RESPONSE} {TO} {EMOTIONAL} {STIMULI} {WITH} {DEPRESSIVE} {SYMPTOMS} {AND} {PROBLEMATIC} {DRINKING}}, - volume = {44}, - booktitle = {Alcoholism-clinical and experimental research}, - author = {Rosenthal, A and Rothkirch, M and Banaschewski, T and Barker, GJ and Bokde, ALW and Quinlan, E Burke and Desrivieres, S and Flor, H and Grigis, A and Garavan, H and {others}}, - year = {2020}, - pages = {114--114}, -} - -@inproceedings{mihailov_multidimensional_2019, - title = {Multidimensional {Approaches} in the {Study} of {Autistic} {Traits} using {Behavioral} and {Imaging} {Data}}, - author = {Mihailov, Angeline and Philippe, Cathy and Grigis, Antoine and Guillemot, Vincent and Laidi, Charles and Piguet, Camille and Abdi, Hervé and Houenou, Josselin and Frouin, Vincent}, - year = {2019}, -} - -@article{scott_prospective_2019, - title = {Prospective cohort study of early biosignatures of response to lithium in bipolar-{I}-disorders: overview of the {H2020}-funded {R}-{LiNK} initiative}, - volume = {7}, - issn = {2194-7511}, - shorttitle = {Prospective cohort study of early biosignatures of response to lithium in bipolar-{I}-disorders}, - url = {https://journalbipolardisorders.springeropen.com/articles/10.1186/s40345-019-0156-x}, - doi = {10.1186/s40345-019-0156-x}, - language = {en}, - number = {1}, - urldate = {2020-10-15}, - journal = {International Journal of Bipolar Disorders}, - author = {Scott, Jan and Hidalgo-Mazzei, Diego and Strawbridge, Rebecca and Young, Allan and Resche-Rigon, Matthieu and Etain, Bruno and Andreassen, Ole A. and Bauer, Michael and Bennabi, Djamila and Blamire, Andrew M. and Boumezbeur, Fawzi and Brambilla, Paolo and Cattane, Nadia and Cattaneo, Annamaria and Chupin, Marie and Coello, Klara and Cointepas, Yann and Colom, Francesc and Cousins, David A. and Dubertret, Caroline and Duchesnay, Edouard and Ferro, Adele and Garcia-Estela, Aitana and Goikolea, Jose and Grigis, Antoine and Haffen, Emmanuel and Høegh, Margrethe C. and Jakobsen, Petter and Kalman, Janos L. and Kessing, Lars V. and Klohn-Saghatolislam, Farah and Lagerberg, Trine V. and Landén, Mikael and Lewitzka, Ute and Lutticke, Ashley and Mazer, Nicolas and Mazzelli, Monica and Mora, Cristina and Muller, Thorsten and Mur-Mila, Estanislao and Oedegaard, Ketil Joachim and Oltedal, Leif and Pålsson, Erik and Papadopoulos Orfanos, Dimitri and Papiol, Sergi and Perez-Sola, Victor and Reif, Andreas and Ritter, Philipp and Rossi, Roberto and Schulze, Thomas and Senner, Fanny and Smith, Fiona E. and Squarcina, Letizia and Steen, Nils Eiel and Thelwall, Pete E. and Varo, Cristina and Vieta, Eduard and Vinberg, Maj and Wessa, Michele and Westlye, Lars T. and Bellivier, Frank}, - month = dec, - year = {2019}, - keywords = {Neuroimaging, Phenotype, Lithium, Response, Actigraphy, Bipolar, Digital, Omics, Personalization, Precision}, - file = {Springer Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TIHK9QC7/Scott et al. - 2019 - Prospective cohort study of early biosignatures of.pdf:application/pdf}, -} - -@misc{poiret_can_2023, - title = {Can we {Agree}? {On} the {Rashomon} {Effect} and the {Reliability} of {Post}-{Hoc} {Explainable} {AI}}, - author = {Poiret, Clement and Grigis, Antoine and Thomas, Justin and Noulhiane, Marion}, - year = {2023}, -} - -@misc{duan_population_2024, - title = {Population clustering of structural brain aging and its association with brain development}, - author = {Duan, Haojing and Shi, Runye and Kang, Jujiao and Banaschewski, Tobias and Bokde, Arun LW and Büchel, Christian and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and {others}}, - year = {2024}, - note = {Publisher: Cold Spring Harbor Laboratory Press}, -} - -@article{ambroise_interpretable_2024, - title = {Interpretable and integrative deep learning for discovering brain-behaviour associations with stability analysis}, - author = {Ambroise, Corentin and Grigis, Antoine and Houenou, Josselin and Frouin, Vincent}, - year = {2024}, -} - -@misc{freichel_unravelling_2023, - title = {Unravelling {Robust} {Brain}-{Behavior} {Links} of {Depressive} {Symptoms} {Through} {Granular} {Network} {Models}: {Understanding} {Heterogeneity} and {Clinical} {Implications}}, - author = {Freichel, René and Lenartowicz, Agatha and Douw, Linda and Kruschwitz, Johann D and Banaschewski, Tobias and Barker, Gareth J and Bokde, Arun LW and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and {others}}, - year = {2023}, - note = {Publisher: Cold Spring Harbor Laboratory Press}, -} - -@misc{korologou-linden_bidirectional_2023, - title = {The bidirectional effects between cognitive ability and brain morphology: {A} life course {Mendelian} randomization analysis}, - author = {Korologou-Linden, Roxanna and Schuurmans, Isabel K and Cecil, Charlotte AM and White, Tonya and Banaschewski, Tobias and Bokde, Arun LW and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and {others}}, - year = {2023}, - note = {Publisher: Cold Spring Harbor Laboratory Preprints}, -} - -@inproceedings{gomez_exploration_2023, - title = {Exploration of the {Neural} {Correlates} of {Consciousness} {Using} {Linear} {Latent} {Model}}, - booktitle = {2023 {IEEE} 20th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - publisher = {IEEE}, - author = {Gomez, C and Tasserie, J and Uhrig, L and Jarraya, B and Grigis, A}, - year = {2023}, - pages = {1--5}, -} - -@article{papanastasiou_examination_2020, - title = {Examination of the neural basis of psychotic-like experiences in adolescenceduring processing of emotional faces}, - journal = {Scientific Reports}, - author = {Papanastasiou, Evangelos and Mouchlianitis, Elias and Joyce, Daniel and McGuire, Philip and Boussebaa, Celia and Banaschewski, Tobias and Bokde, Arun LW and Büchel, Christian and Quinlan, Erin and Desrivieres, Sylvane and {others}}, - year = {2020}, - note = {Publisher: Nature Publishing Group}, -} - -@misc{louiset_separating_2024, - title = {Separating common from salient patterns with {Contrastive} {Representation} {Learning}}, - author = {Louiset, Robin and Duchesnay, Edouard and Grigis, Antoine and Gori, Pietro}, - year = {2024}, -} - -@inproceedings{ambroise_mixup_2023, - title = {{MixUp} brain-cortical augmentations in self-supervised learning}, - booktitle = {International {Workshop} on {Machine} {Learning} in {Clinical} {Neuroimaging}}, - publisher = {Springer}, - author = {Ambroise, Corentin and Frouin, Vincent and Dufumier, Benoit and Duchesnay, Edouard and Grigis, Antoine}, - year = {2023}, - pages = {102--111}, -} - -@article{desrivieres_machine_2024, - title = {Machine learning models for diagnosis and risk prediction in eating disorders, depression, and alcohol use disorder}, - author = {Desrivières, Sylvane and Zhang, Zuo and Robinson, Lauren and Whelan, Robert and Jollans, Lee and Wang, Zijian and Nees, Frauke and Chu, Congying and Bobou, Marina and Du, Dongping and {others}}, - year = {2024}, -} - -@article{cury_genome_2020, - title = {Genome wide association study of incomplete hippocampal inversion in adolescents}, - volume = {15}, - number = {1}, - journal = {PLoS One}, - author = {Cury, Claire and Scelsi, Marzia Antonella and Toro, Roberto and Frouin, Vincent and Artiges, Eric and Grigis, Antoine and Heinz, Andreas and Lemaître, Hervé and Martinot, Jean-Luc and Poline, Jean-Baptiste and {others}}, - year = {2020}, - note = {Publisher: Public Library of Science San Francisco, CA USA}, - pages = {e0227355}, -} - -@inproceedings{el_gueddari_pysap-mri_2020, - title = {{PySAP}-{MRI}: {A} {Python} package for {MR} image reconstruction}, - booktitle = {{ISMRM} workshop on {Data} {Sampling} and {Image} {Reconstruction}}, - author = {El Gueddari, Loubna and Radhakrishna, Chaithya Giliyar and Ramzi, Zaccharie and Farrens, Samuel and Starck, Sophie and Grigis, Antoine and Starck, Jean-Luc and Ciuciu, Philippe}, - year = {2020}, -} - -@article{tasserie_pypreclin_2020, - title = {Pypreclin: {An} automatic pipeline for macaque functional {MRI} preprocessing}, - volume = {207}, - journal = {NeuroImage}, - author = {Tasserie, Jordy and Grigis, Antoine and Uhrig, Lynn and Dupont, Morgan and Amadon, Alexis and Jarraya, Béchir}, - year = {2020}, - note = {Publisher: Academic Press}, - pages = {116353}, -} - -@article{ivanov_substance_2019, - title = {Substance {Use} {Initiation} in {Drug} {Naïve} {Adolescents}-{Possible} {Predictors} and {Consequences} {From} a {Large} {Cohort} {Naturalistic} {Study}}, - author = {Ivanov, Iliyan and Parvaz, Muhammad A and Velthorst, Eva and Sandin, Sven and Shaik, Riaz B and Gan, Gabriella and Spechler, Philip and Mackey, Scott and Banaschewski, Tobias and Bokde, Arun LW and {others}}, - year = {2019}, -} - -@article{jollans_quantifying_2019, - title = {Quantifying performance of machine learning methods for neuroimaging data}, - volume = {199}, - journal = {Neuroimage}, - author = {Jollans, Lee and Boyle, Rory and Artiges, Eric and Banaschewski, Tobias and Desrivières, Sylvane and Grigis, Antoine and Martinot, Jean-Luc and Paus, Tomáš and Smolka, Michael N and Walter, Henrik and {others}}, - year = {2019}, - note = {Publisher: Academic Press}, - pages = {351--365}, -} - -@phdthesis{grigis_approches_2012, - type = {{PhD} {Thesis}}, - title = {Approches statistiques pour la détection de changements en {IRM} de diffusion: application au suivi longitudinal de pathologies neuro-dégénératives}, - school = {Université de Strasbourg}, - author = {Grigis, Antoine}, - year = {2012}, -} - -@inproceedings{cherkaoui_analysis_2018, - title = {Analysis vs synthesis-based regularization for combined compressed sensing and parallel {MRI} reconstruction at 7 tesla}, - booktitle = {2018 26th {European} {Signal} {Processing} {Conference} ({EUSIPCO})}, - publisher = {IEEE}, - author = {Cherkaoui, Hamza and El Gueddari, Loubna and Lazarus, Carole and Grigis, Antoine and Poupon, Fabrice and Vignaud, Alexandre and Farrens, Sammuel and Starck, J-L and Ciuciu, Philippe}, - year = {2018}, - pages = {36--40}, -} - -@inproceedings{grigis_new_2011, - title = {A new high order tensor decomposition: {Application} to reorientation.}, - booktitle = {2011 {IEEE} {International} {Symposium} on {Biomedical} {Imaging}: {From} {Nano} to {Macro}}, - publisher = {IEEE}, - author = {Grigis, Antoine and Renard, Félix and Noblet, Vincent and Heinrich, Christian and Heitz, Fabrice and Armspach, Jean-Paul}, - year = {2011}, - pages = {258--261}, -} - -@inproceedings{renard_comparison_2010, - title = {Comparison of interpolation methods for angular resampling of diffusion weighted images}, - booktitle = {2010 2nd {International} {Conference} on {Image} {Processing} {Theory}, {Tools} and {Applications}}, - publisher = {IEEE}, - author = {Renard, Félix and Noblet, Vincent and Grigis, Antoine and Heinrich, Christian and Kremer, Stéphane}, - year = {2010}, - pages = {207--211}, -} - -@inproceedings{grigis_integration_2011, - title = {On the integration of spatial neighborhood information for detecting longitudinal changes in {MRI} sequences}, - author = {Grigis, Antoine and Noblet, Vincent and Heitz, Fabrice and Armspach, Jean-Paul}, - year = {2011}, -} - -@inproceedings{grigis_change_2010, - title = {Change detection in diffusion {MRI} using multivariate statistical testing on tensors}, - booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention}–{MICCAI} 2010: 13th {International} {Conference}, {Beijing}, {China}, {September} 20-24, 2010, {Proceedings}, {Part} {II} 13}, - publisher = {Springer Berlin Heidelberg}, - author = {Grigis, Antoine and Noblet, Vincent and Renard, Félix and Heitz, Fabrice and Armspach, Jean-Paul and Rumbach, Lucien}, - year = {2010}, - pages = {117--124}, -} - -@inproceedings{grigis_longitudinal_2011, - title = {Longitudinal change detection: inference on the diffusion tensor along white-matter pathways}, - booktitle = {Medical {Image} {Computing} and {Computer}-{Assisted} {Intervention}–{MICCAI} 2011: 14th {International} {Conference}, {Toronto}, {Canada}, {September} 18-22, 2011, {Proceedings}, {Part} {II} 14}, - publisher = {Springer Berlin Heidelberg}, - author = {Grigis, Antoine and Noblet, Vincent and Blanc, Fréderic and Heitz, Fabrice and de Seze, Jérome and Armspach, Jean-Paul}, - year = {2011}, - pages = {1--8}, -} - -@article{grigis_statistical_2012, - title = {Statistical approaches for change detection in diffusion {MRI} (application to the longitudinal follow-up of neuro-degenerative pathologies)}, - author = {Grigis, Antoine}, - year = {2012}, - note = {Publisher: Université de Strasbourg, Strasbourg}, -} - -@inproceedings{goyard_brainomics_2015, - title = {Brainomics: {Harnessing} the {CubicWeb} semantic framework to manage large neuromaging genetics shared resources}, - booktitle = {Journées {RITS} 2015}, - author = {Goyard, David and Grigis, Antoine and Papadopoulos-Orfanos, Dimitri and Vittot, Michel and Frouin, Vincent and Di Mascio, Adrien}, - year = {2015}, - pages = {p34--35}, -} - -@article{xu_causal_2022, - title = {A causal association of {ANKRD37} with human hippocampal volume}, - volume = {27}, - number = {11}, - journal = {Molecular Psychiatry}, - author = {Xu, Jiayuan and Xia, Xianyou and Li, Qiaojun and Dou, Yan and Suo, Xinjun and Sun, Zuhao and Liu, Nana and Han, Yating and Sun, Xiaodi and He, Yukun and Qin, Wen and Zhang, Shijie and Banaschewski, Tobias and Flor, Herta and Grigis, Antoine and Gowland, Penny and {others}}, - year = {2022}, - note = {Publisher: Nature Publishing Group UK London}, - pages = {4432--4445}, -} - -@article{brouwer_genetic_2022, - title = {Genetic variants associated with longitudinal changes in brain structure across the lifespan}, - volume = {25}, - number = {4}, - journal = {Nature neuroscience}, - author = {Brouwer, Rachel M and Klein, Marieke and Grasby, Katrina L and Schnack, Hugo G and Jahanshad, Neda and Teeuw, Jalmar and Thomopoulos, Sophia I and Sprooten, Emma and Franz, Carol E and Gogtay, Nitin and Kremen, William S and Panizzon, Matthew S and Olde Loohuis, Loes M and Whelan, Christopher D and Aghajani, Moji and Alloza, Clara and Alnæs, Dag and Artiges, Eric and Ayesa-Arriola, Rosa and Barker, Gareth J and Bastin, Mark E and Blok, Elisabet and Bøen, Erlend and Breukelaar, Isabella A and Bright, Joanna K and Buimer, Elizabeth E L and Bülow, Robin and Cannon, Dara M and Ciufolini, Simone and Crossley, Nicolas A and Damatac, Christienne G and Dazzan, Paola and de Mol, Casper L and de Zwarte, Sonja M C and Desrivières, Sylvane and Díaz-Caneja, Covadonga M and Doan, Nhat Trung and Dohm, Katharina and Fröhner, Juliane H and Goltermann, Janik and Grigis, Antoine and Grotegerd, Dominik and {others}}, - year = {2022}, - note = {Publisher: Nature Publishing Group US New York}, - pages = {421--432}, -} - -@misc{owens_bayesian_2021, - title = {Bayesian {Causal} {Network} {Modeling} {Suggests} {Adolescent} {Cannabis} {Use} {Promotes} {Accelerated} {Prefrontal} {Cortical} {Thinning}}, - author = {Owens, Max M and Albaugh, Matthew D and Allgaier, Nicholas and Yuan, Dekang and Robert, Gabriel and Cupertino, Renata Basso and Spechler, Philip A. and Juliano, Anthony and Hahn, Sage and Banaschewski, Tobias and Bokde, Arun L.W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny A and {others}}, - year = {2021}, -} - -@article{brouwer_age-dependent_2020, - title = {Age-dependent genetic variants associated with longitudinal changes in brain structure across the lifespan}, - journal = {bioRxiv}, - author = {Brouwer, Rachel M. and Klein, Marieke and Grasby, Katrina L. and Schnack, Hugo G. and Jahanshad, Neda and Teeuw, Jalmar and Thomopoulos, Sophia I. and Sprooten, Emma and Franz, Carol E. and Gogtay, Nitin and Kremen, William S. and Panizzon, Matthew S. and Loohuis, Loes M. Olde and Whelan, Christopher D. and Aghajani, Moji and Alloza, Clara and Alnæs, Dag and Artiges, Eric and Ayesa-Arriola, Rosa and Barker, Gareth J. and Bastin, Mark E. and Blok, Elisabet and Bøen, Erlend and Breukelaar, Isabella A. and Bright, Joanna K. and Buimer, Elizabeth E. L. and Bülow, Robin and Cannon, Dara M. and Ciufolini, Simone and Crossley, Nicolas A. and Damatac, Christienne G. and Dazzan, Paola and Mol, Casper L. de and Zwarte, Sonja M. C. de and Desrivières, Sylvane and Díaz-Caneja, Covadonga M. and Doan, Nhat Trung and Dohm, Katharina and Fröhner, Juliane H. and Goltermann, Janik and Grigis, Antoine and Grotegerd, Dominik and {others}}, - year = {2020}, - note = {Publisher: Cold Spring Harbor Laboratory}, - pages = {2020--04}, -} - -@article{li_anatomical_2022, - title = {Anatomical connectivity profile development constrains medial-lateral topography in the dorsal prefrontal cortex}, - journal = {bioRxiv}, - author = {Li, Wen and Shi, Weiyang and Wang, Haiyan and Li, Jin and Cui, Yue and Li, Kaixin and Cheng, Luqi and Lu, Yuheng and Ma, Liang and Chu, Congying and Song, Ming and Yang, Zhengyi and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and {others}}, - year = {2022}, - note = {Publisher: Cold Spring Harbor Laboratory}, - pages = {2022--02}, -} - -@article{tschorn_differential_2021, - title = {Differential predictors for alcohol use in adolescents as a function of familial risk}, - volume = {11}, - number = {1}, - journal = {Translational psychiatry}, - author = {Tschorn, Mira and Lorenz, Robert C and O’Reilly, Paul F and Reichenberg, Abraham and Banaschewski, Tobias and Bokde, Arun LW and Quinlan, Erin B and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and {others}}, - year = {2021}, - note = {Publisher: Nature Publishing Group UK London}, - pages = {157}, -} - -@misc{korologou-linden_bidirectional_2021, - title = {The bidirectional causal effects of brain morphology across the life course and risk of {Alzheimer}’s disease: {A} cross-cohort comparison and {Mendelian} randomization meta-analysis}, - author = {Korologou-Linden, Roxanna and Xu, Bing and Coulthard, Elizabeth and Walton, Esther and Wearn, Alfie and Hemani, Gibran and White, Tonya and Cecil, Charlotte and Sharp, Tamsin and Tiemeier, Henning and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and {others}}, - year = {2021}, - note = {Publisher: Cold Spring Harbor Laboratory Press}, -} - -@article{wesarg_interaction_2021, - title = {The interaction of child abuse and rs1360780 of the {FKBP5} gene is associated with amygdala resting-state functional connectivity in young adults}, - volume = {42}, - number = {10}, - journal = {Human brain mapping}, - author = {Wesarg, Christiane and Veer, Ilya M and Oei, Nicole Y L and Daedelow, Laura S and Lett, Tristram A and Banaschewski, Tobias and Barker, Gareth J and Bokde, Arun L W and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and {others}}, - year = {2021}, - note = {Publisher: John Wiley \& Sons, Inc. Hoboken, USA}, - pages = {3269--3281}, -} - -@article{claude_identifying_2019, - title = {Identifying a predictive neuroanatomical signature of bipolar disorders reliable across 13 international sites}, - volume = {1}, - journal = {French Journal of Psychiatry}, - author = {Claude, LA and Favre, P and Grigis, A and Piguet, C and Phillips, ML and McDonald, C and Wessa, M and Brambilla, P and Eyler, LT and Polosan, M and {others}}, - year = {2019}, - note = {Publisher: Elsevier}, - pages = {S110--S111}, -} - -@techreport{brouwer_dynamics_2020, - title = {Dynamics of brain structure and its genetic architecture over the lifespan}, - author = {Brouwer, Rachel M. and Klein, Marieke and Grasby, Katrina L. and Schnack, Hugo G. and Jahanshad, Neda and Teeuw, Jalmar and Thomopoulos, Sophia I. and Sprooten, Emma and Franz, Carol E. and Gogtay, Nitin and Kremen, William S. and Panizzon, Matthew S. and Loohuis, Loes M. Olde and Whelan, Christopher D. and Aghajani, Moji and Alloza, Clara and Alnæs, Dag and Artiges, Eric and Ayesa-Arriola, Rosa and Barker, Gareth J. and Blok, Elisabet and Bøen, Erlend and Breukelaar, Isabella A. and Bright, Joanna K. and Buimer, Elizabeth E. L. and Bülow, Robin and Cannon, Dara M. and Ciufolini, Simone and Crossley, Nicolas A. and Damatac, Christienne G. and Dazzan, Paola and Mol, Casper L. de and Zwarte, Sonja M. C. de and Desrivières, Sylvane and Díaz-Caneja, Covadonga M. and Doan, Nhat Trung and Dohm, Katharina and Fröhner, Juliane H. and Goltermann, Janik and Grigis, Antoine and Grotegerd, Dominik and {others}}, - year = {2020}, - note = {Publisher: Strukturelle und funktionelle Organisation des Gehirns}, -} - -@inproceedings{ambroise_multi-view_2023, - title = {Multi-{View} {Variational} {Autoencoders} {Allow} for {Interpretability} {Leveraging} {Digital} {Avatars}: {Application} to the {HBN} {Cohort}}, - copyright = {All rights reserved}, - shorttitle = {Multi-{View} {Variational} {Autoencoders} {Allow} for {Interpretability} {Leveraging} {Digital} {Avatars}}, - doi = {10.1109/ISBI53787.2023.10230552}, - booktitle = {{IEEE} 20th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI}) 2023}, - author = {Ambroise, Corentin and Grigis, Antoine and Duchesnay, Edouard and Frouin, Vincent}, - month = apr, - year = {2023}, -} - -@inproceedings{dufumier_contrastive_2021, - title = {Contrastive {Learning} with {Continuous} {Proxy} {Meta}-{Data} for {3D} {MRI} {Classification}}, - copyright = {All rights reserved}, - url = {https://link.springer.com/chapter/10.1007%2F978-3-030-87196-3_6}, - doi = {10.1007/978-3-030-87196-3_6}, - abstract = {Traditional supervised learning with deep neural networks requires a tremendous amount of labelled data to converge to a good solution. For 3D medical images, it is often impractical to build a large homogeneous annotated dataset for a specific pathology. Self-supervised methods offer a new way to learn a representation of the images in an unsupervised manner with a neural network. In particular, contrastive learning has shown great promises by (almost) matching the performance of fully-supervised CNN on vision tasks. Nonetheless, this method does not take advantage of available meta-data, such as participant's age, viewed as prior knowledge. Here, we propose to leverage continuous proxy metadata, in the contrastive learning framework, by introducing a new loss called y-Aware InfoNCE loss. Specifically, we improve the positive sampling during pre-training by adding more positive examples with similar proxy meta-data with the anchor, assuming they share similar discriminative semantic features.With our method, a 3D CNN model pre-trained on \$10{\textasciicircum}4\$ multi-site healthy brain MRI scans can extract relevant features for three classification tasks: schizophrenia, bipolar diagnosis and Alzheimer's detection. When fine-tuned, it also outperforms 3D CNN trained from scratch on these tasks, as well as state-of-the-art self-supervised methods. Our code is made publicly available here.}, - urldate = {2021-06-17}, - booktitle = {24th {International} {Conference} on {Medical} {Image} {Computing} and {Computer} {Assisted} {Intervention} ({MICCAI}) 2021}, - author = {Dufumier, Benoit and Gori, Pietro and Victor, Julie and Grigis, Antoine and Wessa, Michel and Brambilla, Paolo and Favre, Pauline and Polosan, Mircea and McDonald, Colm and Piguet, Camille Marie and Duchesnay, Edouard}, - month = jun, - year = {2021}, - note = {arXiv: 2106.08808}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition}, - annote = {Comment: MICCAI 2021}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/PEGCWZMR/Dufumier et al. - 2021 - Contrastive Learning with Continuous Proxy Meta-Da.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3NXT9S7C/2106.html:text/html}, -} - -@inproceedings{dufumier_conditional_2021, - title = {Conditional {Alignment} and {Uniformity} for {Contrastive} {Learning} with {Continuous} {Proxy} {Labels}}, - copyright = {All rights reserved}, - url = {https://hal.telecom-paris.fr/hal-03523114}, - abstract = {Contrastive Learning has shown impressive results on natural and medical images, without requiring annotated data. However, a particularity of medical images is the availability of meta-data (such as age or sex) that can be exploited for learning representations. Here, we show that the recently proposed contrastive y-Aware InfoNCE loss, that integrates multi-dimensional meta-data, asymptotically optimizes two properties: conditional alignment and global uniformity. Similarly to [33], conditional alignment means that similar samples should have similar features, but conditionally on the meta-data. Instead, global uniformity means that the (normalized) features should be uniformly distributed on the unit hypersphere, independently of the meta-data. Here, we propose to define conditional uniformity, relying on the meta-data, that repel only samples with dissimilar metadata. We show that direct optimization of both conditional alignment and uniformity improves the representations, in terms of linear evaluation, on both CIFAR-100 and a brain MRI dataset.}, - language = {en}, - urldate = {2022-06-14}, - author = {Dufumier, Benoit and Gori, Pietro and Victor, Julie and Grigis, Antoine and Duchesnay, Edouard}, - month = dec, - year = {2021}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UFCYY32N/hal-03523114v1.html:text/html}, -} - -@inproceedings{louiset_sepvae_2023, - title = {{SepVAE}: a contrastive {VAE} to separate pathological patterns from healthy ones}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - shorttitle = {{SepVAE}}, - url = {http://arxiv.org/abs/2307.06206}, - doi = {10.48550/arXiv.2307.06206}, - abstract = {Contrastive Analysis VAE (CA-VAEs) is a family of Variational auto-encoders (VAEs) that aims at separating the common factors of variation between a background dataset (BG) (i.e., healthy subjects) and a target dataset (TG) (i.e., patients) from the ones that only exist in the target dataset. To do so, these methods separate the latent space into a set of salient features (i.e., proper to the target dataset) and a set of common features (i.e., exist in both datasets). Currently, all models fail to prevent the sharing of information between latent spaces effectively and to capture all salient factors of variation. To this end, we introduce two crucial regularization losses: a disentangling term between common and salient representations and a classification term between background and target samples in the salient space. We show a better performance than previous CA-VAEs methods on three medical applications and a natural images dataset (CelebA). Code and datasets are available on GitHub https://github.com/neurospin-projects/2023\_rlouiset\_sepvae.}, - urldate = {2024-01-31}, - publisher = {arXiv}, - author = {Louiset, Robin and Duchesnay, Edouard and Grigis, Antoine and Dufumier, Benoit and Gori, Pietro}, - month = jul, - year = {2023}, - note = {arXiv:2307.06206 [cs, stat]}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition}, - annote = {Comment: Workshop on Interpretable ML in Healthcare at International Conference on Machine Learning (ICML), Honolulu, Hawaii, USA. 2023}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HW6TQVV4/Louiset et al. - 2023 - SepVAE a contrastive VAE to separate pathological.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3VTKDE2W/2307.html:text/html}, -} - -@inproceedings{louiset_ucsl_2021, - address = {Bilbao, Spain}, - title = {{UCSL} : {A} {Machine} {Learning} {Expectation}-{Maximization} framework for {Unsupervised} {Clustering} driven by {Supervised} {Learning}}, - copyright = {All rights reserved}, - shorttitle = {{UCSL}}, - url = {http://arxiv.org/abs/2107.01988}, - abstract = {Subtype Discovery consists in finding interpretable and consistent sub-parts of a dataset, which are also relevant to a certain supervised task. From a mathematical point of view, this can be defined as a clustering task driven by supervised learning in order to uncover subgroups in line with the supervised prediction. In this paper, we propose a general Expectation-Maximization ensemble framework entitled UCSL (Unsupervised Clustering driven by Supervised Learning). Our method is generic, it can integrate any clustering method and can be driven by both binary classification and regression. We propose to construct a non-linear model by merging multiple linear estimators, one per cluster. Each hyperplane is estimated so that it correctly discriminates - or predict - only one cluster. We use SVC or Logistic Regression for classification and SVR for regression. Furthermore, to perform cluster analysis within a more suitable space, we also propose a dimension-reduction algorithm that projects the data onto an orthonormal space relevant to the supervised task. We analyze the robustness and generalization capability of our algorithm using synthetic and experimental datasets. In particular, we validate its ability to identify suitable consistent sub-types by conducting a psychiatric-diseases cluster analysis with known ground-truth labels. The gain of the proposed method over previous state-of-the-art techniques is about +1.9 points in terms of balanced accuracy. Finally, we make codes and examples available in a scikit-learn-compatible Python package at https://github.com/neurospin-projects/2021\_rlouiset\_ucsl}, - urldate = {2022-02-01}, - booktitle = {Joint {European} {Conference} on {Machine} {Learning} and {Knowledge} {Discovery} in {Databases} ({ECML}/{PKDD}) 2021}, - author = {Louiset, Robin and Gori, Pietro and Dufumier, Benoit and Houenou, Josselin and Grigis, Antoine and Duchesnay, Edouard}, - year = {2021}, - note = {arXiv: 2107.01988}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Computer Science - Artificial Intelligence}, - annote = {Comment: ECML/PKDD 2021}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JX2XAKXU/Louiset et al. - 2021 - UCSL A Machine Learning Expectation-Maximization.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IJHUX3CU/2107.html:text/html}, -} - -@article{dufumier_openbhb_2022, - title = {{OpenBHB}: a {Large}-{Scale} {Multi}-{Site} {Brain} {MRI} {Data}-set for {Age} {Prediction} and {Debiasing}}, - copyright = {All rights reserved}, - issn = {1053-8119}, - shorttitle = {{OpenBHB}}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922007522}, - doi = {10.1016/j.neuroimage.2022.119637}, - abstract = {Prediction of chronological age from neuroimaging in the healthy population is an important issue because the deviations from normal brain age may highlight abnormal trajectories towards brain disorders. As a first step, ML models have emerged to predict chronological age from brain MRI, as a proxy measure of biological age. However, there is currently no consensus w.r.t which Machine Learning (ML) model is best suited for this task, largely because of a lack of public benchmark. Furthermore, new large emerging population neuroimaging datasets are often biased by the acquisition center images are coming from. This bias heavily deteriorates models generalization capacities, especially for Deep Learning (DL) algorithms that are known to overfit rapidly on the simplest features (known as simplicity bias). Here we propose a new public benchmarking resource, namely Open Big Healthy Brains (OpenBHB), along with a challenge for both brain age prediction and site-effect removal through a representation learning framework. OpenBHB is large-scale, gathering {\textgreater}5K 3D T1 brain MRI from Healthy Controls (HC) and highly multi-sites, aggregating {\textgreater}60 centers worldwide and 10 studies. OpenBHB is expected to grow both in terms of available modalities and number of subjects. All OpenBHB datasets are uniformly preprocessed, including quality check, with container technologies that consist in: 3D Voxel-Based Morphometry maps (VBM from CAT12), quasi-raw (simple linear alignment of images), and Surface-Based Morphometry indices (SBM, from FreeSurfer). The OpenBHB challenge is permanent and we provide all tools, materials and tutorials for participants to easily submit and benchmark their model against each other on a public leaderboard.}, - language = {en}, - urldate = {2022-09-20}, - journal = {NeuroImage}, - author = {Dufumier, Benoit and Grigis, Antoine and Victor, Julie and Ambroise, Corentin and Frouin, Vincent and Duchesnay, Edouard}, - month = sep, - year = {2022}, - pages = {119637}, - file = {ScienceDirect Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/XSKTP76F/Dufumier et al. - 2022 - OpenBHB a Large-Scale Multi-Site Brain MRI Data-s.pdf:application/pdf;ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RWBG5P8M/S1053811922007522.html:text/html}, -} - -@article{elandaloussi_understanding_2023, - title = {Understanding the relationship between cerebellar structure and social abilities}, - volume = {14}, - copyright = {All rights reserved}, - issn = {2040-2392}, - url = {https://doi.org/10.1186/s13229-023-00551-8}, - doi = {10.1186/s13229-023-00551-8}, - abstract = {The cerebellum contains more than 50\% of all neurons in the brain and is involved in a broad range of cognitive functions, including social communication and social cognition. Inconsistent atypicalities in the cerebellum have been reported in individuals with autism compared to controls suggesting the limits of categorical case control comparisons. Alternatively, investigating how clinical dimensions are related to neuroanatomical features, in line with the Research Domain Criteria approach, might be more relevant. We hypothesized that the volume of the “cognitive” lobules of the cerebellum would be associated with social difficulties.}, - number = {1}, - urldate = {2023-11-25}, - journal = {Molecular Autism}, - author = {Elandaloussi, Yannis and Floris, Dorothea L. and Coupé, Pierrick and Duchesnay, Edouard and Mihailov, Angeline and Grigis, Antoine and Bègue, Indrit and Victor, Julie and Frouin, Vincent and Leboyer, Marion and Houenou, Josselin and Laidi, Charles}, - month = may, - year = {2023}, - keywords = {MRI, Cerebellum, Autism, Parcellation, Social communication, Volumetry}, - pages = {18}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/37DCRVAS/Elandaloussi et al. - 2023 - Understanding the relationship between cerebellar .pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WRK99LKT/s13229-023-00551-8.html:text/html}, -} - -@article{iftimovici_asynchronous_2023, - title = {Asynchronous neural maturation predicts transition to psychosis}, - copyright = {All rights reserved}, - issn = {1440-1819}, - doi = {10.1111/pcn.13612}, - abstract = {AIM: Neuroimaging-based machine-learning predictions of psychosis onset rely on the hypothesis that structural brain anomalies may reflect the underlying pathophysiology. Yet, current predictors remain difficult to interpret in light of brain structure. Here, we combined an advanced interpretable supervised algorithm and a model of neuroanatomical age to identify the level of brain maturation of the regions most predictive of psychosis. -METHODS: We used the voxel-based morphometry of a healthy control dataset (N = 2024) and a prospective longitudinal UHR cohort (N = 82), of which 27 developed psychosis after one year. In UHR, psychosis was predicted at one year using Elastic-Net-Total-Variation (Enet-TV) penalties within a five-fold cross-validation, providing an interpretable map of distinct predictive regions. Using both the whole brain and each predictive region separately, a brain age predictor was then built and validated in 1605 controls, externally tested in 419 controls from an independent cohort, and applied in UHR. Brain age gaps were computed as the difference between chronological and predicted age, providing a proxy of whole-brain and regional brain maturation. -RESULTS: Psychosis prediction was performant with 80 ± 4\% of area-under-curve and 69 ± 5\% of balanced accuracy (p {\textless} 0.001), and mainly leveraged volumetric increases in the ventromedial prefrontal cortex and decreases in the left precentral gyrus and the right orbitofrontal cortex. These regions were predicted to have, respectively, delayed and accelerated maturational patterns. -CONCLUSION: By combining an interpretable supervised model of conversion to psychosis with a brain age predictor, we showed that inter-regional asynchronous brain maturation underlines the predictive signature of psychosis. This article is protected by copyright. All rights reserved.}, - language = {eng}, - journal = {Psychiatry and Clinical Neurosciences}, - author = {Iftimovici, Anton and Bourgin, Julie and Houenou, Josselin and Gay, Olivier and Grigis, Antoine and Victor, Julie and Chaumette, Boris and Krebs, Marie-Odile and Duchesnay, Edouard and {ICAAR-plus Study Group.}}, - month = oct, - year = {2023}, - pmid = {37904327}, - keywords = {neurodevelopment, psychosis, brain age, machine-learning, voxel-based morphometry}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EXWGEDSW/Iftimovici et al. - 2023 - Asynchronous neural maturation predicts transition.pdf:application/pdf}, -} - -@article{piguet_irritability_2021, - title = {Irritability {Is} {Associated} {With} {Decreased} {Cortical} {Surface} {Area} and {Anxiety} {With} {Decreased} {Gyrification} {During} {Brain} {Development}}, - volume = {12}, - copyright = {All rights reserved}, - issn = {1664-0640}, - doi = {10.3389/fpsyt.2021.744419}, - abstract = {Background: Brain development is of utmost importance for the emergence of psychiatric disorders, as the most severe of them arise before 25 years old. However, little is known regarding how early transdiagnostic symptoms, in a dimensional framework, are associated with cortical development. Anxiety and irritability are central vulnerability traits for subsequent mood and anxiety disorders. In this study, we investigate how these dimensions are related to structural changes in the brain to understand how they may increase the transition risk to full-blown disorders. Methods: We used the opportunity of an open access developmental cohort, the Healthy Brain Network, to investigate associations between cortical surface markers and irritability and anxiety scores as measured by parents and self-reports. Results: We found that in 658 young people (with a mean age of 11.6) the parental report of irritability is associated with decreased surface area in the bilateral rostral prefrontal cortex and the precuneus. Furthermore, parental reports of anxiety were associated with decreased local gyrification index in the anterior cingulate cortex and dorsomedial prefrontal cortex. Conclusions: These results are consistent with current models of emotion regulation network maturation, showing decreased surface area or gyrification index in regions associated with impaired affective control in mood and anxiety disorders. Our results highlight how dimensional traits may increase vulnerability for these disorders.}, - language = {eng}, - journal = {Frontiers in Psychiatry}, - author = {Piguet, Camille and Mihailov, Angeline and Grigis, Antoine and Laidi, Charles and Duchesnay, Edouard and Houenou, Josselin}, - year = {2021}, - pmid = {34630188}, - pmcid = {PMC8492928}, - keywords = {MRI, anxiety, development, dimensional model, gyrification index, irritability}, - pages = {744419}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6S2MLA6N/Piguet et al. - 2021 - Irritability Is Associated With Decreased Cortical.pdf:application/pdf}, -} - -@article{poiret_fast_2023, - title = {A fast and robust hippocampal subfields segmentation: {HSF} revealing lifespan volumetric dynamics}, - volume = {17}, - copyright = {All rights reserved}, - issn = {1662-5196}, - shorttitle = {A fast and robust hippocampal subfields segmentation}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2023.1130845}, - abstract = {The hippocampal subfields, pivotal to episodic memory, are distinct both in terms of cyto- and myeloarchitectony. Studying the structure of hippocampal subfields in vivo is crucial to understand volumetric trajectories across the lifespan, from the emergence of episodic memory during early childhood to memory impairments found in older adults. However, segmenting hippocampal subfields on conventional MRI sequences is challenging because of their small size. Furthermore, there is to date no unified segmentation protocol for the hippocampal subfields, which limits comparisons between studies. Therefore, we introduced a novel segmentation tool called HSF short for hippocampal segmentation factory, which leverages an end-to-end deep learning pipeline. First, we validated HSF against currently used tools (ASHS, HIPS, and HippUnfold). Then, we used HSF on 3,750 subjects from the HCP development, young adults, and aging datasets to study the effect of age and sex on hippocampal subfields volumes. Firstly, we showed HSF to be closer to manual segmentation than other currently used tools (p {\textless} 0.001), regarding the Dice Coefficient, Hausdorff Distance, and Volumetric Similarity. Then, we showed differential maturation and aging across subfields, with the dentate gyrus being the most affected by age. We also found faster growth and decay in men than in women for most hippocampal subfields. Thus, while we introduced a new, fast and robust end-to-end segmentation tool, our neuroanatomical results concerning the lifespan trajectories of the hippocampal subfields reconcile previous conflicting results.}, - urldate = {2023-11-25}, - journal = {Frontiers in Neuroinformatics}, - author = {Poiret, Clement and Bouyeure, Antoine and Patil, Sandesh and Grigis, Antoine and Duchesnay, Edouard and Faillot, Matthieu and Bottlaender, Michel and Lemaitre, Frederic and Noulhiane, Marion}, - year = {2023}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/9MA6ZDZR/Poiret et al. - 2023 - A fast and robust hippocampal subfields segmentati.pdf:application/pdf}, -} - -@article{poiret_attention-gated_2024, - title = {Attention-gated {3D} {CapsNet} for robust hippocampal segmentation}, - volume = {11}, - copyright = {All rights reserved}, - issn = {2329-4302}, - doi = {10.1117/1.JMI.11.1.014003}, - abstract = {PURPOSE: The hippocampus is organized in subfields (HSF) involved in learning and memory processes and widely implicated in pathologies at different ages of life, from neonatal hypoxia to temporal lobe epilepsy or Alzheimer's disease. Getting a highly accurate and robust delineation of sub-millimetric regions such as HSF to investigate anatomo-functional hypotheses is a challenge. One of the main difficulties encountered by those methodologies is related to the small size and anatomical variability of HSF, resulting in the scarcity of manual data labeling. Recently introduced, capsule networks solve analogous problems in medical imaging, providing deep learning architectures with rotational equivariance. Nonetheless, capsule networks are still two-dimensional and unassessed for the segmentation of HSF. -APPROACH: We released a public 3D Capsule Network (3D-AGSCaps, https://github.com/clementpoiret/3D-AGSCaps) and compared it to equivalent architectures using classical convolutions on the automatic segmentation of HSF on small and atypical datasets (incomplete hippocampal inversion, IHI). We tested 3D-AGSCaps on three datasets with manually labeled hippocampi. -RESULTS: Our main results were: (1) 3D-AGSCaps produced segmentations with a better Dice Coefficient compared to CNNs on rotated hippocampi (p=0.004, cohen's d=0.179); (2) on typical subjects, 3D-AGSCaps produced segmentations with a Dice coefficient similar to CNNs while having 15 times fewer parameters (2.285M versus 35.069M). This may greatly facilitate the study of atypical subjects, including healthy and pathological cases like those presenting an IHI. -CONCLUSION: We expect our newly introduced 3D-AGSCaps to allow a more accurate and fully automated segmentation on atypical populations, small datasets, as well as on and large cohorts where manual segmentations are nearly intractable.}, - language = {eng}, - number = {1}, - journal = {Journal of Medical Imaging (Bellingham, Wash.)}, - author = {Poiret, Clement and Bouyeure, Antoine and Patil, Sandesh and Boniteau, Cécile and Duchesnay, Edouard and Grigis, Antoine and Lemaitre, Frederic and Noulhiane, Marion}, - month = jan, - year = {2024}, - pmid = {38173654}, - pmcid = {PMC10760147}, - keywords = {MRI, convolutional neural networks, deep learning, equivariance, hippocampal subfields}, - pages = {014003}, -} - -@article{guevara_disentangling_2022, - title = {Disentangling the variability of the superficial white matter organization using regional-tractogram-based population stratification}, - volume = {255}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922003214}, - doi = {10.1016/j.neuroimage.2022.119197}, - abstract = {Each variation of the cortical folding pattern implies a particular rearrangement of the geometry of the fibers of the underlying white matter. While this rearrangement only impacts the ends of the long pathways, it may affect most of the trajectory of the short bundles. Therefore, mapping the short fibers of the human brain using diffusion-based tractography requires a dedicated strategy to overcome the variability of the folding patterns. In this paper, we propose a fiber-based stratification strategy splitting the population into homogeneous groups for disentangling the superficial white matter bundle organization. This strategy introduces a new refined fiber distance which includes angular considerations for inferring fine-grained atlases of the short bundles surrounding a specific sulcus and a subtractogram distance that quantifies the similitude between fiber sets of two different subjects. The stratification splits the population into groups with similar regional fiber organization using manifold learning. We first successfully test the hypothesis that the main source of variability of the regional fiber organization is the variability of the regional folding pattern. Then, in each group, we proceed with the automatic identification of the most stable bundles, at a higher granularity level than what can be achieved with the non-stratified whole population, enabling the disentanglement of the very variable configuration of the short fibers. Finally, the method searches for bundle correspondence across groups to build a population level atlas. As a proof of concept, the atlas refinement achieved by this strategy is illustrated for the fibers that surround the central sulcus and the superior temporal sulcus using the HCP dataset.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Guevara, Miguel and Sun, Zhong-Yi and Guevara, Pamela and Rivière, Denis and Grigis, Antoine and Poupon, Cyril and Mangin, Jean-François}, - month = jul, - year = {2022}, - keywords = {Tractography, Short association fibers, Diffusion-weighted imaging, Cortical variability, Superficial white matter, U-fibers, White matter bundle}, - pages = {119197}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EWUQUNGE/S1053811922003214.html:text/html}, -} - -@article{gazula_federated_2023, - title = {Federated {Analysis} in {COINSTAC} {Reveals} {Functional} {Network} {Connectivity} and {Spectral} {Links} to {Smoking} and {Alcohol} {Consumption} in {Nearly} 2,000 {Adolescent} {Brains}}, - volume = {21}, - issn = {1559-0089}, - url = {https://doi.org/10.1007/s12021-022-09604-4}, - doi = {10.1007/s12021-022-09604-4}, - abstract = {With the growth of decentralized/federated analysis approaches in neuroimaging, the opportunities to study brain disorders using data from multiple sites has grown multi-fold. One such initiative is the Neuromark, a fully automated spatially constrained independent component analysis (ICA) that is used to link brain network abnormalities among different datasets, studies, and disorders while leveraging subject-specific networks. In this study, we implement the neuromark pipeline in COINSTAC, an open-source neuroimaging framework for collaborative/decentralized analysis. Decentralized exploratory analysis of nearly 2000 resting-state functional magnetic resonance imaging datasets collected at different sites across two cohorts and co-located in different countries was performed to study the resting brain functional network connectivity changes in adolescents who smoke and consume alcohol. Results showed hypoconnectivity across the majority of networks including sensory, default mode, and subcortical domains, more for alcohol than smoking, and decreased low frequency power. These findings suggest that global reduced synchronization is associated with both tobacco and alcohol use. This proof-of-concept work demonstrates the utility and incentives associated with large-scale decentralized collaborations spanning multiple sites.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Neuroinformatics}, - author = {Gazula, Harshvardhan and Rootes-Murdy, Kelly and Holla, Bharath and Basodi, Sunitha and Zhang, Zuo and Verner, Eric and Kelly, Ross and Murthy, Pratima and Chakrabarti, Amit and Basu, Debasish and Bhagyalakshmi Nanjayya, Subodh and Lenin Singh, Rajkumar and Lourembam Singh, Roshan and Kalyanram, Kartik and Kartik, Kamakshi and Kalyanaraman, Kumaran and Ghattu, Krishnaveni and Kuriyan, Rebecca and Kurpad, Sunita Simon and Barker, Gareth J. and Bharath, Rose Dawn and Desrivieres, Sylvane and Purushottam, Meera and Orfanos, Dimitri Papadopoulos and Sharma, Eesha and Hickman, Matthew and Toledano, Mireille and Vaidya, Nilakshi and Banaschewski, Tobias and Bokde, Arun L. W. and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillére Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Paus, Tomás and Poustka, Luise and Fröhner, Juliane H. and Robinson, Lauren and Smolka, Michael N. and Walter, Henrik and Winterer, Jeanne and Whelan, Robert and Turner, Jessica A. and Sarwate, Anand D. and Plis, Sergey M. and Benegal, Vivek and Schumann, Gunter and Calhoun, Vince D. and {IMAGEN Consortium}}, - month = apr, - year = {2023}, - keywords = {IMAGEN, Adolescent health, COINSTAC, CVEDA, Decentralized analysis, Neuromark}, - pages = {287--301}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/G2F8JJJP/Gazula et al. - 2023 - Federated Analysis in COINSTAC Reveals Functional .pdf:application/pdf}, -} - -@article{xie_shared_2023, - title = {A shared neural basis underlying psychiatric comorbidity}, - volume = {29}, - copyright = {2023 The Author(s)}, - issn = {1546-170X}, - url = {https://www.nature.com/articles/s41591-023-02317-4}, - doi = {10.1038/s41591-023-02317-4}, - abstract = {Recent studies proposed a general psychopathology factor underlying common comorbidities among psychiatric disorders. However, its neurobiological mechanisms and generalizability remain elusive. In this study, we used a large longitudinal neuroimaging cohort from adolescence to young adulthood (IMAGEN) to define a neuropsychopathological (NP) factor across externalizing and internalizing symptoms using multitask connectomes. We demonstrate that this NP factor might represent a unified, genetically determined, delayed development of the prefrontal cortex that further leads to poor executive function. We also show this NP factor to be reproducible in multiple developmental periods, from preadolescence to early adulthood, and generalizable to the resting-state connectome and clinical samples (the ADHD-200 Sample and the STRATIFY \& ESTRA Project). In conclusion, we identify a reproducible and general neural basis underlying symptoms of multiple mental health disorders, bridging multidimensional evidence from behavioral, neuroimaging and genetic substrates. These findings may help to develop new therapeutic interventions for psychiatric comorbidities.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Nature Medicine}, - author = {Xie, Chao and Xiang, Shitong and Shen, Chun and Peng, Xuerui and Kang, Jujiao and Li, Yuzhu and Cheng, Wei and He, Shiqi and Bobou, Marina and Broulidakis, M. John and van Noort, Betteke Maria and Zhang, Zuo and Robinson, Lauren and Vaidya, Nilakshi and Winterer, Jeanne and Zhang, Yuning and King, Sinead and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Lemaître, Hervé and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Schmidt, Ulrike and Sinclair, Julia and Smolka, Michael N. and Stringaris, Argyris and Walter, Henrik and Whelan, Robert and Desrivières, Sylvane and Sahakian, Barbara J. and Robbins, Trevor W. and Schumann, Gunter and Jia, Tianye and Feng, Jianfeng}, - month = may, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychiatric disorders, Cognitive control}, - pages = {1232--1242}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JWPTJBLY/Xie et al. - 2023 - A shared neural basis underlying psychiatric comor.pdf:application/pdf}, -} - -@article{albaugh_differential_2023, - title = {Differential associations of adolescent versus young adult cannabis initiation with longitudinal brain change and behavior}, - copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {1476-5578}, - url = {https://www.nature.com/articles/s41380-023-02148-2}, - doi = {10.1038/s41380-023-02148-2}, - abstract = {Leveraging {\textasciitilde}10 years of prospective longitudinal data on 704 participants, we examined the effects of adolescent versus young adult cannabis initiation on MRI-assessed cortical thickness development and behavior. Data were obtained from the IMAGEN study conducted across eight European sites. We identified IMAGEN participants who reported being cannabis-naïve at baseline and had data available at baseline, 5-year, and 9-year follow-up visits. Cannabis use was assessed with the European School Survey Project on Alcohol and Drugs. T1-weighted MR images were processed through the CIVET pipeline. Cannabis initiation occurring during adolescence (14–19 years) and young adulthood (19–22 years) was associated with differing patterns of longitudinal cortical thickness change. Associations between adolescent cannabis initiation and cortical thickness change were observed primarily in dorso- and ventrolateral portions of the prefrontal cortex. In contrast, cannabis initiation occurring between 19 and 22 years of age was associated with thickness change in temporal and cortical midline areas. Follow-up analysis revealed that longitudinal brain change related to adolescent initiation persisted into young adulthood and partially mediated the association between adolescent cannabis use and past-month cocaine, ecstasy, and cannabis use at age 22. Extent of cannabis initiation during young adulthood (from 19 to 22 years) had an indirect effect on psychotic symptoms at age 22 through thickness change in temporal areas. Results suggest that developmental timing of cannabis exposure may have a marked effect on neuroanatomical correlates of cannabis use as well as associated behavioral sequelae. Critically, this work provides a foundation for neurodevelopmentally informed models of cannabis exposure in humans.}, - language = {en}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Albaugh, Matthew D. and Owens, Max M. and Juliano, Anthony and Ottino-Gonzalez, Jonatan and Cupertino, Renata and Cao, Zhipeng and Mackey, Scott and Lepage, Claude and Rioux, Pierre and Evans, Alan and Banaschewski, Tobias and Bokde, Arun L. W. and Conrod, Patricia and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Potter, Alexandra and Garavan, Hugh}, - month = jun, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Neuroscience, Addiction}, - pages = {1--10}, -} - -@article{de_matos_temporo-basal_2023, - title = {Temporo-basal sulcal connections: a manual annotation protocol and an investigation of sexual dimorphism and heritability}, - volume = {228}, - issn = {1863-2661}, - shorttitle = {Temporo-basal sulcal connections}, - url = {https://doi.org/10.1007/s00429-023-02663-6}, - doi = {10.1007/s00429-023-02663-6}, - abstract = {The temporo-basal region of the human brain is composed of the collateral, the occipito-temporal, and the rhinal sulci. We manually rated (using a novel protocol) the connections between rhinal/collateral (RS-CS), collateral/occipito-temporal (CS-OTS) and rhinal/occipito-temporal (RS-OTS) sulci, using the MRI of nearly 3400 individuals including around 1000 twins. We reported both the associations between sulcal polymorphisms as well with a wide range of demographics (e.g. age, sex, handedness). Finally, we also estimated the heritability, and the genetic correlation between sulcal connections. We reported the frequency of the sulcal connections in the general population, which were hemisphere dependent. We found a sexual dimorphism of the connections, especially marked in the right hemisphere, with a CS-OTS connection more frequent in females (approximately 35–40\% versus 20–25\% in males) and an RS-CS connection more common in males (approximately 40–45\% versus 25–30\% in females). We confirmed associations between sulcal connections and characteristics of incomplete hippocampal inversion (IHI). We estimated the broad sense heritability to be 0.28–0.45 for RS-CS and CS-OTS connections, with hints of dominant contribution for the RS-CS connection. The connections appeared to share some of their genetic causing factors as indicated by strong genetic correlations. Heritability appeared much smaller for the (rarer) RS-OTS connection.}, - language = {en}, - number = {6}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {de Matos, Kevin and Cury, Claire and Chougar, Lydia and Strike, Lachlan T. and Rolland, Thibault and Riche, Maximilien and Hemforth, Lisa and Martin, Alexandre and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Frouin, Vincent and Bach Cuadra, Meritxell and Colliot, Olivier and Couvy-Duchesne, Baptiste and {IMAGEN Consortium}}, - month = jul, - year = {2023}, - keywords = {Collateral sulcus, Occipito-temporal sulcus, Rhinal sulcus, Sulcal variability, Temporal lobe, Twin heritability}, - pages = {1459--1478}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AW47W7SD/de Matos et al. - 2023 - Temporo-basal sulcal connections a manual annotat.pdf:application/pdf}, -} - -@article{prignitz_role_2023, - title = {The {Role} of {Empathy} in {Alcohol} {Use} of {Bullying} {Perpetrators} and {Victims}: {Lower} {Personal} {Empathic} {Distress} {Makes} {Male} {Perpetrators} of {Bullying} {More} {Vulnerable} to {Alcohol} {Use}}, - volume = {20}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - issn = {1660-4601}, - shorttitle = {The {Role} of {Empathy} in {Alcohol} {Use} of {Bullying} {Perpetrators} and {Victims}}, - url = {https://www.mdpi.com/1660-4601/20/13/6286}, - doi = {10.3390/ijerph20136286}, - abstract = {Bullying often results in negative coping in victims, including an increased consumption of alcohol. Recently, however, an increase in alcohol use has also been reported among perpetrators of bullying. The factors triggering this pattern are still unclear. We investigated the role of empathy in the interaction between bullying and alcohol use in an adolescent sample (IMAGEN) at age 13.97 (±0.53) years (baseline (BL), N = 2165, 50.9\% female) and age 16.51 (±0.61) years (follow-up 1 (FU1), N = 1185, 54.9\% female). General empathic distress served as a significant moderator of alcohol use in perpetrators (F9, 493 = 17.978, p {\textless} 0.01), which was specific for males and FU1. Male perpetrators, who are generally less sensitive to distress, might thus be more vulnerable to alcohol abuse.}, - language = {en}, - number = {13}, - urldate = {2024-03-12}, - journal = {International Journal of Environmental Research and Public Health}, - author = {Prignitz, Maren and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Robinson, Lauren and Smolka, Michael N. and Walter, Henrik and Winterer, Jeanne M. and Whelan, Robert and Schumann, Gunter and Nees, Frauke and Flor, Herta and on behalf of the IMAGEN Consortium}, - month = jan, - year = {2023}, - note = {Number: 13 -Publisher: Multidisciplinary Digital Publishing Institute}, - keywords = {adolescence, alcohol, bullying, distress, empathy}, - pages = {6286}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QPYVVZPI/Prignitz et al. - 2023 - The Role of Empathy in Alcohol Use of Bullying Per.pdf:application/pdf}, -} - -@article{kuhn_trees_2023, - title = {Trees for brains: {Current} residential tree cover density and its association with brain structure in young adults}, - volume = {89}, - issn = {0272-4944}, - shorttitle = {Trees for brains}, - url = {https://www.sciencedirect.com/science/article/pii/S0272494423000956}, - doi = {10.1016/j.jenvp.2023.102047}, - abstract = {Previous research has suggested an association between living environment during the first 15 years of life and brain structure. More precisely, urbanicity during upbringing has been shown to be negatively related to prefrontal cortex grey matter. The present study focusses instead on the current living environment of 677 younger adults recruited from different cities across Europe. We observed a positive association between amount of tree cover density, in a radius of 500m around the current home address and grey matter volume in right orbitofrontal cortex (rOFC). Of note, the volume of the rOFC cluster identified, showed a positive association with cognitive performance in the Wechsler Adult Intelligence Scale, namely in the verbal and spatial ability domain (Vocabulary, Block Design), and a negative association with both, self-reported and behavioural markers of impulsivity (delay discounting). Moreover, rOFC volume showed a negative association with self-reported alcohol use problems. The data provide strong evidence in favour of a link between geographical features of the current living environment (particularly trees) and brain structure above and beyond childhood and upbringing. Interestingly, the respective brain correlates are associated with cognitive, behavioural and personality characteristics which have been considered as risk factors for several psychiatric disorders. Environmental neuroscience may in the long run provide a knowledge base for evidence-based urban landscape planning to facilitate mental health.}, - urldate = {2024-03-12}, - journal = {Journal of Environmental Psychology}, - author = {Kühn, Simone and Banaschewski, Tobias and Bokde, Arun L. W. and Büchel, Christian and Burke Quinlan, Erin and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie Laure and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Vaidya, Nilakshi and Meyer-Lindenberg, Andreas and Gallinat, Jürgen}, - month = aug, - year = {2023}, - keywords = {Neuroimaging, Voxel-based morphometry, Environmental neuroscience, Exposure, Tree cover density}, - pages = {102047}, -} - -@article{nweze_trajectories_2023, - title = {Trajectories of cortical structures associated with stress across adolescence: a bivariate latent change score approach}, - volume = {64}, - copyright = {© 2023 The Authors. Journal of Child Psychology and Psychiatry published by John Wiley \& Sons Ltd on behalf of Association for Child and Adolescent Mental Health.}, - issn = {1469-7610}, - shorttitle = {Trajectories of cortical structures associated with stress across adolescence}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jcpp.13793}, - doi = {10.1111/jcpp.13793}, - abstract = {Background Stress exposure in childhood and adolescence has been linked to reductions in cortical structures and cognitive functioning. However, to date, most of these studies have been cross-sectional, limiting the ability to make long-term inferences, given that most cortical structures continue to develop through adolescence. Methods Here, we used a subset of the IMAGEN population cohort sample (N = 502; assessment ages: 14, 19, and 22 years; mean age: 21.945 years; SD = 0.610) to understand longitudinally the long-term interrelations between stress, cortical development, and cognitive functioning. To these ends, we first used a latent change score model to examine four bivariate relations – assessing individual differences in change in the relations between adolescent stress exposure and volume, surface area, and cortical thickness of cortical structures, as well as cognitive outcomes. Second, we probed for indirect neurocognitive effects linking stress to cortical brain structures and cognitive functions using rich longitudinal mediation modeling. Results Latent change score modeling showed that greater baseline adolescence stress at age 14 predicted a small reduction in the right anterior cingulate volume (Std. β = −.327, p = .042, 95\% CI [−0.643, −0.012]) and right anterior cingulate surface area (Std. β = −.274, p = .038, 95\% CI [−0.533, −0.015]) across ages 14–22. These effects were very modest in nature and became nonsignificant after correcting for multiple comparisons. Our longitudinal analyses found no evidence of indirect effects in the two neurocognitive pathways linking adolescent stress to brain and cognitive outcomes. Conclusion Findings shed light on the impact of stress on brain reductions, particularly in the prefrontal cortex that have consistently been implicated in the previous cross-sectional studies. However, the magnitude of effects observed in our study is smaller than that has been reported in past cross-sectional work. This suggests that the potential impact of stress during adolescence on brain structures may likely be more modest than previously noted.}, - language = {en}, - number = {8}, - urldate = {2024-03-12}, - journal = {Journal of Child Psychology and Psychiatry}, - author = {Nweze, Tochukwu and Banaschewski, Tobias and Ajaelu, Cyracius and Okoye, Chukwuemeka and Ezenwa, Michael and Whelan, Robert and Papadopoulos Orfanos, Dimitri and Bokde, Arun L.W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Schumann, Gunter and Hanson, Jamie L. and Consortium, Imagen}, - year = {2023}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jcpp.13793}, - keywords = {Stress, bivariate latent change score model, cognitive functioning, cortical development, longitudinal mediation analysis, longitudinal models}, - pages = {1159--1175}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3AUT2UY9/Nweze et al. - 2023 - Trajectories of cortical structures associated wit.pdf:application/pdf}, -} - -@article{xiang_association_2023, - title = {Association between {vmPFC} gray matter volume and smoking initiation in adolescents}, - volume = {14}, - copyright = {2023 The Author(s)}, - issn = {2041-1723}, - url = {https://www.nature.com/articles/s41467-023-40079-2}, - doi = {10.1038/s41467-023-40079-2}, - abstract = {Smoking of cigarettes among young adolescents is a pressing public health issue. However, the neural mechanisms underlying smoking initiation and sustenance during adolescence, especially the potential causal interactions between altered brain development and smoking behaviour, remain elusive. Here, using large longitudinal adolescence imaging genetic cohorts, we identify associations between left ventromedial prefrontal cortex (vmPFC) gray matter volume (GMV) and subsequent self-reported smoking initiation, and between right vmPFC GMV and the maintenance of smoking behaviour. Rule-breaking behaviour mediates the association between smaller left vmPFC GMV and smoking behaviour based on longitudinal cross-lagged analysis and Mendelian randomisation. In contrast, smoking behaviour associated longitudinal covariation of right vmPFC GMV and sensation seeking (especially hedonic experience) highlights a potential reward-based mechanism for sustaining addictive behaviour. Taken together, our findings reveal vmPFC GMV as a possible biomarker for the early stages of nicotine addiction, with implications for its prevention and treatment.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Nature Communications}, - author = {Xiang, Shitong and Jia, Tianye and Xie, Chao and Cheng, Wei and Chaarani, Bader and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Büchel, Christian and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny A. and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Garavan, Hugh and Schumann, Gunter and Sahakian, Barbara J. and Robbins, Trevor W. and Feng, Jianfeng}, - month = aug, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Cognitive neuroscience, Predictive markers, Addiction, Genetics of the nervous system}, - pages = {4684}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/APDKY6LA/Xiang et al. - 2023 - Association between vmPFC gray matter volume and s.pdf:application/pdf}, -} - -@article{pijnenburg_autistic_2023, - title = {Autistic traits and alcohol use in adolescents within the general population}, - volume = {32}, - issn = {1435-165X}, - url = {https://doi.org/10.1007/s00787-022-01970-3}, - doi = {10.1007/s00787-022-01970-3}, - abstract = {It has been suggested that autistic traits are associated with less frequent alcohol use in adolescence. Our study seeks to examine the relationship between autistic traits and alcohol use in a large adolescent population. Leveraging data from the IMAGEN cohort, including 2045 14-year-old adolescents that were followed-up to age 18, we selected items on social preference/skills and rigidity from different questionnaires. We used linear regression models to (1) test the effect of the sum scores on the prevalence of alcohol use (AUDIT-C) over time, (2) explore the relationship between autistic traits and alcohol use patterns, and (3) explore the specific effect of each autistic trait on alcohol use. Higher scores on the selected items were associated with trajectories of less alcohol use from the ages between 14 and 18 (b = − 0.030; CI 95\% = − 0.042, − 0.017; p {\textless} 0.001). Among adolescents who used alcohol, those who reported more autistic traits were also drinking less per occasion than their peers and were less likely to engage in binge drinking. We found significant associations between alcohol use and social preference (p {\textless} 0.001), nervousness for new situations (p = 0.001), and detail orientation (p {\textless} 0.001). Autistic traits (social impairment, detail orientation, and anxiety) may buffer against alcohol use in adolescence.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {European Child \& Adolescent Psychiatry}, - author = {Pijnenburg, Lisa J. and Kaplun, Anais and de Haan, Lieuwe and Janecka, Magdalena and Smith, Lauren and Reichenberg, Abraham and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Velthorst, Eva and {IMAGEN Consortium}}, - month = sep, - year = {2023}, - keywords = {Adolescence, Alcohol use, Autistic traits, Social preference}, - pages = {1633--1642}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TMJSP5N7/Pijnenburg et al. - 2023 - Autistic traits and alcohol use in adolescents wit.pdf:application/pdf}, -} - -@article{xue_covariation_2023, - title = {Covariation of preadult environmental exposures, adult brain imaging phenotypes, and adult personality traits}, - volume = {28}, - copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {1476-5578}, - url = {https://www.nature.com/articles/s41380-023-02261-2}, - doi = {10.1038/s41380-023-02261-2}, - abstract = {Exposure to preadult environmental exposures may have long-lasting effects on mental health by affecting the maturation of the brain and personality, two traits that interact throughout the developmental process. However, environment-brain-personality covariation patterns and their mediation relationships remain unclear. In 4297 healthy participants (aged 18–30 years), we combined sparse multiple canonical correlation analysis with independent component analysis to identify the three-way covariation patterns of 59 preadult environmental exposures, 760 adult brain imaging phenotypes, and five personality traits, and found two robust environment-brain-personality covariation models with sex specificity. One model linked greater stress and less support to weaker functional connectivity and activity in the default mode network, stronger activity in subcortical nuclei, greater thickness and volume in the occipital, parietal and temporal cortices, and lower agreeableness, consciousness and extraversion as well as higher neuroticism. The other model linked higher urbanicity and better socioeconomic status to stronger functional connectivity and activity in the sensorimotor network, smaller volume and surface area and weaker functional connectivity and activity in the medial prefrontal cortex, lower white matter integrity, and higher openness to experience. We also conducted mediation analyses to explore the potential bidirectional mediation relationships between adult brain imaging phenotypes and personality traits with the influence of preadult environmental exposures and found both environment-brain-personality and environment-personality-brain pathways. We finally performed moderated mediation analyses to test the potential interactions between macro- and microenvironmental exposures and found that one category of exposure moderated the mediation pathways of another category of exposure. These results improve our understanding of the effects of preadult environmental exposures on the adult brain and personality traits and may facilitate the design of targeted interventions to improve mental health by reducing the impact of adverse environmental exposures.}, - language = {en}, - number = {11}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Xue, Kaizhong and Gao, Bo and Chen, Feng and Wang, Meiyun and Cheng, Jingliang and Zhang, Bing and Zhu, Wenzhen and Qiu, Shijun and Geng, Zuojun and Zhang, Xiaochu and Cui, Guangbin and Yu, Yongqiang and Zhang, Quan and Liao, Weihua and Zhang, Hui and Xu, Xiaojun and Han, Tong and Qin, Wen and Liu, Feng and Liang, Meng and Guo, Lining and Xu, Qiang and Xu, Jiayuan and Fu, Jilian and Zhang, Peng and Li, Wei and Shi, Dapeng and Wang, Caihong and Lui, Su and Yan, Zhihan and Zhang, Jing and Li, Jiance and Wang, Dawei and Xian, Junfang and Xu, Kai and Zuo, Xi-Nian and Zhang, Longjiang and Ye, Zhaoxiang and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Poustka, Luise and Hohmann, Sarah and Holz, Nathalie and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Shen, Wen and Miao, Yanwei and Yu, Chunshui}, - month = nov, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychology, Neuroscience}, - pages = {4853--4866}, -} - -@article{gros_whole-brain_2024, - title = {Whole-brain gray matter maturation trajectories associated with autistic traits from adolescence to early adulthood}, - volume = {229}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-023-02710-2}, - doi = {10.1007/s00429-023-02710-2}, - abstract = {A growing number of evidence supports a continued distribution of autistic traits in the general population. However, brain maturation trajectories of autistic traits as well as the influence of sex on these trajectories remain largely unknown. We investigated the association of autistic traits in the general population, with longitudinal gray matter (GM) maturation trajectories during the critical period of adolescence. We assessed 709 community-based adolescents (54.7\% women) at age 14 and 22. After testing the effect of sex, we used whole-brain voxel-based morphometry to measure longitudinal GM volumes changes associated with autistic traits measured by the Social Responsiveness Scale (SRS) total and sub-scores. In women, we observed that the SRS was associated with slower GM volume decrease globally and in the left parahippocampus and middle temporal gyrus. The social communication sub-score correlated with slower GM volume decrease in the left parahippocampal, superior temporal gyrus, and pallidum; and the social cognition sub-score correlated with slower GM volume decrease in the left middle temporal gyrus, the right ventromedial prefrontal and orbitofrontal cortex. No longitudinal association was found in men. Autistic traits in young women were found to be associated with specific brain trajectories in regions of the social brain and the reward circuit known to be involved in Autism Spectrum Disorder. These findings support both the hypothesis of an earlier GM maturation associated with autistic traits in adolescence and of protective mechanisms in women. They advocate for further studies on brain trajectories associated with autistic traits in women.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Gros, Guillaume and Miranda Marcos, Ruben and Latrille, Anthony and Saitovitch, Ana and Gollier-Briant, Fanny and Fossati, Philippe and Schmidt, Liane and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Holz, Nathalie and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Lemaitre, Hervé and Vulser, Hélène and Artiges, Eric and Aydin, Semiha and Bach, Christine and Banaschewski, Tobias and Barbot, Alexis and Barker, Gareth and Bokde, Arun and Bordas, Nadège and Bricaud, Zuleima and Bromberg, Uli and Bruehl, Ruediger and Büchel, Christian and Cattrell, Anna and Conrod, Patricia and Desrivieres, Sylvane and Fadai, Tahmine and Filippi, Irina and Flor, Herta and Frouin, Vincent and Galinowski, André and Gallinat, Jürgen and Garavan, Hugh and Gollier-Briant, Fanny and Gourlan, Chantal and Gowland, Penny and Guldner, Stella and Heinz, Andreas and Ittermann, Bernd and Jia, Tianye and Lemaitre, Hervé and Martinot, Jean-Luc and Massicotte, Jessica and Miranda, Ruben and Müller, Kathrin and Nees, Frauke and Nymberg, Charlotte and Martinot, Marie Laure Paillère and Paus, Tomas and Pausova, Zdenka and Poline, Jean-Baptiste and Poustka, Luise and Reuter, Jan and Rogers, John and Ruggeri, Barbara and Sarvasmaa, Anna S. and Schmäl, Christine and Schumann, Gunter and Struve, Maren and Smolka, Michael and Sommer, Wolfgang and Vulser, Hélène and Walter, Henrik and Whelan, Robert and {for the IMAGEN Consortium}}, - month = jan, - year = {2024}, - keywords = {MRI, Adolescent, Longitudinal, Gray matter, Autistic traits, Women}, - pages = {15--29}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/U7WZK3HB/Gros et al. - 2024 - Whole-brain gray matter maturation trajectories as.pdf:application/pdf}, -} - -@article{ge_genetic_2024, - title = {Genetic architectures of cerebral ventricles and their overlap with neuropsychiatric traits}, - volume = {8}, - copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {2397-3374}, - url = {https://www.nature.com/articles/s41562-023-01722-6}, - doi = {10.1038/s41562-023-01722-6}, - abstract = {The cerebral ventricles are recognized as windows into brain development and disease, yet their genetic architectures, underlying neural mechanisms and utility in maintaining brain health remain elusive. Here we aggregated genetic and neuroimaging data from 61,974 participants (age range, 9 to 98 years) in five cohorts to elucidate the genetic basis of ventricular morphology and examined their overlap with neuropsychiatric traits. Genome-wide association analysis in a discovery sample of 31,880 individuals identified 62 unique loci and 785 candidate genes associated with ventricular morphology. We replicated over 80\% of loci in a well-matched cohort of lateral ventricular volume. Gene set analysis revealed enrichment of ventricular-trait-associated genes in biological processes and disease pathogenesis during both early brain development and degeneration. We explored the age-dependent genetic associations in cohorts of different age groups to investigate the possible roles of ventricular-trait-associated loci in neurodevelopmental and neurodegenerative processes. We describe the genetic overlap between ventricular and neuropsychiatric traits through comprehensive integrative approaches under correlative and causal assumptions. We propose the volume of the inferior lateral ventricles as a heritable endophenotype to predict the risk of Alzheimer’s disease, which might be a consequence of prodromal Alzheimer’s disease. Our study provides an advance in understanding the genetics of the cerebral ventricles and demonstrates the potential utility of ventricular measurements in tracking brain disorders and maintaining brain health across the lifespan.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Nature Human Behaviour}, - author = {Ge, Yi-Jun and Wu, Bang-Sheng and Zhang, Yi and Chen, Shi-Dong and Zhang, Ya-Ru and Kang, Ju-Jiao and Deng, Yue-Ting and Ou, Ya-Nan and He, Xiao-Yu and Zhao, Yong-Li and Kuo, Kevin and Ma, Qing and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Feng, Jian-Feng and Tan, Lan and Dong, Qiang and Schumann, Gunter and Cheng, Wei and Yu, Jin-Tai}, - month = jan, - year = {2024}, - note = {Publisher: Nature Publishing Group}, - keywords = {Alzheimer's disease, Genetics research, Genetics of the nervous system, Genome-wide association studies}, - pages = {164--180}, -} - -@article{qi_differing_2023, - title = {Differing impact of the {COVID}-19 pandemic on youth mental health: combined population and clinical study}, - volume = {9}, - issn = {2056-4724}, - shorttitle = {Differing impact of the {COVID}-19 pandemic on youth mental health}, - url = {https://www.cambridge.org/core/journals/bjpsych-open/article/differing-impact-of-the-covid19-pandemic-on-youth-mental-health-combined-population-and-clinical-study/939EDB00D962E84F86DC362C16B82A14#}, - doi = {10.1192/bjo.2023.601}, - abstract = {BackgroundIdentifying youths most at risk to COVID-19-related mental illness is essential for the development of effective targeted interventions.AimsTo compare trajectories of mental health throughout the pandemic in youth with and without prior mental illness and identify those most at risk of COVID-19-related mental illness.MethodData were collected from individuals aged 18–26 years (N = 669) from two existing cohorts: IMAGEN, a population-based cohort; and ESTRA/STRATIFY, clinical cohorts of individuals with pre-existing diagnoses of mental disorders. Repeated COVID-19 surveys and standardised mental health assessments were used to compare trajectories of mental health symptoms from before the pandemic through to the second lockdown.ResultsMental health trajectories differed significantly between cohorts. In the population cohort, depression and eating disorder symptoms increased by 33.9\% (95\% CI 31.78–36.57) and 15.6\% (95\% CI 15.39–15.68) during the pandemic, respectively. By contrast, these remained high over time in the clinical cohort. Conversely, trajectories of alcohol misuse were similar in both cohorts, decreasing continuously (a 15.2\% decrease) during the pandemic. Pre-pandemic symptom severity predicted the observed mental health trajectories in the population cohort. Surprisingly, being relatively healthy predicted increases in depression and eating disorder symptoms and in body mass index. By contrast, those initially at higher risk for depression or eating disorders reported a lasting decrease.ConclusionsHealthier young people may be at greater risk of developing depressive or eating disorder symptoms during the COVID-19 pandemic. Targeted mental health interventions considering prior diagnostic risk may be warranted to help young people cope with the challenges of psychosocial stress and reduce the associated healthcare burden.}, - language = {en}, - number = {6}, - urldate = {2024-03-12}, - journal = {BJPsych Open}, - author = {Qi, Lu and Zhang, Zuo and Robinson, Lauren and Bobou, Marina and Gourlan, Chantal and Winterer, Jeanne and Adams, Rebecca and Agunbiade, Kofoworola and Zhang, Yuning and King, Sinead and Vaidya, Nilakshi and Artiges, Eric and Banaschewski, Tobias and Bokde, Arun L. W. and Broulidakis, M. John and Brühl, Rüdiger and Flor, Herta and Fröhner, Juliane H. and Garavan, Hugh and Grigis, Antoine and Heinz, Andreas and Hohmann, Sarah and Martinot, Marie-Laure Paillère and Millenet, Sabina and Nees, Frauke and Noort, Betteke Maria van and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Sinclair, Julia and Smolka, Michael N. and Whelan, Robert and Stringaris, Argyris and Walter, Henrik and Martinot, Jean-Luc and Schumann, Gunter and Schmidt, Ulrike and Desrivières, Sylvane and IMAGEN Consortium, ESTRA Consortium {and} STRATIFY Consortium}, - month = nov, - year = {2023}, - keywords = {depression, adolescent, alcohol use disorder, COVID-19, eating disorders}, - pages = {e217}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Z9A5CFJV/Qi et al. - 2023 - Differing impact of the COVID-19 pandemic on youth.pdf:application/pdf}, -} - -@article{backhausen_adolescent_2024, - title = {Adolescent to young adult longitudinal development of subcortical volumes in two {European} sites with four waves}, - volume = {45}, - copyright = {© 2024 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.}, - issn = {1097-0193}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hbm.26574}, - doi = {10.1002/hbm.26574}, - abstract = {Adolescent subcortical structural brain development might underlie psychopathological symptoms, which often emerge in adolescence. At the same time, sex differences exist in psychopathology, which might be mirrored in underlying sex differences in structural development. However, previous studies showed inconsistencies in subcortical trajectories and potential sex differences. Therefore, we aimed to investigate the subcortical structural trajectories and their sex differences across adolescence using for the first time a single cohort design, the same quality control procedure, software, and a general additive mixed modeling approach. We investigated two large European sites from ages 14 to 24 with 503 participants and 1408 total scans from France and Germany as part of the IMAGEN project including four waves of data acquisition. We found significantly larger volumes in males versus females in both sites and across all seven subcortical regions. Sex differences in age-related trajectories were observed across all regions in both sites. Our findings provide further evidence of sex differences in longitudinal adolescent brain development of subcortical regions and thus might eventually support the relationship of underlying brain development and different adolescent psychopathology in boys and girls.}, - language = {en}, - number = {3}, - urldate = {2024-03-12}, - journal = {Human Brain Mapping}, - author = {Backhausen, Lea L. and Fröhner, Juliane H. and Lemaître, Hervé and Artiges, Eric and Martinot, Marie-Laure Palillère and Herting, Megan M. and Sticca, Fabio and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Nees, Frauke and Papadopoulos-Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Robinson, Lauren and Walter, Henrik and Winterer, Jeanne and Whelan, Robert and Schumann, Gunter and Martinot, Jean-Luc and Smolka, Michael N. and Vetter, Nora C. and Consortium, the IMAGEN}, - year = {2024}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.26574}, - keywords = {neurodevelopment, longitudinal, sex differences, adolescence, structural magnetic resonance imaging (sMRI), subcortical}, - pages = {e26574}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/XF22BI9S/Backhausen et al. - 2024 - Adolescent to young adult longitudinal development.pdf:application/pdf}, -} - -@article{heukamp_adolescents_2024, - title = {Adolescents’ pain-related ontogeny shares a neural basis with adults’ chronic pain in basothalamo-cortical organization}, - volume = {27}, - issn = {25890042}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004224001755}, - doi = {10.1016/j.isci.2024.108954}, - abstract = {During late adolescence, the brain undergoes ontogenic organization altering subcortical-cortical circuitry. This includes regions implicated in pain chronicity, and thus alterations in the adolescent ontogenic organization could predispose to pain chronicity in adulthood - however, evidence is lacking. Using resting-state functional magnetic resonance imaging from a large European longitudinal adolescent cohort and an adult cohort with and without chronic pain, we examined links between painful symptoms and brain connectivity. During late adolescence, thalamo-, caudate-, and red nucleus-cortical connectivity were positively and subthalamo-cortical connectivity negatively associated with painful symptoms. Thalamo-cortical connectivity, but also subthalamo-cortical connectivity, was increased in adults with chronic pain compared to healthy controls. Our results indicate a shared basis in basothalamo-cortical circuitries between adolescent painful symptomatology and adult pain chronicity, with the subthalamic pathway being differentially involved, potentially due to a hyperconnected thalamo-cortical pathway in chronic pain and ontogeny-driven organization. This can inform neuromodulation-based prevention and early intervention.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {iScience}, - author = {Heukamp, Nils Jannik and Banaschewski, Tobias and Bokde, Arun L.W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Kandić, Mina and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Papadopoulos Orfanos, Dimitri and Lemaitre, Herve and Löffler, Martin and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Usai, Katrin and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Flor, Herta and Nees, Frauke}, - month = feb, - year = {2024}, - pages = {108954}, -} - -@article{sibilia_relationship_2024, - title = {The relationship between negative life events and cortical structural connectivity in adolescents}, - volume = {16}, - issn = {2667-2421}, - url = {https://www.sciencedirect.com/science/article/pii/S2667242124000101}, - doi = {10.1016/j.ibneur.2024.01.012}, - abstract = {Adolescence is a crucial period for physical and psychological development. The impact of negative life events represents a risk factor for the onset of neuropsychiatric disorders. This study aims to investigate the relationship between negative life events and structural brain connectivity, considering both graph theory and connectivity strength. A group (n = 487) of adolescents from the IMAGEN Consortium was divided into Low and High Stress groups. Brain networks were extracted at an individual level, based on morphological similarity between grey matter regions with regions defined using an atlas-based region of interest (ROI) approach. Between-group comparisons were performed with global and local graph theory measures in a range of sparsity levels. The analysis was also performed in a larger sample of adolescents (n = 976) to examine linear correlations between stress level and network measures. Connectivity strength differences were investigated with network-based statistics. Negative life events were not found to be a factor influencing global network measures at any sparsity level. At local network level, between-group differences were found in centrality measures of the left somato-motor network (a decrease of betweenness centrality was seen at sparsity 5\%), of the bilateral central visual and the left dorsal attention network (increase of degree at sparsity 10\% at sparsity 30\% respectively). Network-based statistics analysis showed an increase in connectivity strength in the High stress group in edges connecting the dorsal attention, limbic and salience networks. This study suggests negative life events alone do not alter structural connectivity globally, but they are associated to connectivity properties in areas involved in emotion and attention.}, - urldate = {2024-03-12}, - journal = {IBRO Neuroscience Reports}, - author = {Sibilia, Francesca and Jost-Mousseau, Coline and Banaschewski, Tobias and Barker, Gareth J. and Büchel, Christian and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Bokde, Arun L. W.}, - month = jun, - year = {2024}, - keywords = {Adolescence, Cortex, Stress, Brain networks, Edge connectivity, Graph theory}, - pages = {201--210}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Q8SDK2Y9/S2667242124000101.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TZM37KYD/Sibilia et al. - 2024 - The relationship between negative life events and .pdf:application/pdf}, -} - -@article{le_guen_chaotic_2018, - title = {The chaotic morphology of the left superior temporal sulcus is genetically constrained}, - volume = {174}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811918302568}, - doi = {10.1016/j.neuroimage.2018.03.046}, - abstract = {The asymmetry of the superior temporal sulcus (STS) has been identified as a species-specific feature of the human brain. The so-called superior temporal asymmetrical pit (STAP) area is observed from the last trimester of gestation onwards and is far less pronounced in the chimpanzee brain. This asymmetry is associated with more frequent sulcal interruptions, named plis de passage (PPs), leading to the irregular morphology of the left sulcus. In this paper, we aimed to characterize the variability, asymmetry, and heritability of these interruptions in the STS in comparison with the other main sulci. We developed an automated method to extract PPs across the cortex based on a highly reproducible grid of sulcal pits across individuals, which we applied to a subset of Human Connectome Project (HCP) subjects (N = 820). We report that only a few PPs across the cortex are genetically constrained, namely in the collateral, postcentral and superior temporal sulci and the calcarine fissure. Moreover, some PPs occur more often in one hemisphere than the other, namely in the precentral, postcentral, intraparietal sulci, as well as in both inferior and superior temporal sulci. Most importantly, we found that only the interruptions within the STAP region are both asymmetric and genetically constrained. Because this morphological pattern is located in an area of the left hemisphere related to speech, our results suggest structural constraints on the architecture of the linguistic network.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Le Guen, Yann and Leroy, François and Auzias, Guillaume and Riviere, Denis and Grigis, Antoine and Mangin, Jean-François and Coulon, Olivier and Dehaene-Lambertz, Ghislaine and Frouin, Vincent}, - month = jul, - year = {2018}, - keywords = {Heritability, Cortical folding, Imaging genetics, Pli de passage, Structural MRI, STS asymmetry}, - pages = {297--307}, -} - -@inproceedings{le_guen_heritability_2019, - title = {Heritability of surface area and cortical thickness: a comparison between the {Human} {Connectome} {Project} and the {UK} {Biobank} dataset}, - shorttitle = {Heritability of surface area and cortical thickness}, - url = {https://ieeexplore.ieee.org/abstract/document/8759539}, - doi = {10.1109/ISBI.2019.8759539}, - abstract = {Heritability of the regional thickness/surface in human cortex is established. Yet the estimates vary substantially depending on cohorts or the information they are derived from: pedigree or genotyping. Here we present three heritability studies of the cortex phenotype in two cohorts showing: i) both pedigree and genotyping or ii) genotyping only. We obtained clearly correlated heritability values between studies with a shift appearing between cohorts. Spatial pattern of heritability remains highly consistent across cohorts.}, - urldate = {2024-03-12}, - booktitle = {2019 {IEEE} 16th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2019)}, - author = {Le Guen, Yann and Karkar, Slim and Grigis, Antoine and Philippe, Cathy and Mangin, Jean-François and Frouin, Vincent}, - month = apr, - year = {2019}, - note = {ISSN: 1945-8452}, - keywords = {Sociology, Statistics, Magnetic resonance imaging, heritability, imaging-genetic, cortical thickness, Genomics, Bioinformatics, surface area}, - pages = {1887--1890}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FC8YYEQ4/Le Guen et al. - 2019 - Heritability of surface area and cortical thicknes.pdf:application/pdf}, -} - -@article{ji_increased_2019, - title = {Increased and {Decreased} {Superficial} {White} {Matter} {Structural} {Connectivity} in {Schizophrenia} and {Bipolar} {Disorder}}, - volume = {45}, - issn = {0586-7614}, - url = {https://doi.org/10.1093/schbul/sbz015}, - doi = {10.1093/schbul/sbz015}, - abstract = {Schizophrenia (SZ) and bipolar disorder (BD) are often conceptualized as “disconnection syndromes,” with substantial evidence of abnormalities in deep white matter tracts, forming the substrates of long-range connectivity, seen in both disorders. However, the study of superficial white matter (SWM) U-shaped short-range tracts remained challenging until recently, although findings from postmortem studies suggest they are likely integral components of SZ and BD neuropathology. This diffusion weighted imaging (DWI) study aimed to investigate SWM microstructure in vivo in both SZ and BD for the first time. We performed whole brain tractography in 31 people with SZ, 32 people with BD and 54 controls using BrainVISA and Connectomist 2.0. Segmentation and labeling of SWM tracts were performed using a novel, comprehensive U-fiber atlas. Analysis of covariances yielded significant generalized fractional anisotropy (gFA) differences for 17 SWM bundles in frontal, parietal, and temporal cortices. Post hoc analyses showed gFA reductions in both patient groups as compared with controls in bundles connecting regions involved in language processing, mood regulation, working memory, and motor function (pars opercularis, insula, anterior cingulate, precentral gyrus). We also found increased gFA in SZ patients in areas overlapping the default mode network (inferior parietal, middle temporal, precuneus), supporting functional hyperconnectivity of this network evidenced in SZ. We thus illustrate that short U-fibers are vulnerable to the pathological processes in major psychiatric illnesses, encouraging improved understanding of their anatomy and function.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Schizophrenia Bulletin}, - author = {Ji, Ellen and Guevara, Pamela and Guevara, Miguel and Grigis, Antoine and Labra, Nicole and Sarrazin, Samuel and Hamdani, Nora and Bellivier, Frank and Delavest, Marine and Leboyer, Marion and Tamouza, Ryad and Poupon, Cyril and Mangin, Jean-François and Houenou, Josselin}, - month = oct, - year = {2019}, - pages = {1367--1378}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Y7YQ6NHY/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A6NRGXW3/Ji et al. - 2019 - Increased and Decreased Superficial White Matter S.pdf:application/pdf}, -} - -@article{mangin_plis_2019, - title = {“{Plis} de passage” {Deserve} a {Role} in {Models} of the {Cortical} {Folding} {Process}}, - volume = {32}, - issn = {1573-6792}, - url = {https://doi.org/10.1007/s10548-019-00734-8}, - doi = {10.1007/s10548-019-00734-8}, - abstract = {Cortical folding is a hallmark of brain topography whose variability across individuals remains a puzzle. In this paper, we call for an effort to improve our understanding of the pli de passage phenomenon, namely annectant gyri buried in the depth of the main sulci. We suggest that plis de passage could become an interesting benchmark for models of the cortical folding process. As an illustration, we speculate on the link between modern biological models of cortical folding and the development of the Pli de Passage Frontal Moyen (PPFM) in the middle of the central sulcus. For this purpose, we have detected nine interrupted central sulci in the Human Connectome Project dataset, which are used to explore the organization of the hand sensorimotor areas in this rare configuration of the PPFM.}, - language = {en}, - number = {6}, - urldate = {2024-03-12}, - journal = {Brain Topography}, - author = {Mangin, Jean-François and Le Guen, Yann and Labra, Nicole and Grigis, Antoine and Frouin, Vincent and Guevara, Miguel and Fischer, Clara and Rivière, Denis and Hopkins, William D. and Régis, Jean and Sun, Zhong Yi}, - month = nov, - year = {2019}, - keywords = {Cortical folding, Central sulcus, Pli de passage, Sulcal pits, Sulcal roots}, - pages = {1035--1048}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6DSRSA4Q/Mangin et al. - 2019 - “Plis de passage” Deserve a Role in Models of the .pdf:application/pdf}, -} - -@article{maltais_prospective_2020, - title = {Prospective {Associations} {Between} {Diffusion} {Tensor} {Imaging} {Parameters} and {Frailty} in {Older} {Adults}}, - volume = {68}, - copyright = {© 2020 The American Geriatrics Society}, - issn = {1532-5415}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16343}, - doi = {10.1111/jgs.16343}, - abstract = {BACKGROUND Cross-sectional associations have been found between frail individuals and worse white matter (WM) integrity. However, the prospective association between WM integrity and frailty is still unclear. Our objectives were to measure associations between WM integrity using diffusion tensor imaging (DTI) and the 5-year worsening of frailty in community-dwelling older adults. DESIGN Secondary analysis of the randomized controlled Multidomain Alzheimer Preventive Trial (MAPT). SETTING Thirteen memory centers in France and Monaco between 2008 and 2011. PARTICIPANTS Participants (mean age = 74.7 ± 3.9 years) with no dementia at baseline who had functional magnetic resonance imaging performed as part of the MAPT study (n = 227). MEASUREMENTS Fractional anisotropy and mean diffusivity (MD), axial diffusivity (AxD), and radial diffusivity (RD) were acquired for 10 different brain regions. Frailty was assessed by the Fried frailty phenotype (score from 0 to 5, higher is worse) at up to seven time points for 5 years. Mixed effect ordinal logistic regression model was used to assess the prospective association between DTI parameters (independent variables) and frailty (dependent variable). All the analyses were adjusted for age, sex, baseline total intracranial volume, and the presence of one of the following cardiovascular risk factors (hypertension, diabetes, and/or hypercholesterolemia). RESULTS A statistically significant association was found between the RD, AxD, and MD for different brain regions (anterior limb of internal capsule, external capsule, posterior corona radiata, posterior thalamic radiation, superior corona radiata, superior frontal occipital fasciculus, and superior longitudinal fasciculus) and worsening of frailty over 5 years after adjusting for multiple comparisons. CONCLUSIONS This is the first study to show that WM integrity is associated with frailty in older adults. The mechanisms related to these results require further investigation. J Am Geriatr Soc 68:1050–1055, 2020}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Journal of the American Geriatrics Society}, - author = {Maltais, Mathieu and de Souto Barreto, Philipe and Perus, Lisa and Mangin, Jean-François and Grigis, Antoine and Chupin, Marie and Bouyahia, Ali and Gabelle, Audrey and Delrieux, Julien and Rolland, Yves and Vellas, Bruno and Group, for the Multidomain Alzheimer Preventive Trial/Data Sharing Alzheimer (MAPT/DSA) Study}, - year = {2020}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jgs.16343}, - keywords = {brain health, diffusion magnetic resonance imagingfrailty, physical capacity}, - pages = {1050--1055}, -} - -@article{chen_genetic_2024, - title = {The genetic architecture of the human hypothalamus and its involvement in neuropsychiatric behaviours and disorders}, - copyright = {2024 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {2397-3374}, - url = {https://www.nature.com/articles/s41562-023-01792-6}, - doi = {10.1038/s41562-023-01792-6}, - abstract = {Despite its crucial role in the regulation of vital metabolic and neurological functions, the genetic architecture of the hypothalamus remains unknown. Here we conducted multivariate genome-wide association studies (GWAS) using hypothalamic imaging data from 32,956 individuals to uncover the genetic underpinnings of the hypothalamus and its involvement in neuropsychiatric traits. There were 23 significant loci associated with the whole hypothalamus and its subunits, with functional enrichment for genes involved in intracellular trafficking systems and metabolic processes of steroid-related compounds. The hypothalamus exhibited substantial genetic associations with limbic system structures and neuropsychiatric traits including chronotype, risky behaviour, cognition, satiety and sympathetic–parasympathetic activity. The strongest signal in the primary GWAS, the ADAMTS8 locus, was replicated in three independent datasets (N = 1,685–4,321) and was strengthened after meta-analysis. Exome-wide association analyses added evidence to the association for ADAMTS8, and Mendelian randomization showed lower ADAMTS8 expression with larger hypothalamic volumes. The current study advances our understanding of complex structure–function relationships of the hypothalamus and provides insights into the molecular mechanisms that underlie hypothalamic formation.}, - language = {en}, - urldate = {2024-03-12}, - journal = {Nature Human Behaviour}, - author = {Chen, Shi-Dong and You, Jia and Zhang, Wei and Wu, Bang-Sheng and Ge, Yi-Jun and Xiang, Shi-Tong and Du, Jing and Kuo, Kevin and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Baeuchl, Christian and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Feng, Jian-Feng and Dong, Qiang and Cheng, Wei and Yu, Jin-Tai}, - month = jan, - year = {2024}, - note = {Publisher: Nature Publishing Group}, - keywords = {Genetics research, Genetics of the nervous system, Genome-wide association studies}, - pages = {1--15}, -} - -@article{ernst_pubertal_2019, - title = {Pubertal maturation and sex effects on the default-mode network connectivity implicated in mood dysregulation}, - volume = {9}, - copyright = {2019 The Author(s)}, - issn = {2158-3188}, - url = {https://www.nature.com/articles/s41398-019-0433-6}, - doi = {10.1038/s41398-019-0433-6}, - abstract = {This study examines the effects of puberty and sex on the intrinsic functional connectivity (iFC) of brain networks, with a focus on the default-mode network (DMN). Consistently implicated in depressive disorders, the DMN’s function may interact with puberty and sex in the development of these disorders, whose onsets peak in adolescence, and which show strong sex disproportionality (females {\textgreater} males). The main question concerns how the DMN evolves with puberty as a function of sex. These effects are expected to involve within- and between-network iFC, particularly, the salience and the central-executive networks, consistent with the Triple-Network Model. Resting-state scans of an adolescent community sample (n = 304, male/female: 157/147; mean/std age: 14.6/0.41 years), from the IMAGEN database, were analyzed using the AFNI software suite and a data reduction strategy for the effects of puberty and sex. Three midline regions (medial prefrontal, pregenual anterior cingulate, and posterior cingulate), within the DMN and consistently implicated in mood disorders, were selected as seeds. Within- and between-network clusters of the DMN iFC changed with pubertal maturation differently in boys and girls (puberty-X-sex). Specifically, pubertal maturation predicted weaker iFC in girls and stronger iFC in boys. Finally, iFC was stronger in boys than girls independently of puberty. Brain–behavior associations indicated that lower connectivity of the anterior cingulate seed predicted higher internalizing symptoms at 2-year follow-up. In conclusion, weaker iFC of the anterior DMN may signal disconnections among circuits supporting mood regulation, conferring risk for internalizing disorders.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Translational Psychiatry}, - author = {Ernst, Monique and Benson, Brenda and Artiges, Eric and Gorka, Adam X. and Lemaitre, Herve and Lago, Tiffany and Miranda, Ruben and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Brühl, Rüdiger and Büchel, Christian and Cattrell, Anna and Conrod, Patricia and Desrivières, Sylvane and Fadai, Tahmine and Flor, Herta and Grigis, Antoine and Gallinat, Juergen and Garavan, Hugh and Gowland, Penny and Grimmer, Yvonne and Heinz, Andreas and Kappel, Viola and Nees, Frauke and Papadopoulos-Orfanos, Dimitri and Penttilä, Jani and Poustka, Luise and Smolka, Michael N. and Stringaris, Argyris and Struve, Maren and van Noort, Betteke M. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Grillon, Christian and Martinot, Marie-Laure Paillère and Martinot, Jean-Luc}, - month = feb, - year = {2019}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychiatric disorders, Neuroscience, Learning and memory}, - pages = {1--14}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZH5ZVT32/Ernst et al. - 2019 - Pubertal maturation and sex effects on the default.pdf:application/pdf}, -} - -@article{albaugh_amygdalar_2019, - title = {Amygdalar reactivity is associated with prefrontal cortical thickness in a large population-based sample of adolescents}, - volume = {14}, - issn = {1932-6203}, - url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216152}, - doi = {10.1371/journal.pone.0216152}, - abstract = {In structural neuroimaging studies, reduced cerebral cortical thickness in orbital and ventromedial prefrontal regions is frequently interpreted as reflecting an impaired ability to downregulate neuronal activity in the amygdalae. Unfortunately, little research has been conducted in order to test this conjecture. We examine the extent to which amygdalar reactivity is associated with cortical thickness in a population-based sample of adolescents. Data were obtained from the IMAGEN study, which includes 2,223 adolescents. While undergoing functional neuroimaging, participants passively viewed video clips of a face that started from a neutral expression and progressively turned angry, or, instead, turned to a second neutral expression. Left and right amygdala ROIs were used to extract mean BOLD signal change for the angry minus neutral face contrast for all subjects. T1-weighted images were processed through the CIVET pipeline (version 2.1.0). In variable-centered analyses, local cortical thickness was regressed against amygdalar reactivity using first and second-order linear models. In a follow-up person-centered analysis, we defined a “high reactive” group of participants based on mean amygdalar BOLD signal change for the angry minus neutral face contrast. Between-group differences in cortical thickness were examined (“high reactive” versus all other participants). A significant association was revealed between the continuous measure of amygdalar reactivity and bilateral ventromedial prefrontal cortical thickness in a second-order linear model (p {\textless} 0.05, corrected). The “high reactive” group, in comparison to all other participants, possessed reduced cortical thickness in bilateral orbital and ventromedial prefrontal cortices, bilateral anterior temporal cortices, left caudal middle temporal gyrus, and the left inferior and middle frontal gyri (p {\textless} 0.05, corrected). Results are consistent with non-human primate studies, and provide empirical support for an association between reduced prefrontal cortical thickness and amygdalar reactivity. Future research will likely benefit from investigating the degree to which psychopathology qualifies relations between prefrontal cortical structure and amygdalar reactivity.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {PLOS ONE}, - author = {Albaugh, Matthew D. and Hudziak, James J. and Orr, Catherine and Spechler, Philip A. and Chaarani, Bader and Mackey, Scott and Lepage, Claude and Fonov, Vladimir and Rioux, Pierre and Evans, Alan C. and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Potter, Alexandra S. and Garavan, Hugh and Consortium, Imagen}, - year = {2019}, - note = {Publisher: Public Library of Science}, - keywords = {Neuroimaging, Emotions, Prefrontal cortex, Magnetic resonance imaging, Amygdala, Functional magnetic resonance imaging, Face, Adolescents}, - pages = {e0216152}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NAMSAXGP/Albaugh et al. - 2019 - Amygdalar reactivity is associated with prefrontal.pdf:application/pdf}, -} - -@article{kuhn_predicting_2019, - title = {Predicting development of adolescent drinking behaviour from whole brain structure at 14 years of age}, - volume = {8}, - issn = {2050-084X}, - url = {https://doi.org/10.7554/eLife.44056}, - doi = {10.7554/eLife.44056}, - abstract = {Adolescence is a common time for initiation of alcohol use and development of alcohol use disorders. The present study investigates neuroanatomical predictors for trajectories of future alcohol use based on a novel voxel-wise whole-brain structural equation modeling framework. In 1814 healthy adolescents of the IMAGEN sample, the Alcohol Use Disorder Identification Test (AUDIT) was acquired at three measurement occasions across five years. Based on a two-part latent growth curve model, we conducted whole-brain analyses on structural MRI data at age 14, predicting change in alcohol use score over time. Higher grey-matter volumes in the caudate nucleus and the left cerebellum at age 14 years were predictive of stronger increase in alcohol use score over 5 years. The study is the first to demonstrate the feasibility of running separate voxel-wise structural equation models thereby opening new avenues for data analysis in brain imaging.}, - urldate = {2024-03-12}, - journal = {eLife}, - author = {Kühn, Simone and Mascharek, Anna and Banaschewski, Tobias and Bodke, Arun and Bromberg, Uli and Büchel, Christian and Quinlan, Erin Burke and Desrivieres, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny A and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomas and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H and Smolka, Michael N and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Lindenberger, Ulman and Gallinat, Jürgen and {IMAGEN Consortium}}, - editor = {Johansen-Berg, Heidi and Frank, Michael J}, - month = jul, - year = {2019}, - note = {Publisher: eLife Sciences Publications, Ltd}, - keywords = {adolescence, brain structure, alcohol use, structural equation modelling, latent growth curve modelling}, - pages = {e44056}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EJA42DDG/Kühn et al. - 2019 - Predicting development of adolescent drinking beha.pdf:application/pdf}, -} - -@article{kuhn_hierarchical_2020, - title = {Hierarchical associations of alcohol use disorder symptoms in late adolescence with markers during early adolescence}, - volume = {100}, - issn = {0306-4603}, - url = {https://www.sciencedirect.com/science/article/pii/S0306460319303168}, - doi = {10.1016/j.addbeh.2019.106130}, - abstract = {High adolescent alcohol consumption is predictive for alcohol problems later in life. To tailor interventions, early identification of risk groups for adolescent alcohol consumption is important. The IMAGEN dataset was utilized to investigate predictors for problematic alcohol consumption at age 18–20 years as a function self and parental personality and drug-related measures as well as life-events and cognitive variables all assessed at age 14 years (N = 1404). For this purpose the binary partitioning algorithm ctree was used in an explorative analysis. The algorithm recursively selects significant input variables and splits the outcome variable based on these, yielding a conditional inference tree. Four significant split variables, namely Place of residence, the Disorganization subscale of the Temperament and Character Inventory, Sex, and the Sexuality subscale of the life-events questionnaire were found to distinguish between adolescents scoring high or low on the Alcohol Use Disorders Identification Test about five years later (all p {\textless} 0.001). The analyis adds to the literature on predictors of adolescent drinking problems using a large European sample. The identified split variables could easily be collected in community samples. If their validity is proven in independent samples, they could facilitate intervention studies in the field of adolescent alcohol prevention.}, - urldate = {2024-03-12}, - journal = {Addictive Behaviors}, - author = {Kühn, Simone and Lisofsky, Nina and Banaschewski, Tobias and Barker, Gareth and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Brühl, Rüdiger and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Gallinat, Jürgen}, - month = jan, - year = {2020}, - keywords = {Adolescence, Alcohol consumption, Conditional inference trees (ctree), Hierarchical associations}, - pages = {106130}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B8MYEL46/Kühn et al. - 2020 - Hierarchical associations of alcohol use disorder .pdf:application/pdf}, -} - -@article{papanastasiou_examination_2020-1, - title = {Examination of the neural basis of psychotic-like experiences in adolescence during processing of emotional faces}, - volume = {10}, - copyright = {2020 The Author(s)}, - issn = {2045-2322}, - url = {https://www.nature.com/articles/s41598-020-62026-7}, - doi = {10.1038/s41598-020-62026-7}, - abstract = {Contemporary theories propose that dysregulation of emotional perception is involved in the aetiology of psychosis. 298 healthy adolescents were assessed at age 14- and 19-years using fMRI while performing a facial emotion task. Psychotic-like experiences (PLEs) were assessed with the CAPE-42 questionnaire at age 19. The high PLEs group at age 19 years exhibited an enhanced response in right insular cortex and decreased response in right prefrontal, right parahippocampal and left striatal regions; also, a gradient of decreasing response to emotional faces with age, from 14 to 19 years, in the right parahippocampal region and left insular cortical area. The right insula demonstrated an increasing response to emotional faces with increasing age in the low PLEs group, and a decreasing response over time in the high PLEs group. The change in parahippocampal/amygdala and insula responses during the perception of emotional faces in adolescents with high PLEs between the ages of 14 and 19 suggests a potential ‘aberrant’ neurodevelopmental trajectory for critical limbic areas. Our findings emphasize the role of the frontal and limbic areas in the aetiology of psychotic symptoms, in subjects without the illness phenotype and the confounds introduced by antipsychotic medication.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Scientific Reports}, - author = {Papanastasiou, Evangelos and Mouchlianitis, Elias and Joyce, Dan W. and McGuire, Philip and Boussebaa, Celia and Banaschewski, Tobias and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Spechler, Philip and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Shergill, Sukhwinder S.}, - month = mar, - year = {2020}, - note = {Publisher: Nature Publishing Group}, - keywords = {Cognitive neuroscience, Diagnostic markers, Human behaviour}, - pages = {5164}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7UWV7K6X/Papanastasiou et al. - 2020 - Examination of the neural basis of psychotic-like .pdf:application/pdf}, -} - -@article{jia_neurobehavioural_2020, - title = {Neurobehavioural characterisation and stratification of reinforcement-related behaviour}, - volume = {4}, - copyright = {2020 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {2397-3374}, - url = {https://www.nature.com/articles/s41562-020-0846-5}, - doi = {10.1038/s41562-020-0846-5}, - abstract = {Reinforcement-related cognitive processes, such as reward processing, inhibitory control and social–emotional regulation are critical components of externalising and internalising behaviours. It is unclear to what extent the deficit in each of these processes contributes to individual behavioural symptoms, how their neural substrates give rise to distinct behavioural outcomes and whether neural activation profiles across different reinforcement-related processes might differentiate individual behaviours. We created a statistical framework that enabled us to directly compare functional brain activation during reward anticipation, motor inhibition and viewing emotional faces in the European IMAGEN cohort of 2,000 14-year-old adolescents. We observe significant correlations and modulation of reward anticipation and motor inhibition networks in hyperactivity, impulsivity, inattentive behaviour and conduct symptoms, and we describe neural signatures across cognitive tasks that differentiate these behaviours. We thus characterise shared and distinct functional brain activation patterns underling different externalising symptoms and identify neural stratification markers, while accounting for clinically observed comorbidity.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Nature Human Behaviour}, - author = {Jia, Tianye and Ing, Alex and Quinlan, Erin Burke and Tay, Nicole and Luo, Qiang and Francesca, Biondo and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Desrivières, Sylvane and Feng, Jianfeng and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter}, - month = may, - year = {2020}, - note = {Publisher: Nature Publishing Group}, - keywords = {Motivation, Attention, Emotion, Network models}, - pages = {544--558}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/I5Y5UKDZ/Jia et al. - 2020 - Neurobehavioural characterisation and stratificati.pdf:application/pdf}, -} - -@article{bossier_empirical_2020, - title = {The empirical replicability of task-based {fMRI} as a function of sample size}, - volume = {212}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811920300884}, - doi = {10.1016/j.neuroimage.2020.116601}, - abstract = {Replicating results (i.e. obtaining consistent results using a new independent dataset) is an essential part of good science. As replicability has consequences for theories derived from empirical studies, it is of utmost importance to better understand the underlying mechanisms influencing it. A popular tool for non-invasive neuroimaging studies is functional magnetic resonance imaging (fMRI). While the effect of underpowered studies is well documented, the empirical assessment of the interplay between sample size and replicability of results for task-based fMRI studies remains limited. In this work, we extend existing work on this assessment in two ways. Firstly, we use a large database of 1400 subjects performing four types of tasks from the IMAGEN project to subsample a series of independent samples of increasing size. Secondly, replicability is evaluated using a multi-dimensional framework consisting of 3 different measures: (un)conditional test-retest reliability, coherence and stability. We demonstrate not only a positive effect of sample size, but also a trade-off between spatial resolution and replicability. When replicability is assessed voxelwise or when observing small areas of activation, a larger sample size than typically used in fMRI is required to replicate results. On the other hand, when focussing on clusters of voxels, we observe a higher replicability. In addition, we observe variability in the size of clusters of activation between experimental paradigms or contrasts of parameter estimates within these.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Bossier, Han and Roels, Sanne P. and Seurinck, Ruth and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Fröhner Dipl-Psych, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Moerkerke, Beatrijs}, - month = may, - year = {2020}, - keywords = {Reliability, Replicability, Stability, Coherence, Reproducibility, Task-based fMRI}, - pages = {116601}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DZTGSAYV/Bossier et al. - 2020 - The empirical replicability of task-based fMRI as .pdf:application/pdf}, -} - -@article{spechler_longitudinal_2020, - title = {Longitudinal associations between amygdala reactivity and cannabis use in a large sample of adolescents}, - volume = {237}, - issn = {1432-2072}, - url = {https://doi.org/10.1007/s00213-020-05624-7}, - doi = {10.1007/s00213-020-05624-7}, - abstract = {The amygdala is a key brain structure to study in relation to cannabis use as reflected by its high-density of cannabinoid receptors and functional reactivity to processes relevant to drug use. Previously, we identified a correlation between cannabis use in early adolescence and amygdala hyper-reactivity to angry faces (Spechler et al. 2015).}, - language = {en}, - number = {11}, - urldate = {2024-03-12}, - journal = {Psychopharmacology}, - author = {Spechler, Philip A. and Chaarani, Bader and Orr, Catherine and Albaugh, Matthew D. and Fontaine, Nicholas R. and Higgins, Stephen T. and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Artiges, Eric and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Garavan, Hugh}, - month = nov, - year = {2020}, - keywords = {Prediction, Amygdala, Adolescence, Cannabis, Risk, Social threat}, - pages = {3447--3458}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/L26BQJ6D/Spechler et al. - 2020 - Longitudinal associations between amygdala reactiv.pdf:application/pdf}, -} - -@article{kuhn_brain_2020, - title = {Brain structure and habitat: {Do} the brains of our children tell us where they have been brought up?}, - volume = {222}, - issn = {1053-8119}, - shorttitle = {Brain structure and habitat}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811920307114}, - doi = {10.1016/j.neuroimage.2020.117225}, - abstract = {Recently many lifestyle factors have been shown to be associated with brain structural alterations. At present we are facing increasing population shifts from rural to urban areas, which considerably change the living environments of human beings. To investigate the association between rural vs. urban upbringing and brain structure we selected 106 14-year old adolescents of whom half were exclusively raised in rural areas and the other half who exclusively lived in cities. Voxel-based morphometry revealed a group difference in left hippocampal formation (Rural {\textgreater} City), which was positively associated with cognitive performance in a spatial processing task. Moreover, significant group differences were observed in spatial processing (Rural {\textgreater} City). A mediation analysis revealed that hippocampal formation accounted for more than half of the association between upbringing and spatial processing. The results are compatible with studies reporting earlier and more intense opportunities for spatial exploration in children brought up in rural areas. The results are interesting in the light of urban planning where spaces enabling spatial exploration for children may deserve more attention.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Kühn, Simone and Banaschewski, Tobias and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Meyer-Lindenberg, Andreas and Gallinat, Jürgen}, - month = nov, - year = {2020}, - keywords = {Neuroimaging, Voxel-based morphometry, Environmental neuroscience, City living, Rural, Urbanicity}, - pages = {117225}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YNB2IW69/Kühn et al. - 2020 - Brain structure and habitat Do the brains of our .pdf:application/pdf}, -} - -@article{robinson_association_2020, - title = {Association of {Genetic} and {Phenotypic} {Assessments} {With} {Onset} of {Disordered} {Eating} {Behaviors} and {Comorbid} {Mental} {Health} {Problems} {Among} {Adolescents}}, - volume = {3}, - issn = {2574-3805}, - url = {https://doi.org/10.1001/jamanetworkopen.2020.26874}, - doi = {10.1001/jamanetworkopen.2020.26874}, - abstract = {Eating disorders are serious mental disorders with increasing prevalence. Without early identification and treatment, eating disorders may run a long-term course.To characterize any associations among disordered eating behaviors (DEBs) and other mental health disorders and to identify early associations with the development of symptoms over time.This multicenter, population-based, longitudinal cohort study used data from baseline (collected in 2010), follow-up 1 (collected in 2012), and follow-up 2 (collected in 2015) of the IMAGEN Study, which included adolescents recruited from 8 European sites. The present study assessed data from 1623 healthy adolescents, aged 14 years at baseline, recruited from high schools. Data analyses were performed from January 2018 to September 2019.Body mass index (BMI), mental health symptoms, substance use behaviors, and personality variables were investigated as time-varying associations of DEBs (dieting, binge eating, and purging) or change in BMI over time. Polygenic risk scores were calculated to investigate genetic contributions associated with BMI, attention-deficit/hyperactivity disorder (ADHD) and neuroticism to DEBs.In this cohort study of 1623 adolescents (829 girls [51.1\%]) recruited at a mean (SD) age of 14.5 (0.4) years and followed up at ages 16 and 19 years, 278 adolescents (17.1\%) reported binge eating, 334 adolescents (20.6\%) reported purging, and 356 adolescents (21.9\%) reported dieting at 14, 16, or 19 years. Among the precursors of DEBs, high BMI was associated with future dieting (OR, 3.44; 95\% CI, 2.09-5.65). High levels of neuroticism (OR, 1.04; 95\% CI, 1.01-1.06), conduct problems (OR, 1.41; 95\% CI, 1.17-1.69), and deliberate self-harm (OR, 2.18; 95\% CI, 1.37-3.45) were associated with future binge eating. Low agreeableness (OR, 0.95; 95\% CI, 0.92-0.97), deliberate self-harm (OR, 2.59; 95\% CI, 1.69-3.95), conduct problems (OR, 1.42; 95\% CI, 1.20-1.68), alcohol misuse (OR, 1.31; 95\% CI, 1.10-1.54), and drug abuse (OR, 2.91; 95\% CI, 1.78-4.74) were associated with future purging. Polygenetic risk scores for BMI were associated with dieting (at 14 years: OR, 1.27; lower bound 95\% CI, 1.08; at 16 years: OR, 1.38; lower bound 95\% CI, 1.17); ADHD, with purging (at 16 years: OR, 1.25; lower bound 95\% CI, 1.08; at 19 years, OR, 1.23; lower bound 95\% CI, 1.06); and neuroticism, with binge eating (at 14 years: OR, 1.32; lower bound 95\% CI, 1.11; at 16 years: OR, 1.24; lower bound 95\% CI, 1.06), highlighting distinct etiologic overlaps between these traits. The DEBs predated other mental health problems, with dieting at 14 years associated with future symptoms of depression (OR, 2.53; 95\% CI, 1.56-4.10), generalized anxiety (OR, 2.27; 95\% CI, 1.14-4.51), deliberate self-harm (OR, 2.10; 95\% CI, 1.51-4.24), emotional problems (OR, 1.24; 95\% CI, 1.08-1.43), and smoking (OR, 2.16; 95\% CI, 1.36-3.48). Purging at 14 years was also associated with future depression (OR, 2.87; 95\% CI, 1.69-5.01) and anxiety (OR, 2.48; 95\% CI, 1.49-4.12) symptoms.The findings of this study delineate temporal associations and shared etiologies among DEBs and other mental health disorders and emphasize the potential of genetic and phenotypical assessments of obesity, behavioral disorders, and neuroticism to improve early and differential diagnosis of eating disorders.}, - number = {12}, - urldate = {2024-03-12}, - journal = {JAMA Network Open}, - author = {Robinson, Lauren and Zhang, Zuo and Jia, Tianye and Bobou, Marina and Roach, Anna and Campbell, Iain and Irish, Madeleine and Quinlan, Erin Burke and Tay, Nicole and Barker, Edward D. and Banaschewski, Tobias and Bokde, Arun L. W. and Grigis, Antoine and Garavan, Hugh and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Stringaris, Argyris and Penttilä, Jani and van Noort, Betteke and Grimmer, Yvonne and Martinot, Marie-Laure Paillère and Insensee, Corinna and Becker, Andreas and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Schmidt, Ulrike and Desrivières, Sylvane and {IMAGEN Consortium}}, - month = dec, - year = {2020}, - pages = {e2026874}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YPCZ99UM/Robinson et al. - 2020 - Association of Genetic and Phenotypic Assessments .pdf:application/pdf}, -} - -@article{daedelow_are_2021, - title = {Are psychotic-like experiences related to a discontinuation of cannabis consumption in young adults?}, - volume = {228}, - issn = {0920-9964}, - url = {https://www.sciencedirect.com/science/article/pii/S0920996421000220}, - doi = {10.1016/j.schres.2021.01.002}, - abstract = {Objective -To assess changes in cannabis use in young adults as a function of psychotic-like experiences. -Method -Participants were initially recruited at age 14 in high schools for the longitudinal IMAGEN study. All measures presented here were assessed at follow-ups at age 19 and at age 22, respectively. Perceived stress was only assessed once at age 22. Ever users of cannabis (N = 552) gave qualitative and quantitative information on cannabis use and psychotic-like experiences using the Community Assessment of Psychic Experiences (CAPE). Of those, nearly all n = 549 reported to have experienced at least one psychotic experience of any form at age 19. -Results -Mean cannabis use increased from age 19 to 22 and age of first use of cannabis was positively associated with a change in cannabis use between the two time points. Change in cannabis use was not significantly associated with psychotic-like experiences at age 19 or 22. In exploratory analysis, we observed a positive association between perceived stress and the experience of psychotic experiences at age 22. -Conclusion -Age of first use of cannabis influenced trajectories of young cannabis users with later onset leading to higher increase, whereas the frequency of psychotic-like experiences was not associated with a change in cannabis use. The observed association between perceived stress and psychotic-like experiences at age 22 emphasizes the importance of stress experiences in developing psychosis independent of cannabis use.}, - urldate = {2024-03-12}, - journal = {Schizophrenia Research}, - author = {Daedelow, Laura S. and Banaschewski, Tobias and Berning, Moritz and Bokde, Arun L. W. and Brühl, Rüdiger and Burke Quinlan, Erin and Curran, H. Valerie and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Hardon, Anita and Kaminski, Jakob and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Murray, Hayley and Nees, Frauke and Oei, Nicole Y. L. and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Rosenthal, Annika and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Wiers, Reinout W. and Schumann, Gunter and Heinz, Andreas}, - month = feb, - year = {2021}, - keywords = {Age of first use, Cannabis discontinuation hypothesis, Cannabis use, Perceived stress, Psychotic-like experiences}, - pages = {271--279}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/94FVEU6I/Daedelow et al. - 2021 - Are psychotic-like experiences related to a discon.pdf:application/pdf}, -} - -@article{xie_reward_2021, - title = {Reward {Versus} {Nonreward} {Sensitivity} of the {Medial} {Versus} {Lateral} {Orbitofrontal} {Cortex} {Relates} to the {Severity} of {Depressive} {Symptoms}}, - volume = {6}, - issn = {2451-9022}, - url = {https://www.sciencedirect.com/science/article/pii/S2451902220302548}, - doi = {10.1016/j.bpsc.2020.08.017}, - abstract = {Background -The orbitofrontal cortex (OFC) is implicated in depression. The hypothesis investigated was whether the OFC sensitivity to reward and nonreward is related to the severity of depressive symptoms. -Methods -Activations in the monetary incentive delay task were measured in the IMAGEN cohort at ages 14 years (n = 1877) and 19 years (n = 1140) with a longitudinal design. Clinically relevant subgroups were compared at ages 19 (high-severity group: n = 116; low-severity group: n = 206) and 14. -Results -The medial OFC exhibited graded activation increases to reward, and the lateral OFC had graded activation increases to nonreward. In this general population, the medial and lateral OFC activations were associated with concurrent depressive symptoms at both ages 14 and 19 years. In a stratified high-severity depressive symptom group versus control group comparison, the lateral OFC showed greater sensitivity for the magnitudes of activations related to nonreward in the high-severity group at age 19 (p = .027), and the medial OFC showed decreased sensitivity to the reward magnitudes in the high-severity group at both ages 14 (p = .002) and 19 (p = .002). In a longitudinal design, there was greater sensitivity to nonreward of the lateral OFC at age 14 for those who exhibited high depressive symptom severity later at age 19 (p = .003). -Conclusions -Activations in the lateral OFC relate to sensitivity to not winning, were associated with high depressive symptom scores, and at age 14 predicted the depressive symptoms at ages 16 and 19. Activations in the medial OFC were related to sensitivity to winning, and reduced reward sensitivity was associated with concurrent high depressive symptom scores.}, - number = {3}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry: Cognitive Neuroscience and Neuroimaging}, - author = {Xie, Chao and Jia, Tianye and Rolls, Edmund T. and Robbins, Trevor W. and Sahakian, Barbara J. and Zhang, Jie and Liu, Zhaowen and Cheng, Wei and Luo, Qiang and Zac Lo, Chun-Yi and Wang, He and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Hohmann, Sarah and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Feng, Jianfeng and Artiges, Eric and Aydin, Semiha and Banaschewski, Tobias and Barbot, Alexis and Barker, Gareth and Becker, Andreas and Bezivin-Frere, Pauline and Biondo, Francesca and Bokde, Arun and Büchel, Christian and Chu, Congying and Conrod, Patricia and Daedelow, Laura and Dalley, Jeffrey and Desrivieres, Sylvane and Dooley, Eoin and Filippi, Irina and Fillmer, Ariane and Flor, Herta and Fröhner, Juliane and Frouin, Vincent and Garavan, Hugh and Gowland, Penny and Grimmer, Yvonne and Heinz, Andreas and Hohmann, Sarah and Ihlenfeld, Albrecht and Ing, Alex and Isensee, Corinna and Ittermann, Bernd and Jia, Tianye and Lemaitre, Hervé and Lethbridge, Emma and Martinot, Jean-Luc and Millenet, Sabina and Miller, Sarah and Miranda, Ruben and Nees, Frauke and Paillere, Marie-Laure and Papadopoulos, Dimitri and Paus, Tomáš and Pausova, Zdenka and Pentilla, Jani and Poline, Jean-Baptiste and Poustka, Luise and Burke, Erin and Rapp, Michael and Robbins, Trevor and Robert, Gabriel and Rogers, John and Ruggeri, Barbara and Schumann, Gunter and Smolka, Michael and Stringaris, Argyris and van Noort, Betteke and Walter, Henrik and Whelan, Robert and Simon, Roux and Williams, Steve and Zhang, Yuning}, - month = mar, - year = {2021}, - keywords = {Depression, Adolescents, Monetary incentive delay task, Nonreward sensitivity, Orbitofrontal cortex, Reward anticipation, Reward sensitivity, Ventral striatum}, - pages = {259--269}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LA549CQR/Xie et al. - 2021 - Reward Versus Nonreward Sensitivity of the Medial .pdf:application/pdf}, -} - -@article{bottinger_orbitofrontal_2022, - title = {Orbitofrontal control of conduct problems? {Evidence} from healthy adolescents processing negative facial affect}, - volume = {31}, - issn = {1435-165X}, - shorttitle = {Orbitofrontal control of conduct problems?}, - url = {https://doi.org/10.1007/s00787-021-01770-1}, - doi = {10.1007/s00787-021-01770-1}, - abstract = {Conduct problems (CP) in patients with disruptive behavior disorders have been linked to impaired prefrontal processing of negative facial affect compared to controls. However, it is unknown whether associations with prefrontal activity during affective face processing hold along the CP dimension in a healthy population sample, and how subcortical processing is affected. We measured functional brain responses during negative affective face processing in 1444 healthy adolescents [M = 14.39 years (SD = 0.40), 51.5\% female] from the European IMAGEN multicenter study. To determine the effects of CP, we applied a two-step approach: (a) testing matched subgroups of low versus high CP, extending into the clinical range [N = 182 per group, M = 14.44 years, (SD = 0.41), 47.3\% female] using analysis of variance, and (b) considering (non)linear effects along the CP dimension in the full sample and in the high CP group using multiple regression. We observed no significant cortical or subcortical effect of CP group on brain responses to negative facial affect. In the full sample, regression analyses revealed a significant linear increase of left orbitofrontal cortex (OFC) activity with increasing CP up to the clinical range. In the high CP group, a significant inverted u-shaped effect indicated that left OFC responses decreased again in individuals with high CP. Left OFC activity during negative affective processing which is increasing with CP and decreasing in the highest CP range may reflect on the importance of frontal control mechanisms that counteract the consequences of severe CP by facilitating higher social engagement and better evaluation of social content in adolescents.}, - language = {en}, - number = {8}, - urldate = {2024-03-12}, - journal = {European Child \& Adolescent Psychiatry}, - author = {Böttinger, Boris William and Baumeister, Sarah and Millenet, Sabina and Barker, Gareth J. and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Banaschewski, Tobias and Brandeis, Daniel and Nees, Frauke and {IMAGEN Consortium}}, - month = aug, - year = {2022}, - keywords = {FMRI, Adolescence, Orbitofrontal cortex, Affective processing, Conduct problems, Subclinical}, - pages = {1--10}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7RAGULWH/Böttinger et al. - 2022 - Orbitofrontal control of conduct problems Evidenc.pdf:application/pdf}, -} - -@article{wang_functional_2021, - title = {Functional {Connectivity} {Predicts} {Individual} {Development} of {Inhibitory} {Control} during {Adolescence}}, - volume = {31}, - issn = {1047-3211}, - url = {https://doi.org/10.1093/cercor/bhaa383}, - doi = {10.1093/cercor/bhaa383}, - abstract = {Derailment of inhibitory control (IC) underlies numerous psychiatric and behavioral disorders, many of which emerge during adolescence. Identifying reliable predictive biomarkers that place the adolescents at elevated risk for future IC deficits can help guide early interventions, yet the scarcity of longitudinal research has hindered the progress. Here, using a large-scale longitudinal dataset in which the same subjects performed a stop signal task during functional magnetic resonance imaging at ages 14 and 19, we tracked their IC development individually and tried to find the brain features predicting their development by constructing prediction models using 14-year-olds’ functional connections within a network or between a pair of networks. The participants had distinct between-subject trajectories in their IC development. Of the candidate connections used for prediction, ventral attention-subcortical network interconnections could predict the individual development of IC and formed a prediction model that generalized to previously unseen individuals. Furthermore, we found that connectivity between these two networks was related to substance abuse problems, an IC-deficit related problematic behavior, within 5 years. Our study reveals individual differences in IC development from mid- to late-adolescence and highlights the importance of ventral attention-subcortical network interconnections in predicting future IC development and substance abuse in adolescents.}, - number = {5}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Wang, Haiyan and Fan, Lingzhong and Song, Ming and Liu, Bing and Wu, Dongya and Jiang, Rongtao and Li, Jin and Li, Ang and Banaschewski, Tobias and Bokde, Arun L W and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Chaarani, Bader and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H and Smolka, Michael N and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Jiang, Tianzi}, - month = may, - year = {2021}, - pages = {2686--2700}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SKBMV6CC/Wang et al. - 2021 - Functional Connectivity Predicts Individual Develo.pdf:application/pdf}, -} - -@article{wendel_residual_2021, - title = {Residual effects of cannabis-use on neuropsychological functioning}, - volume = {59}, - issn = {0885-2014}, - url = {https://www.sciencedirect.com/science/article/pii/S0885201421000678}, - doi = {10.1016/j.cogdev.2021.101072}, - abstract = {Non-acute effects of cannabis on neurocognition in adolescents remain unclear with most studies being cross-sectional. Therefore, the aim of this longitudinal, multi-center study was to examine the effects of cannabis use on cognitive abilities in participants emerging into adulthood. Data on substance use as well as neurocognitive measures were assessed in 804 adolescents (441 females, 363 males) at age 14 and 19. First, cross-sectional analyses of baseline and follow-up data were conducted using analyses of covariance (ANCOVA). Second, repeated measures ANCOVAs were conducted to quantify longitudinal change. Cross-sectionally, we detected no significant neurocognitive differences before initiation of drug use. However, after controlling for confounders, light cannabis use as well as late-onset thereof was associated with increased decision-making skills both cross-sectionally at follow-up as well as longitudinally compared to non-using controls. In summary, our data suggests that decision-making is not impaired when cannabis is used in moderation and onset of use occurs after the age of 15. In addition, we find no evidence to support the presumption that cannabis consumption leads to a decline in neurocognitive ability.}, - urldate = {2024-03-12}, - journal = {Cognitive Development}, - author = {Wendel, Lena Kristin and Daedelow, Laura and Kaminski, Jakob and Banaschewski, Tobias and Millenet, Sabina and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Whelan, Robert and Schumann, Gunter and Walter, Henrik}, - month = jul, - year = {2021}, - keywords = {Adolescence, Cannabis, Brain development, Decision-making, Marijuana, Neurocognition}, - pages = {101072}, -} - -@article{modabbernia_linked_2021, - title = {Linked patterns of biological and environmental covariation with brain structure in adolescence: a population-based longitudinal study}, - volume = {26}, - copyright = {2020 The Author(s)}, - issn = {1476-5578}, - shorttitle = {Linked patterns of biological and environmental covariation with brain structure in adolescence}, - url = {https://www.nature.com/articles/s41380-020-0757-x}, - doi = {10.1038/s41380-020-0757-x}, - abstract = {Adolescence is a period of major brain reorganization shaped by biologically timed and by environmental factors. We sought to discover linked patterns of covariation between brain structural development and a wide array of these factors by leveraging data from the IMAGEN study, a longitudinal population-based cohort of adolescents. Brain structural measures and a comprehensive array of non-imaging features (relating to demographic, anthropometric, and psychosocial characteristics) were available on 1476 IMAGEN participants aged 14 years and from a subsample reassessed at age 19 years (n = 714). We applied sparse canonical correlation analyses (sCCA) to the cross-sectional and longitudinal data to extract modes with maximum covariation between neuroimaging and non-imaging measures. Separate sCCAs for cortical thickness, cortical surface area and subcortical volumes confirmed that each imaging phenotype was correlated with non-imaging features (sCCA r range: 0.30–0.65, all PFDR {\textless} 0.001). Total intracranial volume and global measures of cortical thickness and surface area had the highest canonical cross-loadings ({\textbar}ρ{\textbar} = 0.31−0.61). Age, physical growth and sex had the highest association with adolescent brain structure ({\textbar}ρ{\textbar} = 0.24−0.62); at baseline, further significant positive associations were noted for cognitive measures while negative associations were observed at both time points for prenatal parental smoking, life events, and negative affect and substance use in youth ({\textbar}ρ{\textbar} = 0.10−0.23). Sex, physical growth and age are the dominant influences on adolescent brain development. We highlight the persistent negative influences of prenatal parental smoking and youth substance use as they are modifiable and of relevance for public health initiatives.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Modabbernia, Amirhossein and Reichenberg, Abraham and Ing, Alex and Moser, Dominik A. and Doucet, Gaelle E. and Artiges, Eric and Banaschewski, Tobias and Barker, Gareth J. and Becker, Andreas and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Fröhner, Juliane H. and Garavan, Hugh and Gowland, Penny and Grigis, Antoine and Grimmer, Yvonne and Heinz, Andreas and Insensee, Corinna and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Millenet, Sabina and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Penttilä, Jani and Poustka, Luise and Smolka, Michael N. and Stringaris, Argyris and van Noort, Betteke M. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Frangou, Sophia}, - month = sep, - year = {2021}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychology, Neuroscience}, - pages = {4905--4918}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A5KDZ2UB/Modabbernia et al. - 2021 - Linked patterns of biological and environmental co.pdf:application/pdf}, -} - -@article{penninck_immune-related_2021, - title = {Immune-{Related} {Genetic} {Overlap} {Between} {Regional} {Gray} {Matter} {Reductions} and {Psychiatric} {Symptoms} in {Adolescents}, and {Gene}-{Set} {Validation} in a {Translational} {Model}}, - volume = {15}, - issn = {1662-5137}, - url = {https://www.frontiersin.org/articles/10.3389/fnsys.2021.725413}, - doi = {10.3389/fnsys.2021.725413}, - abstract = {Here, we investigated a possible common immune-related genetic link between these two phenomena in a population study of human adolescents. Hippocampal and medial prefrontal cortex (mPFC) GM volumes were extracted from the IMAGEN database in 1563 14-year-olds recruited from the community in 4 european countries. Two polygenic risk scores (PRS) were constructed with inflammation-related SNPs; one accounting for hippocampal GM volume at age 14 and another for mPFC GM volume at age 14. We found 26 “independent” SNPs that correlated with the hippocampal volumes and 29 with the mPFC volumes. The predictive ability of both PRSs with regards to the presence of psychiatric symptoms at age 18 was investigated by correlating the PRSs with psychometric questionnaires obtained at age 18. The PRSs (but not control PRSs constructed with random SNPs) were found to have significant predictive power with regards to the presence of depressive symptoms, positive psychotic symptoms and externalizing symptoms in later adolescence. We also found that the effect of childhood maltreatment, one of the major environmental risk factors for depression and other mental disorders, interacted with the inflammation-related genetic effect. We next sought to validate this finding by investigating our set of inflammatory genes in a translational animal model of early life adversity. Mice were subjected to a protocol of maternal separation at an early post-natal age. We evaluated depressive behaviors in separated and non-separated mice at adolescence and their correlations with the concomitant expression of our genes in whole blood samples. We show that in mice, early life adversity affected the expression of our set of genes in peripheral blood, and that levels of expression correlated with symptoms of negative affects at adolescence. Overall, our translational findings in adolescent mice and men provide a novel validated gene-set of immune-related genes for further research in the early stages of mood disorders.}, - language = {English}, - urldate = {2024-03-12}, - journal = {Frontiers in Systems Neuroscience}, - author = {Penninck, Lukas and Ibrahim, El Chérif and Artiges, Eric and Gorgievski, Victor and Desrivières, Sylvane and Farley, Severine and Filippi, Irina and de Macedo, Carlos E. A. and Belzeaux, Raoul and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Grenier, Julien and Schumann, Gunter and Paillère Martinot, Marie-Laure and Tzavara, Eleni T. and Martinot, Jean-Luc and Consortium, for the IMAGEN}, - month = sep, - year = {2021}, - note = {Publisher: Frontiers}, - keywords = {MRI, adolescence, childhood maltreatment, Immunity genes, psychiatric symptoms}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/R6GJRSGK/Penninck et al. - 2021 - Immune-Related Genetic Overlap Between Regional Gr.pdf:application/pdf}, -} - -@article{price_examination_2021, - title = {Examination of the association between exposure to childhood maltreatment and brain structure in young adults: a machine learning analysis}, - volume = {46}, - copyright = {2021 The Author(s), under exclusive licence to American College of Neuropsychopharmacology}, - issn = {1740-634X}, - shorttitle = {Examination of the association between exposure to childhood maltreatment and brain structure in young adults}, - url = {https://www.nature.com/articles/s41386-021-00987-7}, - doi = {10.1038/s41386-021-00987-7}, - abstract = {Exposure to maltreatment during childhood is associated with structural changes throughout the brain. However, the structural differences that are most strongly associated with maltreatment remain unclear given the limited number of whole-brain studies. The present study used machine learning to identify if and how brain structure distinguished young adults with and without a history of maltreatment. Young adults (ages 18–21, n = 384) completed an assessment of childhood trauma exposure and a structural MRI as part of the IMAGEN study. Elastic net regularized regression was used to identify the structural features that identified those with a history of maltreatment. A generalizable model that included 7 cortical thicknesses, 15 surface areas, and 5 subcortical volumes was identified (area under the receiver operating characteristic curve = 0.71, p {\textless} 0.001). Those with a maltreatment history had reduced surface areas and cortical thicknesses primarily in fronto-temporal regions. This group also had larger cortical thicknesses in occipital regions and surface areas in frontal regions. The results suggest childhood maltreatment is associated with multiple measures of structure throughout the brain. The use of a large sample without exposure to adulthood trauma provides further evidence for the unique contribution of childhood trauma to brain structure. The identified regions overlapped with regions associated with psychopathology in adults with maltreatment histories, which offers insights as to how these disorders manifest.}, - language = {en}, - number = {11}, - urldate = {2024-03-12}, - journal = {Neuropsychopharmacology}, - author = {Price, Matthew and Albaugh, Matthew and Hahn, Sage and Juliano, Anthony C. and Fani, Negar and Brier, Zoe M. F. and Legrand, Alison C. and van Stolk-Cooke, Katherine and Chaarani, Bader and Potter, Alexandra and Peck, Kelly and Allgaier, Nicholas and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Garavan, Hugh}, - month = oct, - year = {2021}, - note = {Publisher: Nature Publishing Group}, - keywords = {Trauma, Stress and resilience, Diagnostic markers, Human behaviour}, - pages = {1888--1894}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FDTW88GY/Price et al. - 2021 - Examination of the association between exposure to.pdf:application/pdf}, -} - -@article{qi_reward_2021, - series = {Stress, {Inflammation}, and {Synaptic} {Remodeling} in {Addiction}}, - title = {Reward {Processing} in {Novelty} {Seekers}: {A} {Transdiagnostic} {Psychiatric} {Imaging} {Biomarker}}, - volume = {90}, - issn = {0006-3223}, - shorttitle = {Reward {Processing} in {Novelty} {Seekers}}, - url = {https://www.sciencedirect.com/science/article/pii/S0006322321000780}, - doi = {10.1016/j.biopsych.2021.01.011}, - abstract = {Background -Dysfunctional reward processing is implicated in multiple mental disorders. Novelty seeking (NS) assesses preference for seeking novel experiences, which is linked to sensitivity to reward environmental cues. -Methods -A subset of 14-year-old adolescents (IMAGEN) with the top 20\% ranked high-NS scores was used to identify high-NS–associated multimodal components by supervised fusion. These features were then used to longitudinally predict five different risk scales for the same and unseen subjects (an independent dataset of subjects at 19 years of age that was not used in predictive modeling training at 14 years of age) (within IMAGEN, n ≈1100) and even for the corresponding symptom scores of five types of patient cohorts (non-IMAGEN), including drinking (n = 313), smoking (n = 104), attention-deficit/hyperactivity disorder (n = 320), major depressive disorder (n = 81), and schizophrenia (n = 147), as well as to classify different patient groups with diagnostic labels. -Results -Multimodal biomarkers, including the prefrontal cortex, striatum, amygdala, and hippocampus, associated with high NS in 14-year-old adolescents were identified. The prediction models built on these features are able to longitudinally predict five different risk scales, including alcohol drinking, smoking, hyperactivity, depression, and psychosis for the same and unseen 19-year-old adolescents and even predict the corresponding symptom scores of five types of patient cohorts. Furthermore, the identified reward-related multimodal features can classify among attention-deficit/hyperactivity disorder, major depressive disorder, and schizophrenia with an accuracy of 87.2\%. -Conclusions -Adolescents with higher NS scores can be used to reveal brain alterations in the reward-related system, implicating potential higher risk for subsequent development of multiple disorders. The identified high-NS–associated multimodal reward-related signatures may serve as a transdiagnostic neuroimaging biomarker to predict disease risks or severity.}, - number = {8}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry}, - author = {Qi, Shile and Schumann, Gunter and Bustillo, Juan and Turner, Jessica A. and Jiang, Rongtao and Zhi, Dongmei and Fu, Zening and Mayer, Andrew R. and Vergara, Victor M. and Silva, Rogers F. and Iraji, Armin and Chen, Jiayu and Damaraju, Eswar and Ma, Xiaohong and Yang, Xiao and Stevens, Michael and Mathalon, Daniel H. and Ford, Judith M. and Voyvodic, James and Mueller, Bryon A. and Belger, Aysenil and Potkin, Steven G. and Preda, Adrian and Zhuo, Chuanjun and Xu, Yong and Chu, Congying and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Calhoun, Vince D. and Sui, Jing and Schumann, Gunter and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert}, - month = oct, - year = {2021}, - keywords = {Schizophrenia, Attention-deficit/hyperactivity disorder, ADHD, Major depressive disorders, MDD, Novelty seeking, Reward processing, Substance use}, - pages = {529--539}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GLY4C6GC/Qi et al. - 2021 - Reward Processing in Novelty Seekers A Transdiagn.pdf:application/pdf}, -} - -@article{cao_characterizing_2021, - title = {Characterizing reward system neural trajectories from adolescence to young adulthood}, - volume = {52}, - issn = {1878-9293}, - url = {https://www.sciencedirect.com/science/article/pii/S1878929321001316}, - doi = {10.1016/j.dcn.2021.101042}, - abstract = {Mixed findings exist in studies comparing brain responses to reward in adolescents and adults. Here we examined the trajectories of brain response, functional connectivity and task-modulated network properties during reward processing with a large-sample longitudinal design. Participants from the IMAGEN study performed a Monetary Incentive Delay task during fMRI at timepoint 1 (T1; n = 1304, mean age=14.44 years old) and timepoint 2 (T2; n = 1241, mean age=19.09 years). The Alcohol Use Disorders Identification Test (AUDIT) was administrated at both T1 and T2 to assess a participant’s alcohol use during the past year. Voxel-wise linear mixed effect models were used to compare whole brain response as well as functional connectivity of the ventral striatum (VS) during reward anticipation (large reward vs no-reward cue) between T1 and T2. In addition, task-modulated networks were constructed using generalized psychophysiological interaction analysis and summarized with graph theory metrics. To explore alcohol use in relation to development, participants with no/low alcohol use at T1 but increased alcohol use to hazardous use level at T2 (i.e., participants with AUDIT≤2 at T1 and ≥8 at T2) were compared against those with consistently low scores (i.e., participants with AUDIT≤2 at T1 and ≤7 at T2). Across the whole sample, lower brain response during reward anticipation was observed at T2 compared with T1 in bilateral caudate nucleus, VS, thalamus, midbrain, dorsal anterior cingulate as well as left precentral and postcentral gyrus. Conversely, greater response was observed bilaterally in the inferior and middle frontal gyrus and right precentral and postcentral gyrus at T2 (vs. T1). Increased functional connectivity with VS was found in frontal, temporal, parietal and occipital regions at T2. Graph theory metrics of the task-modulated network showed higher inter-regional connectivity and topological efficiency at T2. Interactive effects between time (T1 vs. T2) and alcohol use group (low vs. high) on the functional connectivity were observed between left middle temporal gyrus and right VS and the characteristic shortest path length of the task-modulated networks. Collectively, these results demonstrate the utility of the MID task as a probe of typical brain response and network properties during development and of differences in these features related to adolescent drinking, a reward-related behaviour associated with heightened risk for future negative health outcomes.}, - urldate = {2024-03-12}, - journal = {Developmental Cognitive Neuroscience}, - author = {Cao, Zhipeng and Ottino-Gonzalez, Jonatan and Cupertino, Renata B. and Juliano, Anthony and Chaarani, Bader and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Robinson, Lauren and Smolka, Michael N. and Walter, Henrik and Winterer, Jeanne and Schumann, Gunter and Whelan, Robert and Mackey, Scott and Garavan, Hugh}, - month = dec, - year = {2021}, - keywords = {Adolescence, Monetary Incentive Delay task, Neural development, Reward system, Task-modulated network}, - pages = {101042}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/U9BWI3V6/Cao et al. - 2021 - Characterizing reward system neural trajectories f.pdf:application/pdf}, -} - -@article{liao_similarity_2021, - title = {Similarity and stability of face network across populations and throughout adolescence and adulthood}, - volume = {244}, - issn = {1053-8119}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811921008600}, - doi = {10.1016/j.neuroimage.2021.118587}, - abstract = {The ability to extract cues from faces is fundamental for social animals, including humans. An individual's profile of functional connectivity across a face network can be shaped by common organizing principles, stable individual traits, and time-varying mental states. In the present study, we used data obtained with functional magnetic resonance imaging in two cohorts, IMAGEN (N = 534) and ALSPAC (N = 465), to investigate - both at group and individual levels - the consistency of the regional profile of functional connectivity across populations (IMAGEN, ALSPAC) and time (Visits 1 to 3 in IMAGEN; age 14 to 22 years). At the group level, we found a robust canonical profile of connectivity both across populations and time. At the individual level, connectivity profiles deviated from the canonical profile, and the magnitude of this deviation related to the presence of psychopathology. These findings suggest that the brain processes faces in a highly stereotypical manner, and that the deviations from this normative pattern may be related to the risk of mental illness.}, - urldate = {2024-03-12}, - journal = {NeuroImage}, - author = {Liao, Zhijie and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Paus, Tomáš}, - month = dec, - year = {2021}, - keywords = {Psychopathology, fMRI, Adolescence, Canonical connectivity profile, Change}, - pages = {118587}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/9965U9TP/Liao et al. - 2021 - Similarity and stability of face network across po.pdf:application/pdf}, -} - -@article{zhang_development_2021, - series = {Corticostriatal {Function} and {Eating} {Disorders}}, - title = {Development of {Disordered} {Eating} {Behaviors} and {Comorbid} {Depressive} {Symptoms} in {Adolescence}: {Neural} and {Psychopathological} {Predictors}}, - volume = {90}, - issn = {0006-3223}, - shorttitle = {Development of {Disordered} {Eating} {Behaviors} and {Comorbid} {Depressive} {Symptoms} in {Adolescence}}, - url = {https://www.sciencedirect.com/science/article/pii/S0006322320316723}, - doi = {10.1016/j.biopsych.2020.06.003}, - abstract = {Background -Eating disorders are common in adolescence and are devastating and strongly comorbid with other psychiatric disorders. Yet little is known about their etiology, knowing which would aid in developing effective preventive measures. -Methods -Longitudinal assessments of disordered eating behaviors (DEBs)—binge-eating, purging, and dieting—and comorbid psychopathology were measured in 1386 adolescents from the IMAGEN study. Development of DEBs and associated mental health problems was investigated by comparing participants who reported symptoms at ages 16 or 19 years, but not at age 14 years, with asymptomatic control participants. Voxel-based morphometry and psychopathological differences at age 14 were investigated to identify risk factors for the development of DEBs and associated mental health problems. -Results -DEBs and depressive symptoms developed together. Emotional and behavioral problems, including symptoms of attention-deficit/hyperactivity disorder and conduct disorder, predated their development. Alterations in frontostriatal brain areas also predated the development of DEBs and depressive symptoms. Specifically, development of binge-eating was predicted by higher gray matter volumes in the right putamen/globus pallidus at age 14. Conversely, development of purging and depressive symptoms was predicted by lower volumes in the medial orbitofrontal, dorsomedial, and dorsolateral prefrontal cortices. Lower gray matter volumes in the orbitofrontal and anterior cingulate cortices mediated the relationship between attention-deficit/hyperactivity disorder and conduct disorder symptoms and future purging and depressive symptoms. -Conclusions -These findings suggest that alterations in frontal brain circuits are part of the shared etiology among eating disorders, attention-deficit/hyperactivity disorder, conduct disorder, and depression and highlight the importance of a transdiagnostic approach to treating these conditions.}, - number = {12}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry}, - author = {Zhang, Zuo and Robinson, Lauren and Jia, Tianye and Quinlan, Erin Burke and Tay, Nicole and Chu, Congying and Barker, Edward D. and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Stringaris, Argyris and Penttilä, Jani and van Noort, Betteke and Grimmer, Yvonne and Paillère Martinot, Marie-Laure and Isensee, Corinna and Becker, Andreas and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Schmidt, Ulrike and Desrivières, Sylvane}, - month = dec, - year = {2021}, - keywords = {Depression, Biomarkers, Eating disorders, Attention-deficit/hyperactivity disorder, Gray matter volume, Conduct disorder}, - pages = {853--862}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WWZNYI77/Zhang et al. - 2021 - Development of Disordered Eating Behaviors and Com.pdf:application/pdf}, -} - -@article{xu_global_2022, - title = {Global urbanicity is associated with brain and behaviour in young people}, - volume = {6}, - copyright = {2021 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {2397-3374}, - url = {https://www.nature.com/articles/s41562-021-01204-7}, - doi = {10.1038/s41562-021-01204-7}, - abstract = {Urbanicity is a growing environmental challenge for mental health. Here, we investigate correlations of urbanicity with brain structure and function, neuropsychology and mental illness symptoms in young people from China and Europe (total n = 3,867). We developed a remote-sensing satellite measure (UrbanSat) to quantify population density at any point on Earth. UrbanSat estimates of urbanicity were correlated with brain volume, cortical surface area and brain network connectivity in the medial prefrontal cortex and cerebellum. UrbanSat was also associated with perspective-taking and depression symptoms, and this was mediated by neural variables. Urbanicity effects were greatest when urban exposure occurred in childhood for the cerebellum, and from childhood to adolescence for the prefrontal cortex. As UrbanSat can be generalized to different geographies, it may enable assessments of correlations of urbanicity with mental illness and resilience globally.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Nature Human Behaviour}, - author = {Xu, Jiayuan and Liu, Xiaoxuan and Li, Qiaojun and Goldblatt, Ran and Qin, Wen and Liu, Feng and Chu, Congying and Luo, Qiang and Ing, Alex and Guo, Lining and Liu, Nana and Liu, Huaigui and Huang, Conghong and Cheng, Jingliang and Wang, Meiyun and Geng, Zuojun and Zhu, Wenzhen and Zhang, Bing and Liao, Weihua and Qiu, Shijun and Zhang, Hui and Xu, Xiaojun and Yu, Yongqiang and Gao, Bo and Han, Tong and Cui, Guangbin and Chen, Feng and Xian, Junfang and Li, Jiance and Zhang, Jing and Zuo, Xi-Nian and Wang, Dawei and Shen, Wen and Miao, Yanwei and Yuan, Fei and Lui, Su and Zhang, Xiaochu and Xu, Kai and Zhang, Longjiang and Ye, Zhaoxiang and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Robinson, Lauren and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Winterer, Jeanne and Patrick, Kevin and Calhoun, Vince and Li, Mulin Jun and Liang, Meng and Gong, Peng and Barker, Edward D. and Clinton, Nicholas and Marquand, Andre and Yu, Le and Yu, Chunshui and Schumann, Gunter}, - month = feb, - year = {2022}, - note = {Publisher: Nature Publishing Group}, - keywords = {Environmental impact, Risk factors}, - pages = {279--293}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JJY2JPPN/Xu et al. - 2022 - Global urbanicity is associated with brain and beh.pdf:application/pdf}, -} - -@article{frohner_associations_2022, - title = {Associations of delay discounting and drinking trajectories from ages 14 to 22}, - volume = {46}, - copyright = {© 2022 The Authors. Alcoholism: Clinical \& Experimental Research published by Wiley Periodicals LLC on behalf of Research Society on Alcoholism.}, - issn = {1530-0277}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acer.14799}, - doi = {10.1111/acer.14799}, - abstract = {Background While drinking alcohol, one must choose between the immediate rewarding effects and the delayed reward of a healthier lifestyle. Individuals differ in their devaluation of a delayed reward based on the time required to receive it, i.e., delay discounting (DD). Previous studies have shown that adolescents discount more steeply than adults and that steeper DD is associated with heavier alcohol use in both groups. Methods In a large-scale longitudinal study, we investigated whether higher rates of DD are an antecedent or a consequence of alcohol use during adolescent development. As part of the IMAGEN project, 2220 adolescents completed the Monetary Choice Questionnaire as a DD measure, the Alcohol Use Disorders Identification Test, and the Timeline Follow Back interview at ages 14, 16, 18, and 22. Bivariate latent growth curve models were applied to investigate the relationship between DD and drinking. To explore the consequences of drinking, we computed the cumulative alcohol consumption and correlated it with the development of discounting. A subsample of 221 participants completed an intertemporal choice task (iTeCh) during functional magnetic resonance imaging at ages 14, 16, and 18. Repeated-measures ANOVA was used to differentiate between high-risk and low-risk drinkers on the development of neural processing during intertemporal choices. Results Overall, high rates of DD at age 14 predicted a greater increase in drinking over 8 years. In contrast, on average, moderate alcohol use did not affect DD from ages 14 to 22. Of note, we found indicators for less brain activity in top-down control areas during intertemporal choices in the participants who drank more. Conclusions Steep DD was shown to be a predictor rather than a consequence of alcohol use in low-level drinking adolescents. Important considerations for future longitudinal studies are the sampling strategies to be used and the reliability of the assessments.}, - language = {en}, - number = {4}, - urldate = {2024-03-12}, - journal = {Alcoholism: Clinical and Experimental Research}, - author = {Fröhner, Juliane H. and Ripke, Stephan and Jurk, Sarah and Li, Shu-Chen and Banaschewski, Tobias and Bokde, Arun L.W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Smolka, Michael N. and Consortium, the IMAGEN}, - year = {2022}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acer.14799}, - keywords = {adolescence, alcohol, delay discounting, latent growth curve modeling, longitudinal fMRI}, - pages = {667--681}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NNDB9MPM/Fröhner et al. - 2022 - Associations of delay discounting and drinking tra.pdf:application/pdf}, -} - -@article{toenders_predicting_2022, - title = {Predicting {Depression} {Onset} in {Young} {People} {Based} on {Clinical}, {Cognitive}, {Environmental}, and {Neurobiological} {Data}}, - volume = {7}, - issn = {2451-9022}, - url = {https://www.sciencedirect.com/science/article/pii/S2451902221000823}, - doi = {10.1016/j.bpsc.2021.03.005}, - abstract = {Background -Adolescent onset of depression is associated with long-lasting negative consequences. Identifying adolescents at risk for developing depression would enable the monitoring of risk factors and the development of early intervention strategies. Using machine learning to combine several risk factors from multiple modalities might allow prediction of depression onset at the individual level. -Methods -A subsample of a multisite longitudinal study in adolescents, the IMAGEN study, was used to predict future (subthreshold) major depressive disorder onset in healthy adolescents. Based on 2-year and 5-year follow-up data, participants were grouped into the following: 1) those developing a diagnosis of major depressive disorder or subthreshold major depressive disorder and 2) healthy control subjects. Baseline measurements of 145 variables from different modalities (clinical, cognitive, environmental, and structural magnetic resonance imaging) at age 14 years were used as input to penalized logistic regression (with different levels of penalization) to predict depression onset in a training dataset (n = 407). The features contributing the highest to the prediction were validated in an independent hold-out sample (three independent IMAGEN sites; n = 137). -Results -The area under the receiver operating characteristic curve for predicting depression onset ranged between 0.70 and 0.72 in the training dataset. Baseline severity of depressive symptoms, female sex, neuroticism, stressful life events, and surface area of the supramarginal gyrus contributed most to the predictive model and predicted onset of depression, with an area under the receiver operating characteristic curve between 0.68 and 0.72 in the independent validation sample. -Conclusions -This study showed that depression onset in adolescents can be predicted based on a combination multimodal data of clinical characteristics, life events, personality traits, and brain structure variables.}, - number = {4}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry: Cognitive Neuroscience and Neuroimaging}, - author = {Toenders, Yara J. and Kottaram, Akhil and Dinga, Richard and Davey, Christopher G. and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Stringaris, Argyris and van Noort, Betteke and Penttilä, Jani and Grimmer, Yvonne and Insensee, Corinna and Becker, Andreas and Schumann, Gunter and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Schmaal, Lianne}, - month = apr, - year = {2022}, - keywords = {Machine learning, Prediction, Depression, Major depressive disorder, Adolescents, Penalized logistic regression}, - pages = {376--384}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/99MNMA73/Toenders et al. - 2022 - Predicting Depression Onset in Young People Based .pdf:application/pdf}, -} - -@article{ottino-gonzalez_brain_2022, - title = {Brain structural covariance network differences in adults with alcohol dependence and heavy-drinking adolescents}, - volume = {117}, - copyright = {© 2022 Society for the Study of Addiction}, - issn = {1360-0443}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/add.15772}, - doi = {10.1111/add.15772}, - abstract = {Background and aims Graph theoretic analysis of structural covariance networks (SCN) provides an assessment of brain organization that has not yet been applied to alcohol dependence (AD). We estimated whether SCN differences are present in adults with AD and heavy-drinking adolescents at age 19 and age 14, prior to substantial exposure to alcohol. Design Cross-sectional sample of adults and a cohort of adolescents. Correlation matrices for cortical thicknesses across 68 regions were summarized with graph theoretic metrics. Setting and participants A total of 745 adults with AD and 979 non-dependent controls from 24 sites curated by the Enhancing NeuroImaging Genetics through Meta Analysis (ENIGMA)–Addiction consortium, and 297 hazardous drinking adolescents and 594 controls at ages 19 and 14 from the IMAGEN study, all from Europe. Measurements Metrics of network segregation (modularity, clustering coefficient and local efficiency) and integration (average shortest path length and global efficiency). Findings The younger AD adults had lower network segregation and higher integration relative to non-dependent controls. Compared with controls, the hazardous drinkers at age 19 showed lower modularity [area-under-the-curve (AUC) difference = −0.0142, 95\% confidence interval (CI) = −0.1333, 0.0092; P-value = 0.017], clustering coefficient (AUC difference = −0.0164, 95\% CI = −0.1456, 0.0043; P-value = 0.008) and local efficiency (AUC difference = −0.0141, 95\% CI = −0.0097, 0.0034; P-value = 0.010), as well as lower average shortest path length (AUC difference = −0.0405, 95\% CI = −0.0392, 0.0096; P-value = 0.021) and higher global efficiency (AUC difference = 0.0044, 95\% CI = −0.0011, 0.0043; P-value = 0.023). The same pattern was present at age 14 with lower clustering coefficient (AUC difference = −0.0131, 95\% CI = −0.1304, 0.0033; P-value = 0.024), lower average shortest path length (AUC difference = −0.0362, 95\% CI = −0.0334, 0.0118; P-value = 0.019) and higher global efficiency (AUC difference = 0.0035, 95\% CI = −0.0011, 0.0038; P-value = 0.048). Conclusions Cross-sectional analyses indicate that a specific structural covariance network profile is an early marker of alcohol dependence in adults. Similar effects in a cohort of heavy-drinking adolescents, observed at age 19 and prior to substantial alcohol exposure at age 14, suggest that this pattern may be a pre-existing risk factor for problematic drinking.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Addiction}, - author = {Ottino-González, Jonatan and Garavan, Hugh and {The ENIGMA-Addiction and IMAGEN consortiums}}, - year = {2022}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/add.15772}, - keywords = {neurodevelopment, graph theory, cortical thickness, Alcohol, structural covariance networks}, - pages = {1312--1325}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EAXQ9KGV/Ottino-González et al. - 2022 - Brain structural covariance network differences in.pdf:application/pdf}, -} - -@article{nees_global_2022, - title = {Global and {Regional} {Structural} {Differences} and {Prediction} of {Autistic} {Traits} during {Adolescence}}, - volume = {12}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - issn = {2076-3425}, - url = {https://www.mdpi.com/2076-3425/12/9/1187}, - doi = {10.3390/brainsci12091187}, - abstract = {Background: Autistic traits are commonly viewed as dimensional in nature, and as continuously distributed in the general population. In this respect, the identification of predictive values of markers such as subtle autism-related alterations in brain morphology for parameter values of autistic traits could increase our understanding of this dimensional occasion. However, currently, very little is known about how these traits correspond to alterations in brain morphology in typically developing individuals, particularly during a time period where changes due to brain development processes do not provide a bias. Therefore, in the present study, we analyzed brain volume, cortical thickness (CT) and surface area (SA) in a cohort of 14–15-year-old adolescents (N = 285, female: N = 162) and tested their predictive value for autistic traits, assessed with the social responsiveness scale (SRS) two years later at the age of 16–17 years, using a regression-based approach. We found that autistic traits were significantly predicted by volumetric changes in the amygdala (r = 0.181), cerebellum (r = 0.128) and hippocampus (r = −0.181, r = −0.203), both in boys and girls. Moreover, the CT of the superior frontal region was negatively correlated (r = −0.144) with SRS scores. Furthermore, we observed a significant association between the SRS total score and smaller left putamen volume, specifically in boys (r = −0.217), but not in girls. Our findings suggest that neural correlates of autistic traits also seem to lie on a continuum in the general population, are determined by limbic–striatal neuroanatomical brain areas, and are partly dependent on sex. As we imaged adolescents from a large population-based cohort within a small age range, these data may help to increase the understanding of autistic-like occasions in otherwise typically developing individuals.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Brain Sciences}, - author = {Nees, Frauke and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Grimmer, Yvonne and Heinz, Andreas and Brühl, Rüdiger and Isensee, Corinna and Becker, Andreas and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Papadopoulos Orfanos, Dimitri and Lemaître, Hervé and Stringaris, Argyris and van Noort, Betteke and Paus, Tomáš and Penttilä, Jani and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Poustka, Luise and on behalf of the IMAGEN Consortium}, - month = sep, - year = {2022}, - note = {Number: 9 -Publisher: Multidisciplinary Digital Publishing Institute}, - keywords = {adolescents, structural imaging, autism spectrum disorder, autistic traits, social responsiveness}, - pages = {1187}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/9VUPC9FZ/Nees et al. - 2022 - Global and Regional Structural Differences and Pre.pdf:application/pdf}, -} - -@article{perkins_assessing_2022, - title = {Assessing general versus specific liability for externalizing problems in adolescence: {Concurrent} and prospective prediction of symptoms of conduct disorder, {ADHD}, and substance use}, - volume = {131}, - issn = {2769-755X}, - shorttitle = {Assessing general versus specific liability for externalizing problems in adolescence}, - doi = {10.1037/abn0000743}, - abstract = {This study explored the generality versus specificity of two trait-liability factors for externalizing problems—disinhibition and callousness—in the concurrent and prospective prediction of symptoms of conduct disorder, attention-deficit/hyperactivity disorder (ADHD), and substance use (i.e., alcohol use disorder and history of illicit substance use). Disinhibition involves an impulsive, unrestrained cognitive–behavioral style; callousness entails a dispositional lack of social-emotional sensitivity. Participants were European adolescents from the multisite IMAGEN project who completed questionnaires and clinical interviews at ages 14 (N = 1,504, Mage = 14.41, 51.13\% female) and 16 (N = 1,407, Mage = 16.46, 51.88\% female). Disinhibition was related concurrently and prospectively to greater symptoms of conduct disorder, ADHD, and alcohol use disorder; higher scores on a general externalizing factor; and greater likelihood of having tried an illicit substance. Callousness was selectively related to greater conduct disorder symptoms. These findings indicate disinhibition confers broad liability for externalizing spectrum disorders, perhaps due to its affiliated deficits in executive function. In contrast, callousness appears to represent more specific liability for antagonistic (aggressive/exploitative) forms of externalizing, as exemplified by antisocial behavior. Results support the utility of developmental-ontogenetic and hierarchical-dimensional models of psychopathology and have important implications for early assessment of risk for externalizing problems. (PsycInfo Database Record (c) 2022 APA, all rights reserved)}, - number = {7}, - journal = {Journal of Psychopathology and Clinical Science}, - author = {Perkins, Emily R. and Joyner, Keanan J. and Foell, Jens and Drislane, Laura E. and Brislin, Sarah J. and Frick, Paul J. and Yancey, James R. and Soto, Elia F. and Ganley, Colleen M. and Keel, Pamela K. and Sica, Claudio and Flor, Herta and Nees, Frauke and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and {The IMAGEN Consortium} and Patrick, Christopher J.}, - year = {2022}, - note = {Place: US -Publisher: American Psychological Association}, - keywords = {Attention Deficit Disorder with Hyperactivity, Conduct Disorder, Adolescent Psychopathology, Alcohol Use Disorder, Behavioral Disinhibition, Callous-Unemotional Traits, Drug Usage, Externalization, Symptoms}, - pages = {793--807}, - file = {Version acceptée:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NYVA462E/Perkins et al. - 2022 - Assessing general versus specific liability for ex.pdf:application/pdf}, -} - -@article{kaiser_developmental_2022, - title = {A {Developmental} {Perspective} on {Facets} of {Impulsivity} and {Brain} {Activity} {Correlates} {From} {Adolescence} to {Adulthood}}, - volume = {7}, - issn = {2451-9022}, - url = {https://www.sciencedirect.com/science/article/pii/S2451902222000428}, - doi = {10.1016/j.bpsc.2022.02.003}, - abstract = {Background -On a theoretical level, impulsivity represents a multidimensional construct associated with acting without foresight, inefficient inhibitory response control, and alterations in reward processing. On an empirical level, relationships and changes in associations between different measures of impulsivity from adolescence into young adulthood and their relation to neural activity during inhibitory control and reward anticipation have not been fully understood. -Methods -We used data from IMAGEN, a longitudinal multicenter, population-based cohort study in which 2034 healthy adolescents were investigated at age 14, and 1383 were reassessed as young adults at age 19. We measured the construct of trait impulsivity using self-report questionnaires and neurocognitive indices of decisional impulsivity. With functional magnetic resonance imaging, we assessed brain activity during inhibition error processing using the stop signal task and during reward anticipation in the monetary incentive delay task. Correlations were analyzed, and mixed-effect models were fitted to explore developmental and predictive effects. -Results -All self-report and neurocognitive measures of impulsivity proved to be correlated during adolescence and young adulthood. Further, pre-supplementary motor area and inferior frontal gyrus activity during inhibition error processing was associated with trait impulsivity in adolescence, whereas in young adulthood, a trend-level association with reward anticipation activity in the ventral striatum was found. For adult delay discounting, a trend-level predictive effect of adolescent neural activity during inhibition error processing emerged. -Conclusions -Our findings help to inform theories of impulsivity about the development of its multidimensional nature and associated brain activity patterns and highlight the need for taking functional brain development into account when evaluating neuromarker candidates.}, - number = {11}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry: Cognitive Neuroscience and Neuroimaging}, - author = {Kaiser, Anna and Holz, Nathalie E. and Banaschewski, Tobias and Baumeister, Sarah and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Fröhner, Juliane H. and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Millenet, Sabina and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Schwarz, Emanuel and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Brandeis, Daniel and Nees, Frauke and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Robinson, Lauren and Smolka, Michael N. and Walter, Henrik and Winterer, Jeanne M. and Whelan, Robert and Schumann, Gunter}, - month = nov, - year = {2022}, - keywords = {Prediction, Biomarker, Impulsivity, Inhibitory control, Reward anticipation, Developmental trajectories}, - pages = {1103--1115}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VRMXJ97U/Kaiser et al. - 2022 - A Developmental Perspective on Facets of Impulsivi.pdf:application/pdf}, -} - -@article{vulser_chronotype_2023, - title = {Chronotype, {Longitudinal} {Volumetric} {Brain} {Variations} {Throughout} {Adolescence}, and {Depressive} {Symptom} {Development}}, - volume = {62}, - issn = {0890-8567}, - url = {https://www.sciencedirect.com/science/article/pii/S0890856722002982}, - doi = {10.1016/j.jaac.2022.06.003}, - abstract = {Objective -Adolescence is a critical period for circadian rhythm, with a strong shift toward eveningness around age 14. Also, eveningness in adolescence has been found to predict later onset of depressive symptoms. However, no previous study has investigated structural variations associated with chronotype in early adolescence and how this adds to the development of depressive symptoms. -Method -Assessment of 128 community-based adolescents (51\% girls) at age 14 and 19 years was performed. Using whole-brain voxel-based morphometry, baseline (at age 14) regional gray matter volumes (GMVs), follow-up (at age 19) regional GMVs, and longitudinal changes (between 14 and 19) associated with Morningness/Eveningness Scale in Children score and sleep habits at baseline were measured. The association of GMV with depressive symptoms at 19 years was studied, and the role of potential clinical and genetic factors as mediators and moderators was assessed. -Results -Higher eveningness was associated with larger GMV in the right medial prefrontal cortex at ages 14 and 19 in the whole sample. GMV in this region related to depressive symptoms at age 19 in catechol-O-methyltransferase (COMT) Val/Val, but not in Met COMT, carriers. Larger GMV also was observed in the right fusiform gyrus at age 14, which was explained by later wake-up time during weekends. -Conclusion -In adolescence, eveningness and its related sleep habits correlated with distinct developmental patterns. Eveningness was specifically associated with GMV changes in the medial prefrontal cortex; this could serve as a brain vulnerability factor for later self-reported depressive symptoms in COMT Val/Val carriers.}, - number = {1}, - urldate = {2024-03-12}, - journal = {Journal of the American Academy of Child \& Adolescent Psychiatry}, - author = {Vulser, Hélène and Lemaître, Hervé S. and Guldner, Stella and Bezivin-Frère, Pauline and Löffler, Martin and Sarvasmaa, Anna S. and Massicotte-Marquez, Jessica and Artiges, Eric and Paillère Martinot, Marie-Laure and Filippi, Irina and Miranda, Ruben and Stringaris, Argyris and van Noort, Betteke Maria and Penttilä, Jani and Grimmer, Yvonne and Becker, Andreas and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Fröhner, Juliane H. and Garavan, Hugh and Grigis, Antoine and Gowland, Penny A. and Heinz, Andreas and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Smolka, Michael N. and Spechler, Philip A. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Flor, Herta and Martinot, Jean-Luc and Nees, Frauke}, - month = jan, - year = {2023}, - keywords = {MRI, longitudinal, adolescent, chronotype, gray matter}, - pages = {48--58}, -} - -@article{pagano_arc_2023, - title = {Arc controls alcohol cue relapse by a central amygdala mechanism}, - volume = {28}, - copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {1476-5578}, - url = {https://www.nature.com/articles/s41380-022-01849-4}, - doi = {10.1038/s41380-022-01849-4}, - abstract = {Alcohol use disorder (AUD) is a chronic and fatal disease. The main impediment of the AUD therapy is a high probability of relapse to alcohol abuse even after prolonged abstinence. The molecular mechanisms of cue-induced relapse are not well established, despite the fact that they may offer new targets for the treatment of AUD. Using a comprehensive animal model of AUD, virally-mediated and amygdala-targeted genetic manipulations by CRISPR/Cas9 technology and ex vivo electrophysiology, we identify a mechanism that selectively controls cue-induced alcohol relapse and AUD symptom severity. This mechanism is based on activity-regulated cytoskeleton-associated protein (Arc)/ARG3.1-dependent plasticity of the amygdala synapses. In humans, we identified single nucleotide polymorphisms in the ARC gene and their methylation predicting not only amygdala size, but also frequency of alcohol use, even at the onset of regular consumption. Targeting Arc during alcohol cue exposure may thus be a selective new mechanism for relapse prevention.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Pagano, Roberto and Salamian, Ahmad and Zielinski, Janusz and Beroun, Anna and Nalberczak-Skóra, Maria and Skonieczna, Edyta and Cały, Anna and Tay, Nicole and Banaschewski, Tobias and Desrivières, Sylvane and Grigis, Antoine and Garavan, Hugh and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Kalita, Katarzyna and Bito, Haruhiko and Müller, Christian P. and Schumann, Gunter and Okuno, Hiroyuki and Radwanska, Kasia}, - month = feb, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Neuroscience, Addiction}, - pages = {733--745}, - file = {Version soumise:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TXJCRIQQ/Pagano et al. - 2023 - Arc controls alcohol cue relapse by a central amyg.pdf:application/pdf}, -} - -@article{chavanne_anxiety_2023, - title = {Anxiety onset in adolescents: a machine-learning prediction}, - volume = {28}, - copyright = {2022 The Author(s)}, - issn = {1476-5578}, - shorttitle = {Anxiety onset in adolescents}, - url = {https://www.nature.com/articles/s41380-022-01840-z}, - doi = {10.1038/s41380-022-01840-z}, - abstract = {Recent longitudinal studies in youth have reported MRI correlates of prospective anxiety symptoms during adolescence, a vulnerable period for the onset of anxiety disorders. However, their predictive value has not been established. Individual prediction through machine-learning algorithms might help bridge the gap to clinical relevance. A voting classifier with Random Forest, Support Vector Machine and Logistic Regression algorithms was used to evaluate the predictive pertinence of gray matter volumes of interest and psychometric scores in the detection of prospective clinical anxiety. Participants with clinical anxiety at age 18–23 (N = 156) were investigated at age 14 along with healthy controls (N = 424). Shapley values were extracted for in-depth interpretation of feature importance. Prospective prediction of pooled anxiety disorders relied mostly on psychometric features and achieved moderate performance (area under the receiver operating curve = 0.68), while generalized anxiety disorder (GAD) prediction achieved similar performance. MRI regional volumes did not improve the prediction performance of prospective pooled anxiety disorders with respect to psychometric features alone, but they improved the prediction performance of GAD, with the caudate and pallidum volumes being among the most contributing features. To conclude, in non-anxious 14 year old adolescents, future clinical anxiety onset 4–8 years later could be individually predicted. Psychometric features such as neuroticism, hopelessness and emotional symptoms were the main contributors to pooled anxiety disorders prediction. Neuroanatomical data, such as caudate and pallidum volume, proved valuable for GAD and should be included in prospective clinical anxiety prediction in adolescents.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Chavanne, Alice V. and Paillère Martinot, Marie Laure and Penttilä, Jani and Grimmer, Yvonne and Conrod, Patricia and Stringaris, Argyris and van Noort, Betteke and Isensee, Corinna and Becker, Andreas and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Martinot, Jean-Luc and Artiges, Eric}, - month = feb, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychiatric disorders, Predictive markers}, - pages = {639--646}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6CKGGYTG/Chavanne et al. - 2023 - Anxiety onset in adolescents a machine-learning p.pdf:application/pdf}, -} - -@article{cao_cortical_2023, - title = {Cortical profiles of numerous psychiatric disorders and normal development share a common pattern}, - volume = {28}, - copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited}, - issn = {1476-5578}, - url = {https://www.nature.com/articles/s41380-022-01855-6}, - doi = {10.1038/s41380-022-01855-6}, - abstract = {The neurobiological bases of the association between development and psychopathology remain poorly understood. Here, we identify a shared spatial pattern of cortical thickness (CT) in normative development and several psychiatric and neurological disorders. Principal component analysis (PCA) was applied to CT of 68 regions in the Desikan-Killiany atlas derived from three large-scale datasets comprising a total of 41,075 neurotypical participants. PCA produced a spatially broad first principal component (PC1) that was reproducible across datasets. Then PC1 derived from healthy adult participants was compared to the pattern of CT differences associated with psychiatric and neurological disorders comprising a total of 14,886 cases and 20,962 controls from seven ENIGMA disease-related working groups, normative maturation and aging comprising a total of 17,697 scans from the ABCD Study® and the IMAGEN developmental study, and 17,075 participants from the ENIGMA Lifespan working group, as well as gene expression maps from the Allen Human Brain Atlas. Results revealed substantial spatial correspondences between PC1 and widespread lower CT observed in numerous psychiatric disorders. Moreover, the PC1 pattern was also correlated with the spatial pattern of normative maturation and aging. The transcriptional analysis identified a set of genes including KCNA2, KCNS1 and KCNS2 with expression patterns closely related to the spatial pattern of PC1. The gene category enrichment analysis indicated that the transcriptional correlations of PC1 were enriched to multiple gene ontology categories and were specifically over-represented starting at late childhood, coinciding with the onset of significant cortical maturation and emergence of psychopathology during the prepubertal-to-pubertal transition. Collectively, the present study reports a reproducible latent pattern of CT that captures interregional profiles of cortical changes in both normative brain maturation and a spectrum of psychiatric disorders. The pubertal timing of the expression of PC1-related genes implicates disrupted neurodevelopment in the pathogenesis of the spectrum of psychiatric diseases emerging during adolescence.}, - language = {en}, - number = {2}, - urldate = {2024-03-12}, - journal = {Molecular Psychiatry}, - author = {Cao, Zhipeng and Cupertino, Renata B. and Ottino-Gonzalez, Jonatan and Murphy, Alistair and Pancholi, Devarshi and Juliano, Anthony and Chaarani, Bader and Albaugh, Matthew and Yuan, Dekang and Schwab, Nathan and Stafford, James and Goudriaan, Anna E. and Hutchison, Kent and Li, Chiang-Shan R. and Luijten, Maartje and Groefsema, Martine and Momenan, Reza and Schmaal, Lianne and Sinha, Rajita and van Holst, Ruth J. and Veltman, Dick J. and Wiers, Reinout W. and Porjesz, Bernice and Lett, Tristram and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Robinson, Lauren and Smolka, Michael N. and Walter, Henrik and Winterer, Jeanne and Schumann, Gunter and Whelan, Robert and Bhatt, Ravi R. and Zhu, Alyssa and Conrod, Patricia and Jahanshad, Neda and Thompson, Paul M. and Mackey, Scott and Garavan, Hugh}, - month = feb, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Psychiatric disorders, Addiction}, - pages = {698--709}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/LDHIZDUL/Cao et al. - 2023 - Cortical profiles of numerous psychiatric disorder.pdf:application/pdf}, -} - -@article{sun_associations_2023, - series = {Stress {Response}: {Circuits} and {Impact}}, - title = {Associations of {DNA} {Methylation} {With} {Behavioral} {Problems}, {Gray} {Matter} {Volumes}, and {Negative} {Life} {Events} {Across} {Adolescence}: {Evidence} {From} the {Longitudinal} {IMAGEN} {Study}}, - volume = {93}, - issn = {0006-3223}, - shorttitle = {Associations of {DNA} {Methylation} {With} {Behavioral} {Problems}, {Gray} {Matter} {Volumes}, and {Negative} {Life} {Events} {Across} {Adolescence}}, - url = {https://www.sciencedirect.com/science/article/pii/S0006322322013567}, - doi = {10.1016/j.biopsych.2022.06.012}, - abstract = {Background -Negative life events (NLEs) increase the risk for externalizing behaviors (EBs) and internalizing behaviors (IBs) in adolescence and adult psychopathology. DNA methylation associated with behavioral problems may reflect this risk and long-lasting effects of NLEs. -Methods -To identify consistent associations between blood DNA methylation and EBs or IBs across adolescence, we conducted longitudinal epigenome-wide association studies (EWASs) using data from the IMAGEN cohort, collected at ages 14 and 19 years (n = 506). Significant findings were validated in a separate subsample (n = 823). Methylation risk scores were generated by 10-fold cross-validation and further tested for their associations with gray matter volumes and NLEs. -Results -No significant findings were obtained for the IB-EWAS. The EB-EWAS identified a genome-wide significant locus in a gene linked to attention-deficit/hyperactivity disorder (ADHD) (IQSEC1, cg01460382; p = 1.26 × 10−8). Other most significant CpG sites were near ADHD-related genes and enriched for genes regulating tumor necrosis factor and interferon-γ signaling, highlighting the relevance of EB-EWAS findings for ADHD. Analyses with the EB methylation risk scores suggested that it partly reflected comorbidity with IBs in late adolescence. Specific to EBs, EB methylation risk scores correlated with smaller gray matter volumes in medial orbitofrontal and anterior/middle cingulate cortices, brain regions known to associate with ADHD and conduct problems. Longitudinal mediation analyses indicated that EB-related DNA methylation were more likely the outcomes of problematic behaviors accentuated by NLEs, and less likely the epigenetic bases of such behaviors. -Conclusions -Our findings suggest that novel epigenetic mechanisms through which NLEs exert short and longer-term effects on behavior may contribute to ADHD.}, - number = {4}, - urldate = {2024-03-12}, - journal = {Biological Psychiatry}, - author = {Sun, Yan and Jia, Tianye and Barker, Edward D. and Chen, Di and Zhang, Zuo and Xu, Jiayuan and Chang, Suhua and Zhou, Guangdong and Liu, Yun and Tay, Nicole and Luo, Qiang and Chang, Xiao and Banaschewski, Tobias and Bokde, Arun L. W. and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Heinz, Andreas and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Lu, Lin and Shi, Jie and Schumann, Gunter and Desrivières, Sylvane}, - month = feb, - year = {2023}, - keywords = {Brain, Adolescents, ADHD, Epigenome-wide association study, Externalizing behaviors, Life events}, - pages = {342--351}, -} - -@article{navarri_biologically_2023, - title = {A biologically informed polygenic score of neuronal plasticity moderates the association between cognitive aptitudes and cortical thickness in adolescents}, - volume = {60}, - issn = {1878-9293}, - url = {https://www.sciencedirect.com/science/article/pii/S1878929323000373}, - doi = {10.1016/j.dcn.2023.101232}, - abstract = {Although many studies of the adolescent brain identified positive associations between cognitive abilities and cortical thickness, little is known about mechanisms underlying such brain-behavior relationships. With experience-induced plasticity playing an important role in shaping the cerebral cortex throughout life, it is likely that some of the inter-individual variations in cortical thickness could be explained by genetic variations in relevant molecular processes, as indexed by a polygenic score of neuronal plasticity (PGS-NP). Here, we studied associations between PGS-NP, cognitive abilities, and thickness of the cerebral cortex, estimated from magnetic resonance images, in the Saguenay Youth Study (SYS, 533 females, 496 males: age=15.0 ± 1.8 years of age; cross-sectional), and the IMAGEN Study (566 females, 556 males; between 14 and 19 years; longitudinal). Using Gene Ontology, we first identified 199 genes implicated in neuronal plasticity, which mapped to 155,600 single nucleotide polymorphisms (SNPs). Second, we estimated their effect sizes from an educational attainment meta-GWAS to build a PGS-NP. Third, we examined a possible moderating role of PGS-NP in the relationship between performance intelligence quotient (PIQ), and its subtests, and the thickness of 34 cortical regions. In SYS, we observed a significant interaction between PGS-NP and object assembly vis-à-vis thickness in male adolescents (p = 0.026). A median-split analysis showed that, in males with a ‘high’ PGS-NP, stronger associations between object assembly and thickness were found in regions with larger age-related changes in thickness (r = 0.55, p = 0.00075). Although the interaction between PIQ and PGS-NP was non-significant (p = 0.064), we performed a similar median-split analysis. Again, in the high PGS-NP males, positive associations between PIQ and thickness were observed in regions with larger age-related changes in thickness (r = 0.40, p = 0.018). In the IMAGEN cohort, we did not replicate the first set of results (interaction between PGS-NP and cognitive abilities via-a-vis cortical thickness) while we did observe the same relationship between the brain-behaviour relationship and (longitudinal) changes in cortical thickness (Matrix reasoning: r = 0.63, p = 6.5e-05). No statistically significant results were observed in female adolescents in either cohort. Overall, these cross-sectional and longitudinal results suggest that molecular mechanisms involved in neuronal plasticity may contribute to inter-individual variations of cortical thickness related to cognitive abilities during adolescence in a sex-specific manner.}, - urldate = {2024-03-12}, - journal = {Developmental Cognitive Neuroscience}, - author = {Navarri, Xavier and Vosberg, Daniel E. and Shin, Jean and Richer, Louis and Leonard, Gabriel and Pike, G. Bruce and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Hohmann, Sarah and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Pausova, Zdenka and Paus, Tomáš}, - month = apr, - year = {2023}, - keywords = {Cognition, Genetics, Adolescence, Cortical Thickness, Fluid intelligence}, - pages = {101232}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/H5Z3MA86/Navarri et al. - 2023 - A biologically informed polygenic score of neurona.pdf:application/pdf}, -} - -@article{kuhn_predicting_2020, - title = {Predicting change trajectories of neuroticism from baseline brain structure using whole brain analyses and latent growth curve models in adolescents}, - volume = {10}, - copyright = {2020 The Author(s)}, - issn = {2045-2322}, - url = {https://www.nature.com/articles/s41598-020-58128-x}, - doi = {10.1038/s41598-020-58128-x}, - abstract = {Adolescence is a vulnerable time for personality development. Especially neuroticism with its link to the development of psychopathology is of interest concerning influential factors. The present study exploratorily investigates neuroanatomical signatures for developmental trajectories of neuroticism based on a voxel-wise whole-brain structural equation modelling framework. In 1,814 healthy adolescents of the IMAGEN sample, the NEO-FFI was acquired at three measurement occasions across five years. Based on a partial measurement invariance second-order latent growth curve model we conducted whole-brain analyses on structural MRI data at age 14 years, predicting change in neuroticism over time. We observed that a reduced volume in the pituitary gland was associated with the slope of neuroticism over time. However, no relations with prefrontal areas emerged. Both findings are discussed against the background of possible genetic and social influences that may account for this result.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Scientific Reports}, - author = {Kühn, Simone and Mascherek, Anna and Banaschewski, Tobias and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Lindenberger, Ulman and Gallinat, Jürgen}, - month = jan, - year = {2020}, - note = {Publisher: Nature Publishing Group}, - keywords = {Development of the nervous system, Agency}, - pages = {1207}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Z7BD6R9Y/Kühn et al. - 2020 - Predicting change trajectories of neuroticism from.pdf:application/pdf}, -} - -@article{rane_structural_2022, - title = {Structural differences in adolescent brains can predict alcohol misuse}, - volume = {11}, - issn = {2050-084X}, - url = {https://doi.org/10.7554/eLife.77545}, - doi = {10.7554/eLife.77545}, - abstract = {Alcohol misuse during adolescence (AAM) has been associated with disruptive development of adolescent brains. In this longitudinal machine learning (ML) study, we could predict AAM significantly from brain structure (T1-weighted imaging and DTI) with accuracies of 73 -78\% in the IMAGEN dataset (n∼1182). Our results not only show that structural differences in brain can predict AAM, but also suggests that such differences might precede AAM behavior in the data. We predicted 10 phenotypes of AAM at age 22 using brain MRI features at ages 14, 19, and 22. Binge drinking was found to be the most predictable phenotype. The most informative brain features were located in the ventricular CSF, and in white matter tracts of the corpus callosum, internal capsule, and brain stem. In the cortex, they were spread across the occipital, frontal, and temporal lobes and in the cingulate cortex. We also experimented with four different ML models and several confound control techniques. Support Vector Machine (SVM) with rbf kernel and Gradient Boosting consistently performed better than the linear models, linear SVM and Logistic Regression. Our study also demonstrates how the choice of the predicted phenotype, ML model, and confound correction technique are all crucial decisions in an explorative ML study analyzing psychiatric disorders with small effect sizes such as AAM.}, - urldate = {2024-03-12}, - journal = {eLife}, - author = {Rane, Roshan Prakash and de Man, Evert Ferdinand and Kim, JiHoon and Görgen, Kai and Tschorn, Mira and Rapp, Michael A and Banaschewski, Tobias and Bokde, Arun LW and Desrivieres, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny A and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillere and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Lemaitre, Herve and Paus, Tomas and Poustka, Luise and Fröhner, Juliane and Robinson, Lauren and Smolka, Michael N and Winterer, Jeanne and Whelan, Robert and Schumann, Gunter and Walter, Henrik and Heinz, Andreas and Ritter, Kerstin and {IMAGEN consortium}}, - editor = {Jbabdi, Saad and Baker, Chris I}, - month = may, - year = {2022}, - note = {Publisher: eLife Sciences Publications, Ltd}, - keywords = {machine learning, magnetic resonance imaging, alcohol use disorder, adolescence alcohol misuse, confound control, data science for psychiatry}, - pages = {e77545}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/I9Z5QERN/Rane et al. - 2022 - Structural differences in adolescent brains can pr.pdf:application/pdf}, -} - -@article{jia_neural_2021, - title = {Neural network involving medial orbitofrontal cortex and dorsal periaqueductal gray regulation in human alcohol abuse}, - volume = {7}, - url = {https://www.science.org/doi/full/10.1126/sciadv.abd4074}, - doi = {10.1126/sciadv.abd4074}, - abstract = {Prompted by recent evidence of neural circuitry in rodent models, functional magnetic resonance imaging and functional connectivity analyses were conducted for a large adolescent population at two ages, together with alcohol abuse measures, to characterize a neural network that may underlie the onset of alcoholism. A network centered on the medial orbitofrontal cortex (mOFC), as well as including the dorsal periaqueductal gray (dPAG), central nucleus of the amygdala, and nucleus accumbens, was identified, consistent with the rodent models, with evidence of both inhibitory and excitatory coregulation by the mOFC over the dPAG. Furthermore, significant relationships were detected between raised baseline excitatory coregulation in this network and impulsivity measures, supporting a role for negative urgency in alcohol dependence.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Science Advances}, - author = {Jia, Tianye and Xie, Chao and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Robbins, Trevor W. and Feng, Jianfeng and {IMAGEN CONSORTIUM}}, - month = feb, - year = {2021}, - note = {Publisher: American Association for the Advancement of Science}, - pages = {eabd4074}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/67GQD7NT/Jia et al. - 2021 - Neural network involving medial orbitofrontal cort.pdf:application/pdf}, -} - -@article{maltais_prospective_2020-1, - title = {Prospective associations between physical activity levels and white matter integrity in older adults: results from the {MAPT} study}, - volume = {137}, - issn = {0378-5122}, - shorttitle = {Prospective associations between physical activity levels and white matter integrity in older adults}, - url = {https://www.sciencedirect.com/science/article/pii/S0378512220302425}, - doi = {10.1016/j.maturitas.2020.04.012}, - abstract = {Background -Higher levels of physical activity (PA) are known to be associated with better white matter integrity measured by diffusion tensor imaging (DTI) in older adults in cross-sectional studies. However, no studies have investigated the association between PA levels and the evolution of DTI parameters (fractional anisotropy and mean diffusivity). -Objectives -To examine the cross-sectional associations between PA levels and DTI parameters, then to investigate the association between baseline PA levels and the evolution of DTI parameters in older adults. -Methods -Data on magnetic resonance imaging with DTI method from the Multidomain Alzheimer’s Preventive Trial (MAPT) study were used; 228 participants had data on DTI measured at three time-points over five years. Fractional anisotropy and mean diffusivity were acquired for six different brain regions. -Results -No significant associations were found in the cross-sectional analyses. Only one association was found: compared with active individuals, a faster worsening in the mean diffusivity of the uncinate fasciculus region was found in inactive individuals (-5.0 × 10-6 (-9.5 × 10-5, 4.9 × 10-6)). -Conclusions -In this study, we found that the condition of the uncinate fasciculus region may be susceptible to changes in PA levels in older adults. Longitudinal studies that assess fitness and PA using objective measurements (e.g. cardiorespiratory fitness and accelerometry) could shed some new light on this topic.}, - urldate = {2024-03-12}, - journal = {Maturitas}, - author = {Maltais, Mathieu and Rolland, Yves and Boisvert-Vigneault, Katherine and Perus, Lisa and Mangin, Jean-François and Grigis, Antoine and Chupin, Marie and Bouyahia, Ali and Gabelle, Audrey and Delrieux, Julien and Vellas, Bruno and de Souto Barreto, Philipe}, - month = jul, - year = {2020}, - keywords = {magnetic resonance imaging, brain imaging, physical activity}, - pages = {24--29}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3SZNLLDX/S0378512220302425.html:text/html}, -} - -@article{holz_stable_2023, - title = {A stable and replicable neural signature of lifespan adversity in the adult brain}, - volume = {26}, - copyright = {2023 The Author(s)}, - issn = {1546-1726}, - url = {https://www.nature.com/articles/s41593-023-01410-8}, - doi = {10.1038/s41593-023-01410-8}, - abstract = {Environmental adversities constitute potent risk factors for psychiatric disorders. Evidence suggests the brain adapts to adversity, possibly in an adversity-type and region-specific manner. However, the long-term effects of adversity on brain structure and the association of individual neurobiological heterogeneity with behavior have yet to be elucidated. Here we estimated normative models of structural brain development based on a lifespan adversity profile in a longitudinal at-risk cohort aged 25 years (n = 169). This revealed widespread morphometric changes in the brain, with partially adversity-specific features. This pattern was replicated at the age of 33 years (n = 114) and in an independent sample at 22 years (n = 115). At the individual level, greater volume contractions relative to the model were predictive of future anxiety. We show a stable neurobiological signature of adversity that persists into adulthood and emphasize the importance of considering individual-level rather than group-level predictions to explain emerging psychopathology.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Nature Neuroscience}, - author = {Holz, Nathalie E. and Zabihi, Mariam and Kia, Seyed Mostafa and Monninger, Maximillian and Aggensteiner, Pascal-M. and Siehl, Sebastian and Floris, Dorothea L. and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Meyer-Lindenberg, Andreas and Brandeis, Daniel and Buitelaar, Jan K. and Nees, Frauke and Beckmann, Christian and Banaschewski, Tobias and Marquand, Andre F.}, - month = sep, - year = {2023}, - note = {Publisher: Nature Publishing Group}, - keywords = {Predictive markers, Stress and resilience}, - pages = {1603--1612}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8B6UIAK3/Holz et al. - 2023 - A stable and replicable neural signature of lifesp.pdf:application/pdf}, -} - -@article{albaugh_association_2021, - title = {Association of {Cannabis} {Use} {During} {Adolescence} {With} {Neurodevelopment}}, - volume = {78}, - issn = {2168-622X}, - url = {https://doi.org/10.1001/jamapsychiatry.2021.1258}, - doi = {10.1001/jamapsychiatry.2021.1258}, - abstract = {Animal studies have shown that the adolescent brain is sensitive to disruptions in endocannabinoid signaling, resulting in altered neurodevelopment and lasting behavioral effects. However, few studies have investigated ties between cannabis use and adolescent brain development in humans.To examine the degree to which magnetic resonance (MR) imaging–assessed cerebral cortical thickness development is associated with cannabis use in a longitudinal sample of adolescents.Data were obtained from the community-based IMAGEN cohort study, conducted across 8 European sites. Baseline data used in the present study were acquired from March 1, 2008, to December 31, 2011, and follow-up data were acquired from January 1, 2013, to December 31, 2016. A total of 799 IMAGEN participants were identified who reported being cannabis naive at study baseline and had behavioral and neuroimaging data available at baseline and 5-year follow-up. Statistical analysis was performed from October 1, 2019, to August 31, 2020.Cannabis use was assessed at baseline and 5-year follow-up with the European School Survey Project on Alcohol and Other Drugs. Anatomical MR images were acquired with a 3-dimensional T1-weighted magnetization prepared gradient echo sequence. Quality-controlled native MR images were processed through the CIVET pipeline, version 2.1.0.The study evaluated 1598 MR images from 799 participants (450 female participants [56.3\%]; mean [SD] age, 14.4 [0.4] years at baseline and 19.0 [0.7] years at follow-up). At 5-year follow-up, cannabis use (from 0 to \>40 uses) was negatively associated with thickness in left prefrontal (peak: t785 = –4.87, cluster size = 1558 vertices; P = 1.10 × 10−6, random field theory cluster corrected) and right prefrontal (peak: t785 = –4.27, cluster size = 1551 vertices; P = 2.81 × 10−5, random field theory cluster corrected) cortices. There were no significant associations between lifetime cannabis use at 5-year follow-up and baseline cortical thickness, suggesting that the observed neuroanatomical differences did not precede initiation of cannabis use. Longitudinal analysis revealed that age-related cortical thinning was qualified by cannabis use in a dose-dependent fashion such that greater use, from baseline to follow-up, was associated with increased thinning in left prefrontal (peak: t815.27 = –4.24, cluster size = 3643 vertices; P = 2.28 × 10−8, random field theory cluster corrected) and right prefrontal (peak: t813.30 = –4.71, cluster size = 2675 vertices; P = 3.72 × 10−8, random field theory cluster corrected) cortices. The spatial pattern of cannabis-related thinning was associated with age-related thinning in this sample (r = 0.540; P \< .001), and a positron emission tomography–assessed cannabinoid 1 receptor–binding map derived from a separate sample of participants (r = −0.189; P \< .001). Analysis revealed that thinning in right prefrontal cortices, from baseline to follow-up, was associated with attentional impulsiveness at follow-up.Results suggest that cannabis use during adolescence is associated with altered neurodevelopment, particularly in cortices rich in cannabinoid 1 receptors and undergoing the greatest age-related thickness change in middle to late adolescence.}, - number = {9}, - urldate = {2024-03-12}, - journal = {JAMA Psychiatry}, - author = {Albaugh, Matthew D. and Ottino-Gonzalez, Jonatan and Sidwell, Amanda and Lepage, Claude and Juliano, Anthony and Owens, Max M. and Chaarani, Bader and Spechler, Philip and Fontaine, Nicholas and Rioux, Pierre and Lewis, Lindsay and Jeon, Seun and Evans, Alan and D’Souza, Deepak and Radhakrishnan, Rajiv and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Conrod, Patricia and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Potter, Alexandra and Garavan, Hugh and {IMAGEN Consortium}}, - month = sep, - year = {2021}, - pages = {1031--1040}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/445K4VGA/Albaugh et al. - 2021 - Association of Cannabis Use During Adolescence Wit.pdf:application/pdf}, -} - -@article{owens_bayesian_2022, - title = {Bayesian causal network modeling suggests adolescent cannabis use accelerates prefrontal cortical thinning}, - volume = {12}, - copyright = {2022 The Author(s)}, - issn = {2158-3188}, - url = {https://www.nature.com/articles/s41398-022-01956-4}, - doi = {10.1038/s41398-022-01956-4}, - abstract = {While there is substantial evidence that cannabis use is associated with differences in human brain development, most of this evidence is correlational in nature. Bayesian causal network (BCN) modeling attempts to identify probable causal relationships in correlational data using conditional probabilities to estimate directional associations between a set of interrelated variables. In this study, we employed BCN modeling in 637 adolescents from the IMAGEN study who were cannabis naïve at age 14 to provide evidence that the accelerated prefrontal cortical thinning found previously in adolescent cannabis users by Albaugh et al. [1] is a result of cannabis use causally affecting neurodevelopment. BCNs incorporated data on cannabis use, prefrontal cortical thickness, and other factors related to both brain development and cannabis use, including demographics, psychopathology, childhood adversity, and other substance use. All BCN algorithms strongly suggested a directional relationship from adolescent cannabis use to accelerated cortical thinning. While BCN modeling alone does not prove a causal relationship, these results are consistent with a body of animal and human research suggesting that adolescent cannabis use adversely affects brain development.}, - language = {en}, - number = {1}, - urldate = {2024-03-12}, - journal = {Translational Psychiatry}, - author = {Owens, Max M. and Albaugh, Matthew D. and Allgaier, Nicholas and Yuan, Dekang and Robert, Gabriel and Cupertino, Renata B. and Spechler, Philip A. and Juliano, Anthony and Hahn, Sage and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaitre, Herve and Paus, Tomáš and Poustka, Luise and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Mackey, Scott and Schumann, Gunter and Garavan, Hugh}, - month = may, - year = {2022}, - note = {Publisher: Nature Publishing Group}, - keywords = {Addiction, Molecular neuroscience}, - pages = {1--9}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/93XRUXAB/Owens et al. - 2022 - Bayesian causal network modeling suggests adolesce.pdf:application/pdf}, -} - -@article{yip_brain_2023, - title = {Brain {Networks} and {Adolescent} {Alcohol} {Use}}, - volume = {80}, - issn = {2168-622X}, - url = {https://doi.org/10.1001/jamapsychiatry.2023.2949}, - doi = {10.1001/jamapsychiatry.2023.2949}, - abstract = {Alcohol misuse in adolescence is a leading cause of disability and mortality in youth and is associated with higher risk for alcohol use disorder. Brain mechanisms underlying risk of alcohol misuse may inform prevention and intervention efforts.To identify neuromarkers of alcohol misuse using a data-driven approach, with specific consideration of neurodevelopmental sex differences.Longitudinal multisite functional magnetic resonance imaging (fMRI) data collected at ages 14 and 19 years were used to assess whole-brain patterns of functional organization associated with current and future alcohol use risk as measured by the Alcohol Use Disorder Identification Test (AUDIT). Primary data were collected by the IMAGEN consortium, a European multisite study of adolescent neurodevelopment. Model generalizability was further tested using data acquired in a single-site study of college alcohol consumption conducted in the US. The primary sample was a developmental cohort of 1359 adolescents with neuroimaging, phenotyping, and alcohol use data. Model generalizability was further assessed in a separate cohort of 114 individuals.Brain-behavior model accuracy, as defined by the correspondence between model-predicted and actual AUDIT scores in held-out testing data, Bonferroni corrected across the number of models run at each time point, 2-tailed α \< .008, as determined via permutation testing.Among 1359 individuals in the study, the mean (SD) age was 14.42 (0.40) years, and 729 individuals (54\%) were female. The data-driven, whole-brain connectivity approach identified networks associated with vulnerability for future and current AUDIT-defined alcohol use risk (primary outcome, as specified above, future: ρ, 0.22; P \< .001 and present: ρ, 0.27; P \< .001). Results further indicated sex divergence in the accuracies of brain-behavior models, such that female-only models consistently outperformed male-only models. Specifically, female-only models identified networks conferring vulnerability for future and current severity using data acquired during both reward and inhibitory fMRI tasks. In contrast, male-only models were successful in accurately identifying networks using data acquired during the inhibitory control—but not reward—task, indicating domain specificity of alcohol use risk networks in male adolescents only.These data suggest that interventions focusing on inhibitory control processes may be effective in combating alcohol use risk in male adolescents but that both inhibitory and reward-related processes are likely of relevance to alcohol use behaviors in female adolescents. They further identify novel networks of alcohol use risk in youth, which may be used to identify adolescents who are at risk and inform intervention efforts.}, - number = {11}, - urldate = {2024-03-12}, - journal = {JAMA Psychiatry}, - author = {Yip, Sarah W. and Lichenstein, Sarah D. and Liang, Qinghao and Chaarani, Bader and Dager, Alecia and Pearlson, Godfrey and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Garavan, Hugh}, - month = nov, - year = {2023}, - pages = {1131--1141}, -} - -@article{judd_cognitive_2020, - title = {Cognitive and brain development is independently influenced by socioeconomic status and polygenic scores for educational attainment}, - volume = {117}, - url = {https://www.pnas.org/doi/abs/10.1073/pnas.2001228117}, - doi = {10.1073/pnas.2001228117}, - abstract = {Genetic factors and socioeconomic status (SES) inequalities play a large role in educational attainment, and both have been associated with variations in brain structure and cognition. However, genetics and SES are correlated, and no prior study has assessed their neural associations independently. Here we used a polygenic score for educational attainment (EduYears-PGS), as well as SES, in a longitudinal study of 551 adolescents to tease apart genetic and environmental associations with brain development and cognition. Subjects received a structural MRI scan at ages 14 and 19. At both time points, they performed three working memory (WM) tasks. SES and EduYears-PGS were correlated (r = 0.27) and had both common and independent associations with brain structure and cognition. Specifically, lower SES was related to less total cortical surface area and lower WM. EduYears-PGS was also related to total cortical surface area, but in addition had a regional association with surface area in the right parietal lobe, a region related to nonverbal cognitive functions, including mathematics, spatial cognition, and WM. SES, but not EduYears-PGS, was related to a change in total cortical surface area from age 14 to 19. This study demonstrates a regional association of EduYears-PGS and the independent prediction of SES with cognitive function and brain development. It suggests that the SES inequalities, in particular parental education, are related to global aspects of cortical development, and exert a persistent influence on brain development during adolescence.}, - number = {22}, - urldate = {2024-03-12}, - journal = {Proceedings of the National Academy of Sciences}, - author = {Judd, Nicholas and Sauce, Bruno and Wiedenhoeft, John and Tromp, Jeshua and Chaarani, Bader and Schliep, Alexander and van Noort, Betteke and Penttilä, Jani and Grimmer, Yvonne and Insensee, Corinna and Becker, Andreas and Banaschewski, Tobias and Bokde, Arun L. W. and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Garavan, Hugh and Klingberg, Torkel}, - month = jun, - year = {2020}, - note = {Publisher: Proceedings of the National Academy of Sciences}, - pages = {12411--12418}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/5BD2TPZ4/Judd et al. - 2020 - Cognitive and brain development is independently i.pdf:application/pdf}, -} - -@article{liao_hemispheric_2023, - title = {Hemispheric asymmetry in cortical thinning reflects intrinsic organization of the neurotransmitter systems and homotopic functional connectivity}, - volume = {120}, - url = {https://www.pnas.org/doi/abs/10.1073/pnas.2306990120}, - doi = {10.1073/pnas.2306990120}, - abstract = {Hemispheric lateralization and its origins have been of great interest in neuroscience for over a century. The left–right asymmetry in cortical thickness may stem from differential maturation of the cerebral cortex in the two hemispheres. Here, we investigated the spatial pattern of hemispheric differences in cortical thinning during adolescence, and its relationship with the density of neurotransmitter receptors and homotopic functional connectivity. Using longitudinal data from IMAGEN study (N = 532), we found that many cortical regions in the frontal and temporal lobes thinned more in the right hemisphere than in the left. Conversely, several regions in the occipital and parietal lobes thinned less in the right (vs. left) hemisphere. We then revealed that regions thinning more in the right (vs. left) hemispheres had higher density of neurotransmitter receptors and transporters in the right (vs. left) side. Moreover, the hemispheric differences in cortical thinning were predicted by homotopic functional connectivity. Specifically, regions with stronger homotopic functional connectivity showed a more symmetrical rate of cortical thinning between the left and right hemispheres, compared with regions with weaker homotopic functional connectivity. Based on these findings, we suggest that the typical patterns of hemispheric differences in cortical thinning may reflect the intrinsic organization of the neurotransmitter systems and related patterns of homotopic functional connectivity.}, - number = {42}, - urldate = {2024-03-12}, - journal = {Proceedings of the National Academy of Sciences}, - author = {Liao, Zhijie and Banaschewski, Tobias and Bokde, Arun L. W. and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Papadopoulos Orfanos, Dimitri and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Paus, Tomáš and {IMAGEN Consortium}}, - month = oct, - year = {2023}, - note = {Publisher: Proceedings of the National Academy of Sciences}, - pages = {e2306990120}, -} - -@article{khalid_multimodal_2023, - title = {Multimodal {MRI} radiomic models to predict genomic mutations in diffuse intrinsic pontine glioma with missing imaging modalities}, - volume = {10}, - issn = {2296-858X}, - url = {https://www.frontiersin.org/articles/10.3389/fmed.2023.1071447}, - abstract = {PurposePredicting H3.1, TP53, and ACVR1 mutations in DIPG could aid in the selection of therapeutic options. The contribution of clinical data and multi-modal MRI were studied for these three predictive tasks. To keep the maximum number of subjects, which is essential for a rare disease, missing data were considered. A multi-modal model was proposed, collecting all available data for each patient, without performing any imputation.MethodsA retrospective cohort of 80 patients with confirmed DIPG and at least one of the four MR modalities (T1w, T1c, T2w, and FLAIR), acquired with two different MR scanners was built. A pipeline including standardization of MR data and extraction of radiomic features within the tumor was applied. The values of radiomic features between the two MR scanners were realigned using the ComBat method. For each prediction task, the most robust features were selected based on a recursive feature elimination with cross-validation. Five different models, one based on clinical data and one per MR modality, were developed using logistic regression classifiers. The prediction of the multi-modal model was defined as the average of all possible prediction results among five for each patient. The performances of the models were compared using a leave-one-out approach.ResultsThe percentage of missing modalities ranged from 6 to 11\% across modalities and tasks. The performance of each individual model was dependent on each specific task, with an AUC of the ROC curve ranging from 0.63 to 0.80. The multi-modal model outperformed the clinical model for each prediction tasks, thus demonstrating the added value of MRI. Furthermore, regardless of performance criteria, the multi-modal model came in the first place or second place (very close to first). In the leave-one-out approach, the prediction of H3.1 (resp. ACVR1 and TP53) mutations achieved a balanced accuracy of 87.8\% (resp. 82.1 and 78.3\%).ConclusionCompared with a single modality approach, the multi-modal model combining multiple MRI modalities and clinical features was the most powerful to predict H3.1, ACVR1, and TP53 mutations and provided prediction, even in the case of missing modality. It could be proposed in the absence of a conclusive biopsy.}, - urldate = {2023-09-07}, - journal = {Frontiers in Medicine}, - author = {Khalid, Fahad and Goya-Outi, Jessica and Escobar, Thibault and Dangouloff-Ros, Volodia and Grigis, Antoine and Philippe, Cathy and Boddaert, Nathalie and Grill, Jacques and Frouin, Vincent and Frouin, Frédérique}, - year = {2023}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/V2SE87HW/Khalid et al. - 2023 - Multimodal MRI radiomic models to predict genomic .pdf:application/pdf}, -} - -@article{chegraoui_object_2021, - title = {Object {Detection} {Improves} {Tumour} {Segmentation} in {MR} {Images} of {Rare} {Brain} {Tumours}}, - volume = {13}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, - issn = {2072-6694}, - url = {https://www.mdpi.com/2072-6694/13/23/6113}, - doi = {10.3390/cancers13236113}, - abstract = {Tumour lesion segmentation is a key step to study and characterise cancer from MR neuroradiological images. Presently, numerous deep learning segmentation architectures have been shown to perform well on the specific tumour type they are trained on (e.g., glioblastoma in brain hemispheres). However, a high performing network heavily trained on a given tumour type may perform poorly on a rare tumour type for which no labelled cases allows training or transfer learning. Yet, because some visual similarities exist nevertheless between common and rare tumours, in the lesion and around it, one may split the problem into two steps: object detection and segmentation. For each step, trained networks on common lesions could be used on rare ones following a domain adaptation scheme without extra fine-tuning. This work proposes a resilient tumour lesion delineation strategy, based on the combination of established elementary networks that achieve detection and segmentation. Our strategy allowed us to achieve robust segmentation inference on a rare tumour located in an unseen tumour context region during training. As an example of a rare tumour, Diffuse Intrinsic Pontine Glioma (DIPG), we achieve an average dice score of 0.62 without further training or network architecture adaptation.}, - language = {en}, - number = {23}, - urldate = {2023-02-06}, - journal = {Cancers}, - author = {Chegraoui, Hamza and Philippe, Cathy and Dangouloff-Ros, Volodia and Grigis, Antoine and Calmon, Raphael and Boddaert, Nathalie and Frouin, Frédérique and Grill, Jacques and Frouin, Vincent}, - month = jan, - year = {2021}, - keywords = {segmentation, deep learning, brain tumour, DIPG, domain adaptation, object-detection}, - pages = {6113}, -} - -@article{mihailov_cortical_2020, - title = {Cortical signatures in behaviorally clustered autistic traits subgroups: a population-based study}, - volume = {10}, - copyright = {2020 The Author(s)}, - issn = {2158-3188}, - shorttitle = {Cortical signatures in behaviorally clustered autistic traits subgroups}, - url = {https://www.nature.com/articles/s41398-020-00894-3}, - doi = {10.1038/s41398-020-00894-3}, - abstract = {Extensive heterogeneity in autism spectrum disorder (ASD) has hindered the characterization of consistent biomarkers, which has led to widespread negative results. Isolating homogenized subtypes could provide insight into underlying biological mechanisms and an overall better understanding of ASD. A total of 1093 participants from the population-based “Healthy Brain Network” cohort (Child Mind Institute in the New York City area, USA) were selected based on score availability in behaviors relevant to ASD, aged 6–18 and IQ {\textgreater}= 70. All participants underwent an unsupervised clustering analysis on behavioral dimensions to reveal subgroups with ASD traits, identified by the presence of social deficits. Analysis revealed three socially impaired ASD traits subgroups: (1) high in emotionally dysfunctional traits, (2) high in ADHD-like traits, and (3) high in anxiety and depressive symptoms. 527 subjects had good quality structural MRI T1 data. Site effects on cortical features were adjusted using the ComBat method. Neuroimaging analyses compared cortical thickness, gyrification, and surface area, and were controlled for age, gender, and IQ, and corrected for multiple comparisons. Structural neuroimaging analyses contrasting one combined heterogeneous ASD traits group against controls did not yield any significant differences. Unique cortical signatures, however, were observed within each of the three individual ASD traits subgroups versus controls. These observations provide evidence of ASD traits subtypes, and confirm the necessity of applying dimensional approaches to extract meaningful differences, thus reducing heterogeneity and paving the way to better understanding ASD traits.}, - language = {en}, - number = {1}, - urldate = {2023-02-06}, - journal = {Translational Psychiatry}, - author = {Mihailov, Angeline and Philippe, Cathy and Gloaguen, Arnaud and Grigis, Antoine and Laidi, Charles and Piguet, Camille and Houenou, Josselin and Frouin, Vincent}, - month = jun, - year = {2020}, - keywords = {Neuroscience, Diagnostic markers, Prognostic markers, Human behaviour, Autism spectrum disorders}, - pages = {1--12}, -} - -@article{le_guen_eqtl_2019, - title = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening: evidence from 15,597 {UK} {Biobank} participants with neuroimaging data}, - volume = {224}, - issn = {1863-2661}, - shorttitle = {{eQTL} of {KCNK2} regionally influences the brain sulcal widening}, - url = {https://doi.org/10.1007/s00429-018-1808-9}, - doi = {10.1007/s00429-018-1808-9}, - abstract = {The grey and white matter volumes are known to reduce with age. This cortical shrinkage is visible on magnetic resonance images and is conveniently identified by the increased volume of cerebrospinal fluid in the sulci between two gyri. Here, we replicated this finding using the UK Biobank dataset and studied the genetic influence on these cortical features of aging. We divided all individuals genetically confirmed of British ancestry into two sub-cohorts (12,162 and 3435 subjects for discovery and replication samples, respectively). We found that the heritability of the sulcal opening ranges from 15 to 45\% (SE = 4.8\%). We identified 4 new loci that contribute to this opening, including one that also affects the sulci grey matter thickness. We identified the most significant variant (rs864736) on this locus as being an expression quantitative trait locus (eQTL) for the KCNK2 gene. This gene regulates the immune-cell into the central nervous system (CNS) and controls the CNS inflammation, which is implicated in cortical atrophy and cognitive decline. These results expand our knowledge of the genetic contribution to cortical shrinking and promote further investigation into these variants and genes in pathological context such as Alzheimer’s disease in which brain shrinkage is a key biomarker.}, - language = {en}, - number = {2}, - urldate = {2023-02-06}, - journal = {Brain Structure and Function}, - author = {Le Guen, Yann and Philippe, Cathy and Riviere, Denis and Lemaitre, Hervé and Grigis, Antoine and Fischer, Clara and Dehaene-Lambertz, Ghislaine and Mangin, Jean-François and Frouin, Vincent}, - month = mar, - year = {2019}, - keywords = {Brain ageing, Imaging genetics, CSF, GM thickness, GWAS, Sulci widening}, - pages = {847--857}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VJK7LZXH/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DBSB6Y6V/Le Guen et al. - 2019 - eQTL of KCNK2 regionally influences the brain sulc.pdf:application/pdf}, -} - -@article{alentorn_p0588_2018, - title = {P05.88 {Radiomics} analysis of brain metastases from non-small cell lung cancer brings relevant supplementary information to clinical scores}, - volume = {20}, - issn = {1522-8517}, - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144734/}, - doi = {10.1093/neuonc/noy139.414}, - abstract = {Background -Lung cancer, and more precisely, non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality due to its high prevalence. Likewise, brain metastases from lung cancer are the most frequent type of secondary brain tumors. Different prognostic scores have been proposed to better stratify the treatment of brain metastases. More recently, lung GPA has been updated considering two frequent molecular characteristics in lung adenocarcinoma: EGFR and ALK alterations. However, to the best of our knowledge, the crosstalk between imaging features and the currently used prognostic scores is unknown.We sought to analyze the clinical value of radiomics data in the prediction of survival in patients with brain mets from NSCLC. - -Material and Methods -We have selected 29 patients with brain metastases of NSCLC treated during 2015–2016 at Pitié-Salpêtrière Hospital. We selected patients with neither previous history of brain mets nor brain surgery and high-quality structural MRI.We extracted 1428 radiomic features per patient, including: first-order statistics, volume, shape, texture and wavelet analysis using pyradiomics on Gadolinium enhanced T1 and FLAIR RM images. Using the plsRcox package, several Cox models were constructed with either clinical (GPA score, EGFR mutation and ALK fusion status) or radiomics features or both. The goodness of fit was assessed with the Harrell’s concordance index using 5 fold cross-validation. - -Results -The performance of the radiomics model (mean Harrell’s C-index 0.88, SD 0.08) to predict OS was the best compared to the prediction using clinical data (mean Harrell’s C-index 0.77, SD 0.25). Surprisingly, the addition of clinical data to the radiomics model decreased the performance of OS prediction (mean Harrell’s C-index 0.83, SD 0.17). - -Conclusion -Radiomics analysis of brain mets from NSCLC may provide additional clinically relevant data on the survival, in a non-invasive way. The results of this small cohort are currently being validated in a larger dataset of patients.}, - number = {Suppl 3}, - urldate = {2023-09-07}, - journal = {Neuro-Oncology}, - author = {Alentorn, A and Philippe, C and Grigis, A and Ibañez-Julia, M and Younan, N and Duran-Peña, A and Royer-Perron, L and Goya-Outi, J and Buvat, I and Frouin, F and Jacob, J and Conforti, R and Hoang-Xuan, K and Frouin, V}, - month = sep, - year = {2018}, - pmid = {null}, - pmcid = {PMC6144734}, - pages = {iii324}, -} - -@article{ivanov_substance_2021, - title = {Substance {Use} {Initiation}, {Particularly} {Alcohol}, in {Drug}-{Naive} {Adolescents}: {Possible} {Predictors} and {Consequences} {From} a {Large} {Cohort} {Naturalistic} {Study}}, - volume = {60}, - issn = {1527-5418}, - shorttitle = {Substance {Use} {Initiation}, {Particularly} {Alcohol}, in {Drug}-{Naive} {Adolescents}}, - doi = {10.1016/j.jaac.2020.08.443}, - abstract = {OBJECTIVE: It is unclear whether deviations in brain and behavioral development, which may underpin elevated substance use during adolescence, are predispositions for or consequences of substance use initiation. Here, we examine behavioral and neuroimaging indices at early and mid-adolescence in drug-naive youths to identify possible predisposing factors for substance use initiation and its possible consequences. -METHOD: Among 304 drug-naive adolescents at baseline (age 14 years) from the IMAGEN dataset, 83 stayed drug-naive, 133 used alcohol on 1 to 9 occasions, 42 on 10 to 19 occasions, 27 on 20 to 39 occasions, and 19 on {\textgreater}40 occasions at follow-up (age 16 years). Baseline measures included brain activation during the Monetary Incentive Delay task. Data at both baseline and follow-up included measures of trait impulsivity and delay discounting. -RESULTS: From baseline to follow-up, impulsivity decreased in the 0 and 1- to 9-occasions groups (p {\textless} .004), did not change in the 10- to 19-occasions and 20- to 29-occasions groups (p {\textgreater} .294), and uncharacteristically increased in the {\textgreater}40-occasions group (p = .046). Furthermore, blunted medial orbitofrontal cortex activation during reward outcome at baseline significantly predicted higher alcohol use frequency at follow-up, above and beyond behavioral and clinical variables (p = .008). -CONCLUSION: These results suggest that the transition from no use to frequent drinking in early to mid-adolescence may disrupt normative developmental changes in behavioral control. In addition, blunted activity of the medial orbitofrontal cortex during reward outcome may underscore a predisposition toward the development of more severe alcohol use in adolescents. This distinction is clinically important, as it informs early intervention efforts in preventing the onset of substance use disorder in adolescents.}, - language = {eng}, - number = {5}, - journal = {Journal of the American Academy of Child and Adolescent Psychiatry}, - author = {Ivanov, Iliyan and Parvaz, Muhammad A. and Velthorst, Eva and Shaik, Riaz B. and Sandin, Sven and Gan, Gabriela and Spechler, Philip and Albaugh, Matthew D. and Chaarani, Bader and Mackey, Scott and Banaschewski, Tobias and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Quinlan, Erin Burke and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Gowland, Penny and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Lemaitre, Herve and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Millenet, Sabina and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Schumann, Gunter and Garavan, Hugh and {IMAGEN Consortium}}, - month = may, - year = {2021}, - pmid = {33011213}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Adolescent, Reward, Substance-Related Disorders, adolescence, IMAGEN, reward processing, alcohol use, impulsivity, Pharmaceutical Preparations}, - pages = {623--636}, -} - -@article{chen_brain_2022, - title = {Brain {Signatures} {During} {Reward} {Anticipation} {Predict} {Persistent} {Attention}-{Deficit}/{Hyperactivity} {Disorder} {Symptoms}}, - volume = {61}, - issn = {1527-5418}, - doi = {10.1016/j.jaac.2021.11.030}, - abstract = {OBJECTIVE: Children experiencing attention-deficit/hyperactivity disorder (ADHD) symptoms may retain symptoms into adulthood, but little is known about the underlying mechanism. -METHOD: To identify biomarkers of persistent ADHD symptom development, we carried out whole-brain analyses of neuroimaging data during the anticipation phase of the Monetary-Incentive-Delay (MID) task in 1,368 adolescents recruited by the IMAGEN Consortium at age 14 years, whose behavioral measurements were followed up longitudinally at age 16. In particular, we focused on comparing individuals with persistent high ADHD symptoms at both ages 14 and 16 years to unaffected control individuals, but also exploring which individuals demonstrating symptom remission (with high ADHD symptoms at age 14 but much reduced at age 16). -RESULTS: We identified reduced activations in the medial frontal cortex and the thalamus during reward anticipation as neuro-biomarkers for persistent ADHD symptoms across time. The genetic relevance of the above findings was further supported by the associations of the polygenic risk scores of ADHD with both the persistent and control status and the activations of both brain regions. Furthermore, in an exploratory analysis, the thalamic activation might also help to distinguish persons with persistent ADHD from those remitted in both an exploratory sample (odds ratio = 9.43, p {\textless} .001) and an independent generalization sample (odds ratio = 4.64, p = .003). -CONCLUSION: Using a well-established and widely applied functional magnetic resonance imaging task, we have identified neural biomarkers that could discriminate ADHD symptoms that persist throughout adolescence from controls and potentially those likely to remit during adolescent development as well.}, - language = {eng}, - number = {8}, - journal = {Journal of the American Academy of Child and Adolescent Psychiatry}, - author = {Chen, Di and Jia, Tianye and Cheng, Wei and Cao, Miao and Banaschewski, Tobias and Barker, Gareth J. and Bokde, Arun L. W. and Bromberg, Uli and Büchel, Christian and Desrivières, Sylvane and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny A. and Heinz, Andreas and Ittermann, Bernd and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Paus, Tomáš and Poustka, Luise and Fröhner, Juliane H. and Smolka, Michael N. and Walter, Henrik and Whelan, Robert and Robbins, T. W. and Sahakian, Barbara J. and Schumann, Gunter and Feng, Jianfeng and {IMAGEN Consortium}}, - month = aug, - year = {2022}, - pmid = {34954028}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Brain Mapping, Adult, Adolescent, Child, Reward, Attention Deficit Disorder with Hyperactivity, functional magnetic resonance imaging, attention-deficit/hyperactivity disorder, polygenic risk score, monetary incentive delay, Strengths and Difficulties Questionnaire}, - pages = {1050--1061}, -} - -@article{dufumier_exploring_2024, - title = {Exploring the potential of representation and transfer learning for anatomical neuroimaging: {Application} to psychiatry}, - volume = {296}, - issn = {1053-8119}, - shorttitle = {Exploring the potential of representation and transfer learning for anatomical neuroimaging}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811924001605}, - doi = {10.1016/j.neuroimage.2024.120665}, - abstract = {The perspective of personalized medicine for brain disorders requires efficient learning models for anatomical neuroimaging-based prediction of clinical conditions. There is now a consensus on the benefit of deep learning (DL) in addressing many medical imaging tasks, such as image segmentation. However, for single-subject prediction problems, recent studies yielded contradictory results when comparing DL with Standard Machine Learning (SML) on top of classical feature extraction. Most existing comparative studies were limited in predicting phenotypes of little clinical interest, such as sex and age, and using a single dataset. Moreover, they conducted a limited analysis of the employed image pre-processing and feature selection strategies. This paper extensively compares DL and SML prediction capacity on five multi-site problems, including three increasingly complex clinical applications in psychiatry namely schizophrenia, bipolar disorder, and Autism Spectrum Disorder (ASD) diagnosis. To compensate for the relative scarcity of neuroimaging data on these clinical datasets, we also evaluate three pre-training strategies for transfer learning from brain imaging of the general healthy population: self-supervised learning, generative modeling and supervised learning with age. Overall, we find similar performance between randomly initialized DL and SML for the three clinical tasks and a similar scaling trend for sex prediction. This was replicated on an external dataset. We also show highly correlated discriminative brain regions between DL and linear ML models in all problems. Nonetheless, we demonstrate that self-supervised pre-training on large-scale healthy population imaging datasets (N≈10k), along with Deep Ensemble, allows DL to learn robust and transferable representations to smaller-scale clinical datasets (N≤1k). It largely outperforms SML on 2 out of 3 clinical tasks both in internal and external test sets. These findings suggest that the improvement of DL over SML in anatomical neuroimaging mainly comes from its capacity to learn meaningful and useful abstract representations of the brain anatomy, and it sheds light on the potential of transfer learning for personalized medicine in psychiatry}, - urldate = {2024-06-12}, - journal = {NeuroImage}, - author = {Dufumier, Benoit and Gori, Pietro and Petiton, Sara and Louiset, Robin and Mangin, Jean-François and Grigis, Antoine and Duchesnay, Edouard}, - month = aug, - year = {2024}, - keywords = {Anatomical neuroimaging, Deep learning, Individual subject prediction, Machine learning, Psychiatric disorders}, - pages = {120665}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/W82F8YSM/S1053811924001605.html:text/html}, -} diff --git a/bibutils/data/signature_v-20240621.bib b/bibutils/data/signature_v-20240621.bib deleted file mode 100644 index 378e866..0000000 --- a/bibutils/data/signature_v-20240621.bib +++ /dev/null @@ -1,1955 +0,0 @@ - -@misc{lofstedt_simulated_2014, - title = {Simulated {Data} for {Linear} {Regression} with {Structured} and {Sparse} {Penalties}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - url = {https://hal-cea.archives-ouvertes.fr/cea-00914960/document}, - abstract = {A very active field of research in Bioinformatics is to integrate structure in Machine Learning methods. Methods recently developed claim that they allow simultaneously to link the computed model to the graphical structure of the data set and to select a handful of important features in the analysis. However, there is still no way to simulate data for which we can separate the three properties that such method claim to achieve. These properties are: (i) the sparsity of the solution, i.e., the fact the the model is based on a few features of the data; (ii) the structure of the model; (iii) the relation between the structure of the model and the graphical model behind the generation of the data.}, - language = {en}, - urldate = {2015-12-15}, - author = {Lofstedt, Tommy and Guillemot, Vincent and Frouin, Vincent and Duchesnay, Édouard and Hadj-Selem, Fouad}, - month = jan, - year = {2014}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CHKA93Q4/Lofstedt et al. - 2014 - Simulated Data for Linear Regression with Structur.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EUQ9D63L/cea-00914960v3.html:text/html}, -} - -@inproceedings{lofstedt_analysis_2014, - address = {Paris}, - title = {Analysis, {Structured} variable selection for generalized canonical correlation}, - copyright = {All rights reserved}, - booktitle = {International {Conference} on {Partial} {Least} {Squares} and {Related} {Methods}}, - author = {Lofstedt, Tommy and Hadj-Selem, Foaud and Guillemot, Vincent and Philippe, Cathy and Duchesnay, Edouard and Tenenhaus, Arthur and Frouin, Vincent}, - year = {2014}, - pages = {127}, -} - -@misc{martinot_cortical_2006, - address = {Nice, France}, - title = {Cortical gyrification and (developmental) pathopsychology}, - copyright = {All rights reserved}, - author = {Martinot, J. L. and Kircher, T. and McGuire and P Paillère-Martinot, M. L. and Galinowski, A. and De Beaurepaire, R. and Januel, D. and Ringuenet, D. and Plaze, M. and Andoh, J. and Artiges, E. and Bellivier, F. and Duchesnay, E. and Cachia, A. and Mangin, J. F.}, - year = {2006}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTNcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, -} - -@misc{martinot_brain_2005, - address = {Vienna, Austria}, - title = {Brain folding in schizophrenia}, - copyright = {All rights reserved}, - author = {Martinot, J. L. and Kircher, T. and Paillère-Martinot, M. L. and Plaze, M. and Januel, D. and Bellivier, F. and Andoh, J. and De Beaurepaire, R. and Chanraud, S. and Artiges, E. and Duchesnay, E. and Mangin, J. F. and Kellermann, T. and Leube, D. and Bartrés-Faz, D. and Cachia, A.}, - year = {2005}, - keywords = {Sulci,Anatomy}, - annote = {The following values have no corresponding Zotero field:label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {The following values have no corresponding Zotero field:pages: 57label: ACTIcustom1: NeuroSpincustom2: In}, - annote = {Unati - inproceedings}, - annote = {Unati - inproceedings}, -} - -@inproceedings{martinot_brain_2005-1, - address = {Vienna, Austria}, - title = {Brain folding in schizophrenia}, - copyright = {All rights reserved}, - booktitle = {Proc. 8th {World} congress of biological psychiatry. {The} world journal of biological psychiatry vol 6 (1)}, - author = {Martinot, J.-L. and Kircher, T and Paillère-Martinot, M-L and Plaze, M and Januel, D and Bellivier, F and Andoh, J and De Beaurepaire, R and Chanraud, S and Artiges, E and Duchesnay, E and Mangin, J.-F. and Kellermann, T and Leube, D and Bartrés-Faz, D and Cachia, A}, - year = {2005}, - pages = {57}, -} - -@article{duchesnay_methodes_2015, - title = {Méthodes de prédiction multivariées basées sur la neuroimagerie : application aux maladies psychiatriques}, - copyright = {All rights reserved}, - shorttitle = {Méthodes de prédiction multivariées basées sur la neuroimagerie}, - journal = {Annales Médico-psychologiques, revue psychiatrique}, - author = {Duchesnay, Edouard and Bourgin, Julie and Hadj-Selem, Fouad and Frouin, Vincent}, - year = {2015}, -} - -@article{de_pierrefeu_prediction_2018, - title = {Prediction of activation patterns preceding hallucinations in patients with schizophrenia using machine learning with structured sparsity}, - volume = {39}, - copyright = {All rights reserved}, - issn = {1097-0193}, - url = {http://onlinelibrary.wiley.com/doi/10.1002/hbm.23953/abstract}, - doi = {10.1002/hbm.23953}, - abstract = {Despite significant progress in the field, the detection of fMRI signal changes during hallucinatory events remains difficult and time-consuming. This article first proposes a machine-learning algorithm to automatically identify resting-state fMRI periods that precede hallucinations versus periods that do not. When applied to whole-brain fMRI data, state-of-the-art classification methods, such as support vector machines (SVM), yield dense solutions that are difficult to interpret. We proposed to extend the existing sparse classification methods by taking the spatial structure of brain images into account with structured sparsity using the total variation penalty. Based on this approach, we obtained reliable classifying performances associated with interpretable predictive patterns, composed of two clearly identifiable clusters in speech-related brain regions. The variation in transition-to-hallucination functional patterns not only from one patient to another but also from one occurrence to the next (e.g., also depending on the sensory modalities involved) appeared to be the major difficulty when developing effective classifiers. Consequently, second, this article aimed to characterize the variability within the prehallucination patterns using an extension of principal component analysis with spatial constraints. The principal components (PCs) and the associated basis patterns shed light on the intrinsic structures of the variability present in the dataset. Such results are promising in the scope of innovative fMRI-guided therapy for drug-resistant hallucinations, such as fMRI-based neurofeedback.}, - language = {en}, - number = {4}, - urldate = {2018-03-16}, - journal = {Human Brain Mapping}, - author = {de Pierrefeu, Amicie and Fovet, Thomas and Hadj-Selem, Fouad and Löfstedt, Tommy and Ciuciu, Philippe and Lefebvre, Stephanie and Thomas, Pierre and Lopes, Renaud and Jardri, Renaud and Duchesnay, Edouard}, - month = apr, - year = {2018}, - keywords = {hallucinations, machine learning, real-time fMRI, resting-state networks, schizophrenia}, - pages = {1777--1788}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NRKPT4KC/de Pierrefeu et al. - 2018 - Prediction of activation patterns preceding halluc.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B47VFCKD/abstract.html:text/html;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/G7JAWTUA/de Pierrefeu et al. - 2018 - Prediction of activation patterns preceding halluc.pdf:application/pdf}, -} - -@article{de_guio_loss_2014, - title = {Loss of {Venous} {Integrity} in {Cerebral} {Small} {Vessel} {Disease}: {A} 7-{T} {MRI} {Study} in {Cerebral} {Autosomal}-{Dominant} {Arteriopathy} {With} {Subcortical} {Infarcts} and {Leukoencephalopathy} ({CADASIL})}, - volume = {45}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1524-4628}, - shorttitle = {Loss of {Venous} {Integrity} in {Cerebral} {Small} {Vessel} {Disease}}, - doi = {10.1161/STROKEAHA.114.005726}, - abstract = {BACKGROUND AND PURPOSE: Previous pathological studies in humans or in animal models have shown alterations of small arteries and veins within white matter lesions in cerebral small vessel disease. We aimed to evaluate in vivo, the integrity of the cerebral venous network using high-resolution MRI both within and outside white matter hyperintensities in cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). -METHODS: High-resolution T2*-weighted images were obtained at 7-T in 13 CADASIL patients with no or only mild symptoms and 13 age- and sex-matched controls. Macroscopic veins were automatically counted in the centrum semiovale and compared between patients and controls. In addition, T2* was compared between groups in the normal-appearing white matter. -RESULTS: Vein density was found lower in CADASIL patients compared with that in controls (-14.6\% in patients, P{\textless}0.001). This was detected both within and outside white matter hyperintensities. Mean T2*, that is presumably inversely related to the venous density, was also found increased in normal-appearing white matter of patients (+7.2\%, P=0.006). All results were independent from the extent of white matter hyperintensities. -CONCLUSIONS: A significant reduction in the number of visible veins was observed in the centrum semiovale of CADASIL patients both within and outside white matter hyperintensities, together with an increase of T2* in the normal-appearing white matter. Additional studies are needed to decipher the exact implication of such vasculature changes in the appearance of white matter lesions.}, - language = {eng}, - number = {7}, - journal = {Stroke; a Journal of Cerebral Circulation}, - author = {De Guio, François and Vignaud, Alexandre and Ropele, Stefan and Duering, Marco and Duchesnay, Edouard and Chabriat, Hugues and Jouvent, Eric}, - month = jul, - year = {2014}, - pmid = {24867926}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Middle Aged, Aged, CADASIL, magnetic resonance imaging, Cerebral Veins, Cerebrum, veins}, - pages = {2124--2126}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VLY25IQ6/De Guio et al. - 2014 - Loss of venous integrity in cerebral small vessel .pdf:application/pdf}, -} - -@article{de_guio_vivo_2014, - title = {In {Vivo} {High}-{Resolution} 7 {Tesla} {MRI} {Shows} {Early} and {Diffuse} {Cortical} {Alterations} in {CADASIL}}, - volume = {9}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0106311}, - abstract = {BACKGROUND AND PURPOSE: Recent data suggest that early symptoms may be related to cortex alterations in CADASIL (Cerebral Autosomal-Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), a monogenic model of cerebral small vessel disease (SVD). The aim of this study was to investigate cortical alterations using both high-resolution T2* acquisitions obtained with 7 Tesla MRI and structural T1 images with 3 Tesla MRI in CADASIL patients with no or only mild symptomatology (modified Rankin's scale ≤1 and Mini Mental State Examination (MMSE) ≥24). -METHODS: Complete reconstructions of the cortex using 7 Tesla T2* acquisitions with 0.7 mm isotropic resolution were obtained in 11 patients (52.1±13.2 years, 36\% male) and 24 controls (54.8±11.0 years, 42\% male). Seven Tesla T2* within the cortex and cortical thickness and morphology obtained from 3 Tesla images were compared between CADASIL and control subjects using general linear models. -RESULTS: MMSE, brain volume, cortical thickness and global sulcal morphology did not differ between groups. By contrast, T2* measured by 7 Tesla MRI was significantly increased in frontal, parietal, occipital and cingulate cortices in patients after correction for multiple testing. These changes were not related to white matter lesions, lacunes or microhemorrhages in patients having no brain atrophy compared to controls. -CONCLUSIONS: Seven Tesla MRI, by contrast to state of the art post-processing of 3 Tesla acquisitions, shows diffuse T2* alterations within the cortical mantle in CADASIL whose origin remains to be determined.}, - language = {eng}, - number = {8}, - journal = {PloS One}, - author = {De Guio, François and Reyes, Sonia and Vignaud, Alexandre and Duering, Marco and Ropele, Stefan and Duchesnay, Edouard and Chabriat, Hugues and Jouvent, Eric}, - year = {2014}, - pmid = {25165824}, - pmcid = {PMC4148432}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Cerebral Cortex, Middle Aged, CADASIL, Organ Size, Case-Control Studies}, - pages = {e106311}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JXEABKX4/De Guio et al. - 2014 - In vivo high-resolution 7 Tesla MRI shows early an.pdf:application/pdf}, -} - -@inproceedings{damon_discriminating_2008, - title = {Discriminating between populations of subjects based on {FMRI} data using sparse features selection and {SRDA} classifier}, - copyright = {All rights reserved}, - booktitle = {{MICCAI} {Analysis} of {Functional} {Medical} {Images} {Workshop}}, - author = {Damon, Cécilia and Pinel, Philippe and Perrot, Matthieu and Michel, Vincent and Duchesnay, Edouard and Poline, Jean-Baptiste and Thirion, Bertrand}, - year = {2008}, - pages = {25--32}, - file = {Fulltext:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ENXC7Y6Y/Damon et al. - 2008 - Discriminating between populations of subjects bas.pdf:application/pdf}, -} - -@article{mangin_object-based_2004, - title = {Object-based morphometry of the cerebral cortex}, - volume = {23}, - copyright = {All rights reserved}, - number = {8}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Mangin, J. F. and Rivière, D. and Cachia, A. and Duchesnay, E. and Cointepas, Y. and Papadopoulos-Orfanos, D. and Collins, D. L. and Evans, A. C. and Régis, J.}, - month = aug, - year = {2004}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Subtraction Technique, Numerical Analysis, Computer-Assisted, Signal Processing, Computer-Assisted, Expert Systems}, - pages = {968--982}, -} - -@inproceedings{jacquelet_combinatorial_2002, - title = {Combinatorial pyramid transposed to behavioural space for object recognition process}, - volume = {1}, - copyright = {All rights reserved}, - booktitle = {Systems, {Man} and {Cybernetics}, 2002 {IEEE} {International} {Conference} on}, - publisher = {IEEE}, - author = {Jacquelet, Y and Montois, J and Duchesnay, E. and Kinic, A}, - year = {2002}, - pages = {212--217}, -} - -@inproceedings{kinie_segmentation_2001, - title = {Segmentation vectorielle des signaux épileptiques une approche expérimentale multi-agents}, - copyright = {All rights reserved}, - booktitle = {18° {Colloque} sur le traitement du signal et des images, {FRA}, 2001}, - publisher = {GRETSI, Groupe d’Etudes du Traitement du Signal et des Images}, - author = {Kinie, Abel and Duchesnay, Edouard and Wendling, Fabrice and Montois, Jean-Jacques and Jacquelet, Yann}, - year = {2001}, -} - -@inproceedings{jacquelet_architecture_2001, - title = {Architecture pyramidale agent pour la segmentation d'image: {Application} à l'extraction d'une zone lobulaire issue d'une mammographie}, - copyright = {All rights reserved}, - booktitle = {18° {Colloque} sur le traitement du signal et des images, {FRA}, 2001}, - publisher = {GRETSI, Groupe d’Etudes du Traitement du Signal et des Images}, - author = {Jacquelet, Yann and Montois, Jean-Jacques and Duchesnay, Edouard and GARREAU, Mireille and KINIE, Abel}, - year = {2001}, -} - -@inproceedings{duchesnay_multiagent_2000, - address = {Lyon}, - title = {A {Multiagent} {System} for a {Cooperative} and {Distributed} {Vision} {System}}, - copyright = {All rights reserved}, - booktitle = {Advances in {Concurrent} {Engineering}: {CE2000} {Proceedings}}, - author = {Duchesnay, Edouard and Montois, Jean-Jacques and Jacquelet, Yann}, - year = {2000}, - pages = {453--462}, -} - -@inproceedings{duchesnay_agent-based_2001, - title = {An agent-based implementation of irregular pyramid for distributed image segmentation}, - copyright = {All rights reserved}, - booktitle = {Emerging {Technologies} and {Factory} {Automation}, 2001. {Proceedings}. 2001 8th {IEEE} {International} {Conference} on}, - publisher = {IEEE}, - author = {Duchesnay, Edouard and Montois, J-J and Jacquelet, Yann and Kinie, Abel}, - year = {2001}, - pages = {409--415}, -} - -@inproceedings{duchesnay_resolution_2000, - address = {Dinard, France}, - title = {Résolution distribuée de conflits dans un réseau d'agents}, - copyright = {All rights reserved}, - booktitle = {10ème {Journées} {Neurosciences} et {Sciences} de l'{Ingénieur}}, - author = {Duchesnay, E. and Montois, J.J. and Jacquelet, Y.}, - year = {2000}, - pages = {191--194}, -} - -@article{duchesnay_methodes_2015-1, - title = {Méthodes de prédiction multivariées basées sur la neuroimagerie : application aux maladies psychiatriques}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {0003-4487}, - shorttitle = {Méthodes de prédiction multivariées basées sur la neuroimagerie}, - url = {http://www.sciencedirect.com/science/article/pii/S0003448715000621}, - doi = {10.1016/j.amp.2015.03.002}, - abstract = {Résumé -L’étude en neuroimagerie des maladies mentales (troubles de l’humeur, schizophrénie, trouble du spectre autistique) a, jusqu’alors, été abordée par des méthodes classiques d’analyses statistiques dites « univariées ». Ces méthodes ont permis d’identifier de nombreuses modifications cérébrales structurelles et fonctionnelles associées à ces pathologies. Ce type d’analyse répond à la question : « Où, dans le cerveau et à l’échelle d’une cohorte de sujets/patients, y a-t-il des associations entre la pathologie et le signal associé à de l’imagerie structurelle ou fonctionnelle ? » Ce type d’analyse n’a pas de pouvoir prédictif nécessaire pour aider au diagnostic ou au pronostic de la réponse à un traitement à un niveau individuel. De plus, ces analyses impliquent généralement l’examen de chaque voxel (locus de mesure du signal) séparément les uns des autres, ce qui empêche l’identification de « patterns » impliquant conjointement plusieurs régions cérébrales. Tenant compte du fait que dans les pathologies psychiatriques, les altérations du cerveau impliquent des réseaux largement distribués sur plusieurs régions cérébrales, la communauté de neuroimagerie s’est tournée vers des méthodes de prédiction multivariées en raison de leur capacité à examiner conjointement toutes les régions cérébrales ainsi que pour leur potentiel à produire des inférences au niveau individuel. Cet article donne un aperçu critique des applications actuelles des méthodes de prédiction multivariées dans le cadre des maladies mentales. Nous abordons l’identification de biomarqueurs fondée sur la neuroimagerie dans la perspective d’utiliser ces derniers pour le diagnostic, la détection précoce et la réponse au traitement. -Abstract -The study of mental illness (mood disorders, schizophrenia, autism spectrum disorder) in neuroimaging has been addressed by standard “univariate” statistical analysis methods. These methods have revealed many structural and functional brain changes associated with these diseases. Such analysis answers the question: “Where in the brain and on the scale of a cohort of subjects/patients, are the associations between the pathology and any structural or functional related signal”. This type of analysis has no predictive power to assist in the diagnosis or the prognosis of the response to a treatment at an individual level. In addition, these analyses typically involve examining each voxel separately (measured signal at given locus), thus limiting the identification of “patterns” that jointly involve several brain regions. Taking into account the fact that brain alterations in psychiatric diseases expand over a widely distributed network of brain regions, the neuroimaging community turned to multivariate predictive methods because of their ability to examine voxels jointly and their potential for making inferences at a single-subject level. This article provides a critical overview of the current applications of multivariate prediction methods for the identification of biomarkers based on neuroimaging in the prospect of using these for the diagnosis, early detection and response to treatment of mental illness.}, - urldate = {2015-04-02}, - journal = {Annales Médico-psychologiques, revue psychiatrique}, - author = {Duchesnay, Edouard and Bourgin, Julie and Hadj-Selem, Fouad and Frouin, Vincent}, - year = {2015}, - keywords = {imagerie cérébrale, marqueur biologique, médecine prédictive, Biomarker, Imagerie par résonance magnétique, Pathologie psychiatrique, Predictive medicine, Psychiatric pathology, Statistics, Statistique, brain imaging}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GCU7IFM7/S0003448715000621.html:text/html}, -} - -@inproceedings{martinot_brain_2005-2, - address = {Vienna, Austria}, - title = {Brain folding in schizophrenia}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Proc. 8th {World} congress of biological psychiatry. {The} world journal of biological psychiatry vol 6 (1)}, - author = {Martinot, J.-L. and Kircher, T and Paillère-Martinot, M-L and Plaze, M and Januel, D and Bellivier, F and Andoh, J and De Beaurepaire, R and Chanraud, S and Artiges, E and Duchesnay, E and Mangin, J.-F. and Kellermann, T and Leube, D and Bartrés-Faz, D and Cachia, A}, - year = {2005}, - keywords = {anatomy, conference, sulci}, - pages = {57}, -} - -@inproceedings{da_mota_permuted_2014, - title = {Permuted {Voxelwise} {Genome}-{Wide} {Association}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Human {Brain} {Mapping}}, - author = {Da Mota, Benoit and LI, Jinpeng and Cadenne, M and Ducrot, Vincent and Monnot, Sebastien and Frouin, Vincent}, - year = {2014}, -} - -@article{bourgin_hyper-responsivity_2015, - title = {Hyper-responsivity to stress in rats is associated with a large increase in amygdala volume. {A} {7T} {MRI} study}, - volume = {25}, - copyright = {All rights reserved}, - issn = {1873-7862}, - doi = {10.1016/j.euroneuro.2015.02.010}, - abstract = {Stress is known to precipitate psychiatric disorders in vulnerable people. Individual differences in the stress responsivity can dramatically affect the onset of these illnesses. Animal models of repeated stress represent valuable tools to identify region-specific volumetric changes in the brain. Here, using high resolution 7T MRI, we found that amygdala is the most significant parameter for distinction between F344 and SD rats known to have differential response to stress. A significant substantial increase (45\%) was found in the amygdala volume of rats that do not habituate to the repeated stress procedure (F344 rats) compared to SD rats. This strain-specific effect of stress was evidenced by a significant strain-by-stress interaction. There were no significant strain differences in the volumes of hippocampi and prefrontal cortices though stress produces significant reductions of smaller amplitude in the medial prefrontal cortex (mPFC) (9\% and 12\%) and dorsal hippocampus (5\% and 6\%) in both strains. Our data further demonstrate the feasibility and relevance of high isotropic resolution structural ex vivo 7T MRI in the study of the brain effects of stress in small animals. Neuroimaging is a valuable tool to follow up brain volumetric reorganization during the stress response and could also be easily used to test pharmacological interventions to prevent the deleterious effects of stress.}, - language = {eng}, - number = {6}, - journal = {European Neuropsychopharmacology: The Journal of the European College of Neuropsychopharmacology}, - author = {Bourgin, J. and Cachia, A. and Boumezbeur, F. and Djemaï, B. and Bottlaender, M. and Duchesnay, E. and Mériaux, S. and Jay, T. M.}, - month = jun, - year = {2015}, - pmid = {25823695}, - keywords = {Magnetic Resonance Imaging, Male, Animals, Rats, Disease Models, Animal, Hippocampus, Corticosterone, Cortico-limbic network, High-resolution structural MRI, Rat, Amygdala, Electroencephalography, Rats, Inbred F344, Rats, Sprague-Dawley, Stress, Psychological, Analysis of Variance, Species Specificity, Stress/*metabolism, Stress}, - pages = {828--835}, - annote = {The following values have no corresponding Zotero field:number: 6label: ACL}, - annote = {UnirsPMID: 25823695}, -} - -@patent{duchesnay_method_2010, - title = {Method for {Developing} an {Information} {Prediction} {Device}, {Use} {Thereof}, and {Corresponding} {Storage} {Medium} and {Apparatus}}, - url = {https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2010103248}, - abstract = {(EN)The invention relates to the method for developing a prediction device (102) for predicting a phenotype (110) of a person (108) from imaging data (106) of said person (108). The method includes the following steps: determining imaging descriptors (step 10), said step including the following steps: acquiring multidimensional images of people (130) by means of an imaging apparatus (122) (step 20); and extracting multidimensional image elements from the acquired multidimensional images to serve as descriptors (step 24); classifying the predetermined descriptors on the basis of the capability thereof to predict said phenotype (110) (step 12); selecting, from among the classified descriptors, a relevant number of the best-classified descriptors that is sufficient to predict said phenotype (step 14); and constructing the prediction device (102) from the selected descriptors (step 16).(FR)Le procédé d'élaboration d'un dispositif de prédiction (102) destiné à pré¬ dire un phénotype (1 10) d'un individu (108) à partir de données d'imagerie (106) dudit individu (108). Il comprend les étapes suivantes : - détermination de descripteurs d'imagerie (étape 10), cette étape compre¬ nant les étapes suivantes : - acquisition d'images multidimensionnelles d'individus (130) au moyen d'un appareil d'imagerie (122) (étape 20); et - extraction d'éléments d'images multidimensionnelles en tant que descripteurs à partir des images multidimensionnelles acquises (étape 24); - classement des descripteurs déterminés en fonction de leur capacité à prédire ledit phénotype (110) (étape 12); - sélection parmi les descripteurs classés d'un nombre pertinent de descrip¬ teurs les mieux classés suffisant à prédire ledit phénotype (110) (étape 14); et - construction du dispositif de prédiction (102) à partir des descripteurs sé¬ lectionnés (étape 16).}, - language = {French (FR)}, - assignee = {COMMISSARIAT À L'ÉNERGIE ATOMIQUE ET AUX ÉNERGIES ALTERNATIVES, ASSISTANCE PUBLIQUE - HOPITAUX DE PARIS, DUCHESNAY, Edouard, PAILLERE, Marie-Laure, CACHIA, Arnaud, MARTINOT, Jean-Luc, ARTIGES, Eric}, - number = {WO/2010/103248}, - urldate = {2018-05-28}, - author = {Duchesnay, Edouard and Paillere, Marie-Laure and Cachia, Arnaud and Martinot, Jean-Luc and Artiges, Eric}, - month = sep, - year = {2010}, - keywords = {And Corresponding Storage Medium and Apparatus, Method for Developing an Information Prediction Device, Use Thereof}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B2N9PHK7/detail.html:text/html}, -} - -@inproceedings{thirion_reading_2006, - title = {Reading the brain visual system as an inverse problem}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {International {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Thirion, Bertrand and Duchesnay, Edouard and Hubbard, Edward and Dubois, Jessica and Poline, Jean-Baptiste and Dehaene, Stanislas}, - year = {2006}, - keywords = {conference}, - pages = {1060--1063}, -} - -@inproceedings{thirion_reading_2005, - address = {Toronto, Canada}, - title = {Reading in the subject's mind: the case of low-level vision}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Proc. 11th {HBM} {CD}-{Rom} {Neuroimage} vol 26 (1)}, - publisher = {SHFJ-CEA, Orsay}, - author = {Thirion, Bertrand and Duchesnay, Edouard and Dubois, Jessica and Poline, Jean-Baptiste and Le Bihan, Denis}, - year = {2005}, - keywords = {conference}, -} - -@article{thirion_inverse_2006, - title = {Inverse retinotopy: inferring the visual content of images from brain activation patterns}, - volume = {33}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - shorttitle = {Inverse retinotopy}, - doi = {10.1016/j.neuroimage.2006.06.062}, - abstract = {Traditional inference in neuroimaging consists in describing brain activations elicited and modulated by different kinds of stimuli. Recently, however, paradigms have been studied in which the converse operation is performed, thus inferring behavioral or mental states associated with activation images. Here, we use the well-known retinotopy of the visual cortex to infer the visual content of real or imaginary scenes from the brain activation patterns that they elicit. We present two decoding algorithms: an explicit technique, based on the current knowledge of the retinotopic structure of the visual areas, and an implicit technique, based on supervised classifiers. Both algorithms predicted the stimulus identity with significant accuracy. Furthermore, we extend this principle to mental imagery data: in five data sets, our algorithms could reconstruct and predict with significant accuracy a pattern imagined by the subjects.}, - language = {eng}, - number = {4}, - journal = {NeuroImage}, - author = {Thirion, Bertrand and Duchesnay, Edouard and Hubbard, Edward and Dubois, Jessica and Poline, Jean-Baptiste and Lebihan, Denis and Dehaene, Stanislas}, - month = dec, - year = {2006}, - pmid = {17029988}, - keywords = {Humans, Imagination, Models, Theoretical, Retina, Visual Cortex, Visual Perception}, - pages = {1104--1116}, - annote = {Journal ArticleUnited States}, - annote = {Journal ArticleUnited States}, - annote = {The following values have no corresponding Zotero field:auth-address: INRIA Futurs, Service Hospitalier Frederic Joliot, 4, Place du General Leclerc 91401 Orsay Cedex, France. bertrand.thirion@inria.fralt-title: NeuroImagenumber: 4accession-num: 17029988label: ACL}, - annote = {The following values have no corresponding Zotero field:auth-address: INRIA Futurs, Service Hospitalier Frederic Joliot, 4, Place du General Leclerc 91401 Orsay Cedex, France. bertrand.thirion@inria.fralt-title: NeuroImagenumber: 4accession-num: 17029988label: ACLcustom1: NEUROSPIN}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: NeuroSpin}, - annote = {Unati - articlejb}, -} - -@inproceedings{teillac_colocalization_2016, - series = {Mathematics and {Visualization}}, - title = {Colocalization of {Functional} {Activity} and {Neurite} {Density} {Within} {Cortical} {Areas}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-3-319-54129-7 978-3-319-54130-3}, - url = {https://link.springer.com/chapter/10.1007/978-3-319-54130-3_15}, - doi = {10.1007/978-3-319-54130-3_15}, - abstract = {In this work, we investigated the link between the blood-oxygen-level dependant (BOLD) effect observed using functional magnetic resonance imaging (fMRI) and the neurite density inferred from the Neurite Orientation Dispersion and Density Imaging (NODDI) model in some well-known lateralized cortical areas. We found a strong colocalization between those two parameters in lateralized areas such as the primary motor cortex, the language network, but also the primary visual cortex, which might indicate a strong link between microstructure and functional activity.}, - language = {en}, - urldate = {2017-12-29}, - booktitle = {Computational {Diffusion} {MRI}}, - publisher = {Springer, Cham}, - author = {Teillac, Achille and Lefrance, Sandrine and Duchesnay, Edouard and Poupon, Fabrice and Fuster, Maite Alaitz Ripoll and Bihan, Denis Le and Mangin, Jean-Francois and Poupon, Cyril}, - month = oct, - year = {2016}, - pages = {175--186}, - annote = {The following values have no corresponding Zotero field:pub-location: Athens, Greecelabel: ACTI}, - annote = {UnirsPart of the Mathematics and Visualization book series (MATHVISUAL)}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VEPDYHA5/978-3-319-54130-3_15.html:text/html}, -} - -@inproceedings{sun_defining_2008, - title = {Defining cortical sulcus patterns using partial clustering based on bootstrap and bagging}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-1-4244-2002-5}, - shorttitle = {Biomedical {Imaging}: {From} {Nano} to {Macro}, 2008. {ISBI}}, - url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4541325}, - doi = {10.1109/ISBI.2008.4541325}, - abstract = {The cortical folding patterns are very different from one individual to another. Here we try to find folding patterns automatically using large-scale datasets by non-supervised clustering analysis. The sulci of each brain are detected and identified using the brain VIS A open software. The 3D moment invariants are calculated and used as the shape descriptors of the sulci identified. A partial clustering algorithm using bootstrap sampling and bagging (PCBB) is devised for cortical pattern mining. Partial clusters are found using a modified hierarchical clustering method constrained by an objective function which looks for the most compact and dissimilar clusters. Bagging is used to increase stability. Experiments on simulated and real datasets are used to demonstrate the strength and stability of this algorithm compared to other standard approaches. Some cortical patterns are found using our method. In particular, the patterns found for the left cingulate sulcus are consistent with the patterns described in the atlas of Ono.}, - booktitle = {2008 5th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}: {From} {Nano} to {Macro}}, - publisher = {IEEE}, - author = {Sun, Zhong Yi and Riviere, Denis and Duchesnay, Edouard and Thirion, Bertrand and Poupon, Fabrice and Mangin, Jean-Francois}, - month = may, - year = {2008}, - keywords = {conference, Sampling methods, Clustering, Bagging, Large-scale systems, 3D moment invariant, bootstrap sampling, Clustering algorithms, Clustering methods, cortical pattern mining, cortical sulcus pattern, Data analysis, Frequency, hierarchical clustering, left cingulate sulcus, morphometry, nonsupervised clustering analysis, partial clustering, Pattern analysis, pattern clustering, patterns, Shape, Stability, sulcus, Cortical folding pattern}, - pages = {1629--1632}, -} - -@inproceedings{poline_imaging_2010, - address = {Heidelberg}, - title = {Imaging {Genetics}: {Bio}-{Informatics} and {Bio}-{Statistics} {Challenges}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-3-7908-2603-6}, - url = {http://www.springerlink.com/index/10.1007/978-3-7908-2604-3}, - doi = {10.1007/978-3-7908-2604-3}, - booktitle = {compstat}, - publisher = {Physica-Verlag HD}, - author = {Poline, Jean-Baptiste and Lalanne, Christophe and Tenenhaus, Arthur and Duchesnay, Edouard and Thirion, Bertrand and Frouin, Vincent}, - editor = {Lechevallier, Yves and Saporta, Gilbert}, - year = {2010}, - keywords = {conference}, - pages = {101--110}, - file = {Poline et al. - 2010 - Imaging Genetics Bio-Informatics and Bio-Statisti.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HB7SW2DG/Poline et al. - 2010 - Imaging Genetics Bio-Informatics and Bio-Statisti.pdf:application/pdf}, -} - -@article{penttila_cortical_2009, - title = {Cortical folding in patients with bipolar disorder or unipolar depression}, - volume = {34}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1488-2434}, - abstract = {BACKGROUND: Analysis of cortical folding may provide insight into neurodevelopment deviations, which, in turn, can predispose to depression that responds particularly poorly to medications. We hypothesized that patients with treatment-resistant depression would exhibit measurable alterations in cortical folding. -METHODS: We computed hemispheric global sulcal indices (g-SIs) in T(1)-weighted magnetic resonance images obtained from 76 patients and 70 healthy controls. We separately searched for anatomic deviations in patients with bipolar disorder (16 patients with treatment-resistant depression, 25 with euthymia) and unipolar depression (35 patients with treatment-resistant depression). -RESULTS: Compared with healthy controls, both groups of patients with treatment-resistant depression exhibited reduced g-SIs: in the right hemisphere among patients with bipolar disorder and in both hemispheres among those with unipolar depression. Patients with euthymic bipolar disorder did not differ significantly from depressed patients or healthy controls. Among patients with bipolar disorder who were taking lithium, we found positive correlations between current lithium dose and g-SIs in both hemispheres. -LIMITATIONS: We cannot estimate the extent to which the observed g-SI reductions are linked to treatment resistance and to what extent they are state-dependent. Furthermore, we cannot disentangle the impact of medications from that of the affective disorder. Finally, there is interindividual variation and overlap of g-SIs among patients and healthy controls that need to be considered when interpreting our results. -CONCLUSION: Reduced global cortical folding surface appears to be characteristic of patients with treatment-resistant depression, either unipolar or bipolar. In patients with bipolar disorder, treatment with lithium may modify cortical folding surface.}, - language = {eng}, - number = {2}, - journal = {Journal of psychiatry \& neuroscience: JPN}, - author = {Penttilä, Jani and Paillère-Martinot, Marie-Laure and Martinot, Jean-Luc and Ringuenet, Damien and Wessa, Michèle and Houenou, Josselin and Gallarda, Thierry and Bellivier, Frank and Galinowski, André and Bruguière, Pascale and Pinabel, François and Leboyer, Marion and Olié, Jean-Pierre and Duchesnay, Edouard and Artiges, Eric and Mangin, Jean-François and Cachia, Arnaud}, - month = mar, - year = {2009}, - pmid = {19270763}, - pmcid = {PMC2647564}, - keywords = {Humans, Adult, Female, Male, Cerebral Cortex, Depressive Disorder, Middle Aged, Functional Laterality, Psychiatric Status Rating Scales, Antidepressive Agents, Antimanic Agents, Drug Resistance, Electroconvulsive Therapy, Lithium Carbonate}, - pages = {127--135}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Penttila-PsychiatryNeurosci09.pdfarticle}, -} - -@article{penttila_cortical_2009-1, - title = {Cortical folding difference between patients with early-onset and patients with intermediate-onset bipolar disorder}, - volume = {11}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1399-5618}, - doi = {10.1111/j.1399-5618.2009.00683.x}, - abstract = {OBJECTIVES: Cerebral abnormalities have been detected in patients with bipolar disorder (BD). In comparison to BD with a later onset, early-onset BD has been found to have a poorer outcome. However, it is yet unknown whether neuroanatomical abnormalities differ between age-at-onset subgroups of the illness. We searched for cortical folding differences between early-onset (before 25 years) and intermediate-onset (between 25 and 45 years) BD patients. -METHODS: Magnetic resonance images of 22 early-onset BD patients, 14 intermediate-onset BD patients, and 50 healthy participants were analyzed using a fully automated method to extract, label, and measure the sulcal area in the whole cortex. Cortical folding was assessed by computing global sulcal indices (the ratio between total sulcal area and total outer cortex area) for each hemisphere, and local sulcal indices for 12 predefined regions in both hemispheres. -RESULTS: Intermediate-onset BD patients had a significantly reduced local sulcal index in the right dorsolateral prefrontal cortex in comparison to both early-onset BD patients and healthy subjects, and lower global sulcal indices in both hemispheres in comparison to healthy subjects (p {\textless} 0.05, Bonferroni corrected). Brain tissue volumes did not differ between groups. -CONCLUSIONS: This study provided the first evidence of a neuroanatomic difference between intermediate-onset and early-onset BD, which lends further support to the existence of different age-at-onset subgroups of BD.}, - language = {eng}, - number = {4}, - journal = {Bipolar Disorders}, - author = {Penttilä, Jani and Cachia, Arnaud and Martinot, Jean-Luc and Ringuenet, Damien and Wessa, Michèle and Houenou, Josselin and Galinowski, André and Bellivier, Frank and Gallarda, Thierry and Duchesnay, Edouard and Artiges, Eric and Leboyer, Marion and Olié, Jean-Pierre and Mangin, Jean-François and Paillère-Martinot, Marie-Laure}, - month = jun, - year = {2009}, - pmid = {19500089}, - keywords = {Humans, Imaging, Three-Dimensional, Brain Mapping, Adult, Female, Male, Cerebral Cortex, Middle Aged, Functional Laterality, Age Factors, Age of Onset, Suicide, Attempted}, - pages = {361--370}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Penttila-BP2009.pdfarticle}, -} - -@article{pedregosa_scikit-learn:_2012, - title = {Scikit-learn: {Machine} {Learning} in {Python}}, - volume = {12}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - shorttitle = {Scikit-learn}, - url = {http://arxiv.org/abs/1201.0490}, - abstract = {Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net.}, - number = {Oct}, - urldate = {2014-07-28}, - journal = {Journal of Machine Learning Research}, - author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Edouard}, - month = jan, - year = {2012}, - note = {arXiv: 1201.0490}, - keywords = {Computer Science - Learning, Computer Science - Mathematical Software}, - pages = {2825--2830}, - annote = {arXiv: 1201.0490}, - file = {arXiv\:1201.0490 PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WP6A5AMP/Pedregosa et al. - 2012 - Scikit-learn Machine Learning in Python.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8D7CDP3S/1201.html:text/html}, -} - -@inproceedings{pauling_bipolar_2017, - series = {Abstracts of the 30th {ECNP} {Congress}}, - title = {Bipolar disorder and white matter microstructure: {ENIGMA} bipolar disorder fractional anisotropy {DTI} results}, - volume = {27}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - shorttitle = {P.2.d.044 - {Bipolar} disorder and white matter microstructure}, - url = {http://www.sciencedirect.com/science/article/pii/S0924977X17315110}, - doi = {10.1016/S0924-977X(17)31511-0}, - urldate = {2017-12-29}, - booktitle = {European {Neuropsychopharmacology}}, - author = {Pauling, M. and Henry, C. and Sarrazin, S. and Duchesnay, E. and Stout, J. and Hibar, D. and Jahanshad, N. and Andreassen, O. and Thompson, P. and Houenou, J.}, - month = oct, - year = {2017}, - pages = {S839--S840}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/XC2BGPDT/S0924977X17315110.html:text/html}, -} - -@article{maroy_segmentation_2008, - title = {Segmentation of rodent whole-body dynamic {PET} images: an unsupervised method based on voxel dynamics}, - volume = {27}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {0278-0062}, - shorttitle = {Segmentation of rodent whole-body dynamic {PET} images}, - doi = {10.1109/TMI.2007.905106}, - abstract = {Positron emission tomography (PET) is a useful tool for pharmacokinetics studies in rodents during the preclinical phase of drug and tracer development. However, rodent organs are small as compared to the scanner's intrinsic resolution and are affected by physiological movements. We present a new method for the segmentation of rodent whole-body PET images that takes these two difficulties into account by estimating the pharmacokinetics far from organ borders. The segmentation method proved efficient on whole-body numerical rat phantom simulations, including 3-14 organs, together with physiological movements (heart beating, breathing, and bladder filling). The method was resistant to spillover and physiological movements, while other methods failed to obtain a correct segmentation. The radioactivity concentrations calculated with this method also showed an excellent correlation with the manual delineation of organs in a large set of preclinical images. In addition, it was faster, detected more organs, and extracted organs' mean time activity curves with a better confidence on the measure than manual delineation.}, - language = {eng}, - number = {3}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Maroy, Renaud and Boisgard, Raphaël and Comtat, Claude and Frouin, Vincent and Cathier, Pascal and Duchesnay, Edouard and Dollé, Frédéric and Nielsen, Peter E. and Trébossen, Régine and Tavitian, Bertrand}, - month = mar, - year = {2008}, - pmid = {18334430}, - keywords = {Algorithms, Artificial Intelligence, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Animals, Rats, Phantoms, Imaging, Positron-Emission Tomography, Whole Body Imaging}, - pages = {342--354}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Maroy-TMI08.pdfarticle}, -} - -@incollection{lofstedt_structured_2016, - series = {The {Multiple} {Facets} of {Partial} {Least} {Squares} and {Related} {Methods}}, - title = {Structured {Variable} {Selection} for {Regularized} {Generalized} {Canonical} {Correlation} {Analysis}, {The} {Multiple} {Facets} of {Partial} {Least} {Squares} and {Related} {Methods}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - url = {https://hal-centralesupelec.archives-ouvertes.fr/hal-01396614}, - language = {en}, - urldate = {2017-01-10}, - booktitle = {Springer {Proceedings} in {Mathematics} and {Statistics}}, - author = {Lofstedt, Tommy and Hadj-Selem, Fouad and Guillemot, Vincent and Philippe, Cathy and Duchesnay, Edouard and Frouin, Vincent and Tenenhaus, Arthur}, - year = {2016}, - pages = {129--139}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/A3HTWHWC/hal-01396614.html:text/html}, -} - -@inproceedings{li_embarrassingly_2013, - title = {Embarrassingly {Parallel} {Array} {Computing} ({EPAC})}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - author = {LI, Jinpeng and Duchesnay, Edouard and Duboism, Mathieu and Hugo, Laure and Mota, Benoit Da}, - year = {2013}, - note = {http://mloss.org/software/view/515/}, - keywords = {conference}, - annote = {http://mloss.org/software/view/515/}, -} - -@article{leroy_striatal_2012, - title = {Striatal and extrastriatal dopamine transporter in cannabis and tobacco addiction: a high-resolution {PET} study}, - volume = {17}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1369-1600}, - shorttitle = {Striatal and extrastriatal dopamine transporter in cannabis and tobacco addiction}, - doi = {10.1111/j.1369-1600.2011.00356.x}, - abstract = {The dopamine (DA) system is known to be involved in the reward and dependence mechanisms of addiction. However, modifications in dopaminergic neurotransmission associated with long-term tobacco and cannabis use have been poorly documented in vivo. In order to assess striatal and extrastriatal dopamine transporter (DAT) availability in tobacco and cannabis addiction, three groups of male age-matched subjects were compared: 11 healthy non-smoker subjects, 14 tobacco-dependent smokers (17.6 ± 5.3 cigarettes/day for 12.1 ± 8.5 years) and 13 cannabis and tobacco smokers (CTS) (4.8 ± 5.3 cannabis joints/day for 8.7 ± 3.9 years). DAT availability was examined in positron emission tomography (HRRT) with a high resolution research tomograph after injection of [11C]PE2I, a selective DAT radioligand. Region of interest and voxel-by-voxel approaches using a simplified reference tissue model were performed for the between-group comparison of DAT availability. Measurements in the dorsal striatum from both analyses were concordant and showed a mean 20\% lower DAT availability in drug users compared with controls. Whole-brain analysis also revealed lower DAT availability in the ventral striatum, the midbrain, the middle cingulate and the thalamus (ranging from -15 to -30\%). The DAT availability was slightly lower in all regions in CTS than in subjects who smoke tobacco only, but the difference does not reach a significant level. These results support the existence of a decrease in DAT availability associated with tobacco and cannabis addictions involving all dopaminergic brain circuits. These findings are consistent with the idea of a global decrease in cerebral DA activity in dependent subjects.}, - language = {eng}, - number = {6}, - journal = {Addiction Biology}, - author = {Leroy, Claire and Karila, Laurent and Martinot, Jean-Luc and Lukasiewicz, Michaël and Duchesnay, Edouard and Comtat, Claude and Dollé, Frédéric and Benyamina, Amine and Artiges, Eric and Ribeiro, Maria-Joao and Reynaud, Michel and Trichard, Christian}, - month = nov, - year = {2012}, - pmid = {21812871}, - keywords = {Humans, Adult, Male, Basal Ganglia, Positron-Emission Tomography, Case-Control Studies, Caudate Nucleus, Dopamine Plasma Membrane Transport Proteins, Marijuana Abuse, Nortropanes, Putamen, Radiopharmaceuticals, Substantia Nigra, Thalamic Nuclei, Tobacco Use Disorder}, - pages = {981--990}, -} - -@inproceedings{le_floch_bridging_2011, - title = {Bridging the gap between imaging and genetics : a multivariate statistical investigation}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Human brain mapping}, - author = {Le Floch, Edith and Lalanne, Christophe and Pinel, Philippe and Moreno, Antonio and Trinchera, Laura and Tenenhaus, Arthur and Thirion, Bertrand and Poline, Jean-Baptiste and Frouin, Vincent and Duchesnay, Edouard}, - year = {2011}, - keywords = {conference}, -} - -@inproceedings{le_floch_cluster-level_2010, - title = {Cluster-level {Inference} and {Resampling}-{Based} {Multiple} {Testing} applied to {Imaging} {Genetics} {Studies}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Human brain mapping}, - author = {Le Floch, Edith and Keller, Merlin and Frouin, Vincent and Lalanne, Christophe and Pinel, Philippe and Poline, Jean-Baptiste and Duchesnay, Edouard}, - year = {2010}, - keywords = {conference}, - file = {Le Floc, Edith et al. - 2010 - Cluster-level Inference and Resampling-Based Multi.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WIMFRYVC/Le Floc, Edith et al. - 2010 - Cluster-level Inference and Resampling-Based Multi.pdf:application/pdf}, -} - -@article{le_floch_significant_2012, - title = {Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse {Partial} {Least} {Squares}}, - volume = {63}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1095-9572}, - doi = {10.1016/j.neuroimage.2012.06.061}, - abstract = {Brain imaging is increasingly recognised as an intermediate phenotype to understand the complex path between genetics and behavioural or clinical phenotypes. In this context, a first goal is to propose methods to identify the part of genetic variability that explains some neuroimaging variability. Classical univariate approaches often ignore the potential joint effects that may exist between genes or the potential covariations between brain regions. In this paper, we propose instead to investigate an exploratory multivariate method in order to identify a set of Single Nucleotide Polymorphisms (SNPs) covarying with a set of neuroimaging phenotypes derived from functional Magnetic Resonance Imaging (fMRI). Recently, Partial Least Squares (PLS) regression or Canonical Correlation Analysis (CCA) have been proposed to analyse DNA and transcriptomics. Here, we propose to transpose this idea to the DNA vs. imaging context. However, in very high-dimensional settings like in imaging genetics studies, such multivariate methods may encounter overfitting issues. Thus we investigate the use of different strategies of regularisation and dimension reduction techniques combined with PLS or CCA to face the very high dimensionality of imaging genetics studies. We propose a comparison study of the different strategies on a simulated dataset first and then on a real dataset composed of 94 subjects, around 600,000 SNPs and 34 functional MRI lateralisation indexes computed from reading and speech comprehension contrast maps. We estimate the generalisability of the multivariate association with a cross-validation scheme and demonstrate the significance of this link, using a permutation procedure. Univariate selection appears to be necessary to reduce the dimensionality. However, the significant association uncovered by this two-step approach combining univariate filtering and L1-regularised PLS suggests that discovering meaningful genetic associations calls for a multivariate approach.}, - language = {eng}, - number = {1}, - journal = {NeuroImage}, - author = {Le Floch, Edith and Guillemot, Vincent and Frouin, Vincent and Pinel, Philippe and Lalanne, Christophe and Trinchera, Laura and Tenenhaus, Arthur and Moreno, Antonio and Zilbovicius, Monica and Bourgeron, Thomas and Dehaene, Stanislas and Thirion, Bertrand and Poline, Jean-Baptiste and Duchesnay, Edouard}, - month = oct, - year = {2012}, - pmid = {22781162}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Brain Mapping, Data Interpretation, Statistical, Adult, Female, Male, Young Adult, Cognition, Least-Squares Analysis, Nerve Net, Polymorphism, Single Nucleotide}, - pages = {11--24}, - annote = {Times Cited: 14}, -} - -@inproceedings{le_floch_dimension_2012, - title = {Dimension reduction and regularisation combined with {Partial} {Least} {Squares} in high dimensional imaging-genetics studies}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Partial {Least} {Squares}}, - author = {Le Floch, E. and Trinchera, L. and Tenenhaus, A. and Poline, J.B. and Frouin, V. and Duchesnay, E.}, - year = {2012}, - keywords = {conference}, -} - -@misc{hadj-selem_supplementary_2018, - title = {Supplementary material: {Continuation} of {Nesterov}'s {Smoothing} for {Regression} with {Structured} {Sparsity} in {High}-{Dimensional} {Neuroimaging}}, - copyright = {All rights reserved}, - shorttitle = {Supplementary material}, - url = {https://hal-cea.archives-ouvertes.fr/cea-01324021/document}, - abstract = {Predictive models can be used on high-dimensional brain images for diagnosis of a clinical condition. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total Variation (TV) enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties but reasonable precision requires a small smoothing parameter, which slows down the convergence speed. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed towards any globally desired precision. Our main contributions are: To propose an expression of the duality gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the convergence speed. We provide a convergence rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.}, - language = {en}, - urldate = {2018-04-23}, - author = {Hadj-Selem, Fouad and Löfstedt, Tommy and Dohmatob, Elvis and Frouin, Vincent and Dubois, Mathieu and Guillemot, Vincent and Duchesnay, Edouard and Lofstedt, Tommy}, - year = {2018}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/4Y4QZ9X6/Hadj-Selem et al. - 2016 - Supplementary material Continuation of Nesterov's.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CAUV2ZBV/cea-01324021.html:text/html}, -} - -@inproceedings{guillemot_multi-block_2013, - title = {A multi-block approach in imaging genetics}, - copyright = {All rights reserved}, - booktitle = {9th {International} {Imaging} {Genetics} {Conference}}, - author = {Guillemot, Vincent and Tenenhaus, Arthur and Duchesnay, Edouard and Poline, Jean-Baptiste and Frouin, Vincent}, - year = {2013}, - pages = {Poster--13}, -} - -@article{fouquet_longitudinal_2009, - title = {Longitudinal brain metabolic changes from amnestic mild cognitive impairment to {Alzheimer}'s disease}, - volume = {132}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1460-2156}, - doi = {10.1093/brain/awp132}, - abstract = {A sensitive marker for monitoring progression of early Alzheimer's disease would help to develop and test new therapeutic strategies. The present study is aimed at investigating brain metabolism changes over time, as a potential monitoring marker, in patients with amnestic mild cognitive impairment, according to their clinical outcome (converters or non-converters), and in relation to their cognitive decline. Seventeen amnestic mild cognitive impairment patients underwent magnetic resonance imaging and 18FDG-positron emission tomography scans both at inclusion and 18 months later. Baseline and follow-up positron emission tomography data were corrected for partial volume effects and spatially normalized using magnetic resonance imaging data, scaled to the vermis and compared using SPM2. 'PET-PAC' maps reflecting metabolic per cent annual changes were created for correlation analyses with cognitive decline. In the whole sample, the greatest metabolic decrease concerned the posterior cingulate-precuneus area. Converters had significantly greater metabolic decrease than non-converters in two ventro-medial prefrontal areas, the subgenual (BA25) and anterior cingulate (BA24/32). PET-PAC in BA25 and BA24/32 combined allowed complete between-group discrimination. BA25 PET-PAC significantly correlated with both cognitive decline and PET-PAC in the hippocampal region and temporal pole, while BA24/32 PET-PAC correlated with posterior cingulate PET-PAC. Finally, the metabolic change in BA8/9/10 was inversely related to that in BA25 and showed relative increase with cognitive decline, suggesting that compensatory processes may occur in this dorso-medial prefrontal region. The observed ventro-medial prefrontal disruption is likely to reflect disconnection from the hippocampus, both indirectly through the cingulum bundle and posterior cingulate cortex for BA24/32, and directly through the uncinate fasciculus for BA25. Altogether, our findings emphasize the potential of 18FDG-positron emission tomography for monitoring early Alzheimer's disease progression.}, - language = {eng}, - number = {Pt 8}, - journal = {Brain: A Journal of Neurology}, - author = {Fouquet, Marine and Desgranges, Béatrice and Landeau, Brigitte and Duchesnay, Edouard and Mézenge, Florence and de la Sayette, Vincent and Viader, Fausto and Baron, Jean-Claude and Eustache, Francis and Chételat, Gaël}, - month = aug, - year = {2009}, - pmid = {19477964}, - pmcid = {PMC2936690}, - keywords = {Brain, Humans, Image Interpretation, Computer-Assisted, Brain Mapping, Alzheimer Disease, Female, Male, Neuropsychological Tests, Middle Aged, Positron-Emission Tomography, Aged, Aged, 80 and over, Disease Progression, Follow-Up Studies, Amnesia, Cognition Disorders, Fluorodeoxyglucose F18}, - pages = {2058--2067}, - annote = {The following values have no corresponding Zotero field:label: ACLcustom1: NeuroSpin}, - annote = {Unati - article}, -} - -@article{dubois_asynchrony_2008, - title = {Asynchrony of the early maturation of white matter bundles in healthy infants: quantitative landmarks revealed noninvasively by diffusion tensor imaging}, - volume = {29}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1065-9471}, - shorttitle = {Asynchrony of the early maturation of white matter bundles in healthy infants}, - doi = {10.1002/hbm.20363}, - abstract = {Normal cognitive development in infants follows a well-known temporal sequence, which is assumed to be correlated with the structural maturation of underlying functional networks. Postmortem studies and, more recently, structural MR imaging studies have described qualitatively the heterogeneous spatiotemporal progression of white matter myelination. However, in vivo quantification of the maturation phases of fiber bundles is still lacking. We used noninvasive diffusion tensor MR imaging and tractography in twenty-three 1-4-month-old healthy infants to quantify the early maturation of the main cerebral fascicles. A specific maturation model, based on the respective roles of different maturational processes on the diffusion phenomena, was designed to highlight asynchronous maturation across bundles by evaluating the time-course of mean diffusivity and anisotropy changes over the considered developmental period. Using an original approach, a progression of maturation in four relative stages was determined in each tract by estimating the maturation state and speed, from the diffusion indices over the infants group compared with an adults group on one hand, and in each tract compared with the average over bundles on the other hand. Results were coherent with, and extended previous findings in 8 of 11 bundles, showing the anterior limb of the internal capsule and cingulum as the most immature, followed by the optic radiations, arcuate and inferior longitudinal fascicles, then the spinothalamic tract and fornix, and finally the corticospinal tract as the most mature bundle. Thus, this approach provides new quantitative landmarks for further noninvasive research on brain-behavior relationships during normal and abnormal development.}, - language = {eng}, - number = {1}, - journal = {Human Brain Mapping}, - author = {Dubois, Jessica and Dehaene-Lambertz, Ghislaine and Perrin, Muriel and Mangin, Jean-François and Cointepas, Yann and Duchesnay, Edouard and Le Bihan, Denis and Hertz-Pannier, Lucie}, - month = jan, - year = {2008}, - pmid = {17318834}, - keywords = {Humans, Adult, Female, Male, Cerebral Cortex, Corpus Callosum, Anisotropy, Diffusion Magnetic Resonance Imaging, Aging, Diffusion, Fornix, Brain, Infant, Internal Capsule, Nerve Fibers, Myelinated, Neural Pathways, Pyramidal Tracts, Spinothalamic Tracts, Diffusion magnetic resonance imaging}, - pages = {14--27}, -} - -@article{dubois_quantitative_2008, - title = {Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes: application to unilateral visual stimulation}, - volume = {40}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - shorttitle = {Quantitative validation of voxel-wise statistical analyses of autoradiographic rat brain volumes}, - doi = {10.1016/j.neuroimage.2007.11.054}, - abstract = {PET scanners devoted to in vivo functional study have recently been developed, but autoradiography remains the reference technique for assessing cerebral glucose metabolism (CMRGlu) in rodents. Autoradiographs are conventionally subjected to region of interest (ROI) analysis, which is intrinsically hypothesis-driven and therefore not suitable for whole-brain investigation. Voxel-wise statistical methods of analysis have long been used to determine differences in brain activity during in vivo functional neuroimaging experiments. They have also recently been applied to 3D reconstructed autoradiographic volume images from rat brains. We present here a fully automated analysis for autoradiographic data combining (1) computerized procedures for the acquisition and 3D reconstruction of postmortem volume images and (2) spatial normalization followed by classical whole-brain voxel-wise statistical analysis. We also describe an additional procedure for characterizing functional differences between the right and left hemispheres of the brain. We compared two spatial normalization techniques and evaluated how the effect of choosing a particular normalization technique impacted on the statistical analysis. We also propose a small volume correction analysis to address the problem of multiple statistical comparisons. Lastly, we investigated the reliability of such analyses, by comparing their results qualitatively and quantitatively with those previously obtained with our semiautomated ROI-based analysis [Dubois, A., Dauguet, J., Herard, A.-S., Besret, L., Duchesnay, E., Frouin, V., Hantraye, P., Bonvento, G., Delzescaux, T., 2007. Automated three-dimensional analysis of histologic and autoradiographic rat brain sections: application to an activation study. J. Cereb. Blood Flow Metab. 27 (10), 1742-1755.]. Both voxel-wise statistical analyses led to the detection of consistent interhemispheric differences in CMRGlu. This work demonstrates the potential value and robustness of voxel-wise statistical methods for analyzing autoradiographic data sets.}, - language = {eng}, - number = {2}, - journal = {NeuroImage}, - author = {Dubois, Albertine and Hérard, Anne-Sophie and Flandin, Guillaume and Duchesnay, Edouard and Besret, Laurent and Frouin, Vincent and Hantraye, Philippe and Bonvento, Gilles and Delzescaux, Thierry}, - month = apr, - year = {2008}, - pmid = {18234520}, - keywords = {Brain, Animals, Autoradiography, Rats, Organ Size, Photic Stimulation, glucose}, - pages = {482--494}, - annote = {The following values have no corresponding Zotero field:number: 2label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/ADubois-NI08.pdfarticle}, -} - -@article{sarrazin_multicenter_2014, - title = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder: psychotic features and interhemispheric disconnectivity}, - volume = {71}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {2168-6238}, - shorttitle = {A multicenter tractography study of deep white matter tracts in bipolar {I} disorder}, - doi = {10.1001/jamapsychiatry.2013.4513}, - abstract = {IMPORTANCE: Tractography studies investigating white matter (WM) abnormalities in patients with bipolar disorder have yielded heterogeneous results owing to small sample sizes. The small size limits their generalizability, a critical issue for neuroimaging studies of biomarkers of bipolar I disorder (BPI). -OBJECTIVES: To study WM abnormalities using whole-brain tractography in a large international multicenter sample of BPI patients and to compare these alterations between patients with or without a history of psychotic features during mood episodes. -DESIGN, SETTING, AND PARTICIPANTS: A cross-sectional, multicenter, international, Q-ball imaging tractography study comparing 118 BPI patients and 86 healthy control individuals. In addition, among the patient group, we compared those with and without a history of psychotic features. University hospitals in France, Germany, and the United States contributed participants. -INTERVENTIONS: Participants underwent assessment using the Diagnostic Interview for Genetic Studies at the French sites or the Structured Clinical Interview for DSM-IV at the German and US sites. Diffusion-weighted magnetic resonance images were acquired using the same acquisition parameters and scanning hardware at each site. We reconstructed 22 known deep WM tracts using Q-ball imaging tractography and an automatized segmentation technique. -MAIN OUTCOMES AND MEASURES: Generalized fractional anisotropy values along each reconstructed WM tract. -RESULTS: Compared with controls, BPI patients had significant reductions in mean generalized fractional anisotropy values along the body and the splenium of the corpus callosum, the left cingulum, and the anterior part of the left arcuate fasciculus when controlling for age, sex, and acquisition site (corrected for multiple testing). Patients with a history of psychotic features had a lower mean generalized fractional anisotropy value than those without along the body of the corpus callosum (corrected for multiple testing). -CONCLUSIONS AND RELEVANCE: In this multicenter sample, BPI patients had reduced WM integrity in interhemispheric, limbic, and arcuate WM tracts. Interhemispheric pathways are more disrupted in patients with than in those without psychotic symptoms. Together these results highlight the existence of an anatomic disconnectivity in BPI and further underscore a role for interhemispheric disconnectivity in the pathophysiological features of psychosis in BPI.}, - language = {eng}, - number = {4}, - journal = {JAMA psychiatry}, - author = {Sarrazin, Samuel and Poupon, Cyril and Linke, Julia and Wessa, Michèle and Phillips, Mary and Delavest, Marine and Versace, Amelia and Almeida, Jorge and Guevara, Pamela and Duclap, Delphine and Duchesnay, Edouard and Mangin, Jean-François and Le Dudal, Katia and Daban, Claire and Hamdani, Nora and D'Albis, Marc-Antoine and Leboyer, Marion and Houenou, Josselin}, - month = apr, - year = {2014}, - pmid = {24522197}, - keywords = {Brain, Humans, Brain Mapping, Image Processing, Computer-Assisted, Reference Values, Adult, Female, Male, Bipolar Disorder, Cerebral Cortex, Corpus Callosum, Anisotropy, Neural Pathways, Dominance, Cerebral, Psychiatric Status Rating Scales, Diffusion Tensor Imaging, Leukoencephalopathies, Psychotic Disorders}, - pages = {388--396}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QXSGCF5P/Sarrazin et al. - 2014 - A multicenter tractography study of deep white mat.pdf:application/pdf}, -} - -@inproceedings{guen_regional_2017, - title = {Regional study of the genetic influence on the sulcal pits}, - isbn = {978-1-5090-1172-8}, - doi = {10.1109/ISBI.2017.7950472}, - booktitle = {14th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}, {ISBI} 2017, {Melbourne}, {Australia}, {April} 18-21, 2017}, - publisher = {IEEE}, - author = {Guen, Yann Le and Auzias, Guillaume and Dehaene-Lambertz, Ghislaine and Leroy, François and Mangin, Jean-Francois and Duchesnay, Edouard and Coulon, Olivier and Frouin, Vincent}, - year = {2017}, - keywords = {Brain, Biomarkers, Additives, Correlation, cortical structures, genetic control, genetic influence, genomics, imaging-genetic, Junctions, Olfactory, Organizations, sulcal depth, sulcal pits}, - pages = {77--80}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QJPSNRWG/7950472.html:text/html}, -} - -@article{nunes_using_2018, - title = {Using structural {MRI} to identify bipolar disorders - 13 site machine learning study in 3020 individuals from the {ENIGMA} {Bipolar} {Disorders} {Working} {Group}}, - issn = {1476-5578}, - doi = {10.1038/s41380-018-0228-9}, - abstract = {Bipolar disorders (BDs) are among the leading causes of morbidity and disability. Objective biological markers, such as those based on brain imaging, could aid in clinical management of BD. Machine learning (ML) brings neuroimaging analyses to individual subject level and may potentially allow for their diagnostic use. However, fair and optimal application of ML requires large, multi-site datasets. We applied ML (support vector machines) to MRI data (regional cortical thickness, surface area, subcortical volumes) from 853 BD and 2167 control participants from 13 cohorts in the ENIGMA consortium. We attempted to differentiate BD from control participants, investigated different data handling strategies and studied the neuroimaging/clinical features most important for classification. Individual site accuracies ranged from 45.23\% to 81.07\%. Aggregate subject-level analyses yielded the highest accuracy (65.23\%, 95\% CI = 63.47-67.00, ROC-AUC = 71.49\%, 95\% CI = 69.39-73.59), followed by leave-one-site-out cross-validation (accuracy = 58.67\%, 95\% CI = 56.70-60.63). Meta-analysis of individual site accuracies did not provide above chance results. There was substantial agreement between the regions that contributed to identification of BD participants in the best performing site and in the aggregate dataset (Cohen's Kappa = 0.83, 95\% CI = 0.829-0.831). Treatment with anticonvulsants and age were associated with greater odds of correct classification. Although short of the 80\% clinically relevant accuracy threshold, the results are promising and provide a fair and realistic estimate of classification performance, which can be achieved in a large, ecologically valid, multi-site sample of BD participants based on regional neurostructural measures. Furthermore, the significant classification in different samples was based on plausible and similar neuroanatomical features. Future multi-site studies should move towards sharing of raw/voxelwise neuroimaging data.}, - language = {eng}, - journal = {Molecular Psychiatry}, - author = {Nunes, Abraham and Schnack, Hugo G. and Ching, Christopher R. K. and Agartz, Ingrid and Akudjedu, Theophilus N. and Alda, Martin and Alnæs, Dag and Alonso-Lana, Silvia and Bauer, Jochen and Baune, Bernhard T. and Bøen, Erlend and Bonnin, Caterina Del Mar and Busatto, Geraldo F. and Canales-Rodríguez, Erick J. and Cannon, Dara M. and Caseras, Xavier and Chaim-Avancini, Tiffany M. and Dannlowski, Udo and Díaz-Zuluaga, Ana M. and Dietsche, Bruno and Doan, Nhat Trung and Duchesnay, Edouard and Elvsåshagen, Torbjørn and Emden, Daniel and Eyler, Lisa T. and Fatjó-Vilas, Mar and Favre, Pauline and Foley, Sonya F. and Fullerton, Janice M. and Glahn, David C. and Goikolea, Jose M. and Grotegerd, Dominik and Hahn, Tim and Henry, Chantal and Hibar, Derrek P. and Houenou, Josselin and Howells, Fleur M. and Jahanshad, Neda and Kaufmann, Tobias and Kenney, Joanne and Kircher, Tilo T. J. and Krug, Axel and Lagerberg, Trine V. and Lenroot, Rhoshel K. and López-Jaramillo, Carlos and Machado-Vieira, Rodrigo and Malt, Ulrik F. and McDonald, Colm and Mitchell, Philip B. and Mwangi, Benson and Nabulsi, Leila and Opel, Nils and Overs, Bronwyn J. and Pineda-Zapata, Julian A. and Pomarol-Clotet, Edith and Redlich, Ronny and Roberts, Gloria and Rosa, Pedro G. and Salvador, Raymond and Satterthwaite, Theodore D. and Soares, Jair C. and Stein, Dan J. and Temmingh, Henk S. and Trappenberg, Thomas and Uhlmann, Anne and van Haren, Neeltje E. M. and Vieta, Eduard and Westlye, Lars T. and Wolf, Daniel H. and Yüksel, Dilara and Zanetti, Marcus V. and Andreassen, Ole A. and Thompson, Paul M. and Hajek, Tomas and {ENIGMA Bipolar Disorders Working Group}}, - month = aug, - year = {2018}, - pmid = {30171211}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/9DWDC8AC/Nunes et al. - 2018 - Using structural MRI to identify bipolar disorders.pdf:application/pdf}, -} - -@inproceedings{de_pierrefeu_interpretable_2018, - address = {Singapore}, - title = {Interpretable and stable prediction of schizophrenia on a large multisite dataset using machine learning with structured sparsity}, - copyright = {All rights reserved}, - isbn = {978-1-5386-6859-7}, - url = {https://ieeexplore.ieee.org/document/8423946/}, - doi = {10.1109/PRNI.2018.8423946}, - urldate = {2018-09-27}, - booktitle = {2018 {International} {Workshop} on {Pattern} {Recognition} in {Neuroimaging} ({PRNI})}, - publisher = {IEEE}, - author = {de Pierrefeu, Amicie and Lofstedt, Tommy and Laidi, Charles and Hadj-Selem, Fouad and Leboyer, Marion and Ciuciu, Philippe and Houenou, Josselin and Duchesnay, Edouard}, - month = jun, - year = {2018}, - pages = {1--4}, -} - -@article{duchesnay_classification_2007, - title = {Classification based on cortical folding patterns}, - volume = {26}, - issn = {0278-0062}, - doi = {10.1109/TMI.2007.892501}, - abstract = {We describe here a classification system based on automatically identified cortical sulci. Multivariate recognition methods are required for the detection of complex brain patterns with a spatial distribution. However, such methods may face the well-known issue of the curse of dimensionality-the risk of overfitting the training dataset in high-dimensional space. We overcame this problem, using a classifier pipeline with one- or two-stage of descriptor selection based on machine-learning methods, followed by a support vector machine classifier or linear discriminant analysis. We compared alternative designs of the pipeline on two different datasets built from the same database corresponding to 151 brains. The first dataset dealt with cortex asymmetry and the second dealt with the effect of the subject's sex. Our system successfully (98\%) distinguished between the left and right hemispheres on the basis of sulcal shape (size, depth, etc.). The sex of the subject could be determined with a success rate of 85\%. These results highlight the attractiveness of multivariate recognition models combined with appropriate descriptor selection. The sulci selected by the pipeline are consistent with previous whole-brain studies on sex effects and hemispheric asymmetries.}, - language = {eng}, - number = {4}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Duchesnay, Edouard and Cachia, Arnaud and Roche, Alexis and Rivière, Denis and Cointepas, Yann and Papadopoulos-Orfanos, Dimitri and Zilbovicius, Monica and Martinot, Jean-Luc and Régis, Jean and Mangin, Jean-François}, - month = apr, - year = {2007}, - pmid = {17427742}, - keywords = {Algorithms, Artificial Intelligence, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Cerebral Cortex, Numerical Analysis, Computer-Assisted, Classification,Sulci,Anatomy,brainvisa}, - pages = {553--565}, - annote = {The following values have no corresponding Zotero field:number: 4label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - http://brainvisa.info/pdf/duchesnay-TMI07.pdfarticle}, -} - -@article{magalhaes_white_2017, - title = {White matter changes in microstructure associated with a maladaptive response to stress in rats}, - volume = {7}, - issn = {2158-3188}, - doi = {10.1038/tp.2016.283}, - abstract = {In today's society, every individual is subjected to stressful stimuli with different intensities and duration. This exposure can be a key trigger in several mental illnesses greatly affecting one's quality of life. Yet not all subjects respond equally to the same stimulus and some are able to better adapt to them delaying the onset of its negative consequences. The neural specificities of this adaptation can be essential to understand the true dynamics of stress as well as to design new approaches to reduce its consequences. In the current work, we employed ex vivo high field diffusion magnetic resonance imaging (MRI) to uncover the differences in white matter properties in the entire brain between Fisher 344 (F344) and Sprague-Dawley (SD) rats, known to present different responses to stress, and to examine the effects of a 2-week repeated inescapable stress paradigm. We applied a tract-based spatial statistics (TBSS) analysis approach to a total of 25 animals. After exposure to stress, SD rats were found to have lower values of corticosterone when compared with F344 rats. Overall, stress was found to lead to an overall increase in fractional anisotropy (FA), on top of a reduction in mean and radial diffusivity (MD and RD) in several white matter bundles of the brain. No effect of strain on the white matter diffusion properties was observed. The strain-by-stress interaction revealed an effect on SD rats in MD, RD and axial diffusivity (AD), with lower diffusion metric levels on stressed animals. These effects were localized on the left side of the brain on the external capsule, corpus callosum, deep cerebral white matter, anterior commissure, endopiriform nucleus, dorsal hippocampus and amygdala fibers. The results possibly reveal an adaptation of the SD strain to the stressful stimuli through synaptic and structural plasticity processes, possibly reflecting learning processes.}, - language = {eng}, - number = {1}, - journal = {Translational Psychiatry}, - author = {Magalhães, R. and Bourgin, J. and Boumezbeur, F. and Marques, P. and Bottlaender, M. and Poupon, C. and Djemaï, B. and Duchesnay, E. and Mériaux, S. and Sousa, N. and Jay, T. M. and Cachia, A.}, - year = {2017}, - pmid = {28117841}, - pmcid = {PMC5545740}, - keywords = {Brain, Male, Corpus Callosum, Anisotropy, Diffusion Magnetic Resonance Imaging, Animals, Rats, White Matter, Hippocampus, Corticosterone, Amygdala, Adaptation, Physiological, Anterior Cerebellar Commissure, External Capsule, Rats, Inbred F344, Rats, Sprague-Dawley, Stress, Psychological, Hippocampal layers, IN-VIVO, KeyWords Plus:PREFRONTAL CORTEX, LIFE EVENTS, OPTIC-NERVE, RADIAL DIFFUSIVITY, RETINAL ISCHEMIA}, - pages = {e1009}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:number: 1}, - annote = {The following values have no corresponding Zotero field:number: 1label: ACL}, - annote = {Unirs}, - annote = {UnirsPMID: 28117841 DOI: 10.1038/tp.2016.283}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BPAQNAWL/Magalhães et al. - 2017 - White matter changes in microstructure associated .pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/437MPGMD/tp2016283a.html:text/html;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/J5IQSBU2/tp2016283a.html:text/html}, -} - -@article{gesierich_features_2016, - title = {Features and {Determinants} of {Lacune} {Shape}: {Relationship} {With} {Fiber} {Tracts} and {Perforating} {Arteries}}, - volume = {47}, - issn = {1524-4628}, - shorttitle = {Features and {Determinants} of {Lacune} {Shape}}, - doi = {10.1161/STROKEAHA.116.012779}, - abstract = {BACKGROUND AND PURPOSE: Lacunes are a major manifestation of cerebral small vessel disease. Although still debated, the morphological features of lacunes may offer mechanistic insights. We systematically analyzed the shape of incident lacunes in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, a genetically defined small vessel disease. -METHODS: A total of 88 incident lacunes from 57 patients were segmented from 3-dimensional T1 magnetic resonance images and 3 dimensionally reconstructed. Anatomic location, diameter, volume, surface area, and compactness of lacunes were assessed. The shape was analyzed using a size, orientation, and position invariant spectral shape descriptor. We further investigated the relationship with perforating arteries and fiber tracts. -RESULTS: Lacunes were most abundant in the centrum semiovale and the basal ganglia. Diameter, volume, and surface area of lacunes in the basal ganglia and centrum semiovale were larger than in other brain regions. The spectral shape descriptor revealed a continuum of shapes with no evidence for distinct classes of lacunes. Shapes varied mostly in elongation and planarity. The main axis and plane of lacunes were found to align with the orientation of perforating arteries but not with fiber tracts. -CONCLUSIONS: Elongation and planarity are the primary shape principles of lacunes. Their main axis and plane align with perforating arteries. Our findings add to current concepts on the mechanisms of lacunes.}, - language = {eng}, - number = {5}, - journal = {Stroke}, - author = {Gesierich, Benno and Duchesnay, Edouard and Jouvent, Eric and Chabriat, Hugues and Schmidt, Reinhold and Mangin, Jean-Francois and Duering, Marco and Dichgans, Martin}, - year = {2016}, - pmid = {27048698}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Basal Ganglia, Middle Aged, Aged, CADASIL, White Matter, cerebral small vessel diseases, neuroimaging, magnetic resonance imaging, Aftercare}, - pages = {1258--1264}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JF7ZBKIR/Gesierich et al. - 2016 - Features and Determinants of Lacune Shape Relatio.pdf:application/pdf}, -} - -@article{jouvent_prediction_2016, - title = {Prediction of 3-year clinical course in {CADASIL}}, - volume = {87}, - issn = {1526-632X}, - doi = {10.1212/WNL.0000000000003252}, - abstract = {OBJECTIVE: To obtain simple models predicting disease evolution at 3 years for a given patient with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). -METHODS: Based on data obtained in a prospective study of 236 patients, we built and validated models predicting, at the individual level, 3-year changes in Mini-Mental State Examination (MMSE), Mattis Dementia Rating Scale (MDRS), Trail Making Test version B (TMTB), and modified Rankin Scale (mRS). These models were based on different sets of predictors obtained at baseline, including either clinical data (epidemiologic data and cardiovascular risk factors) or clinical data and quantitative MRI markers (volume of lacunes [LLV], volume of white matter hyperintensities, normalized brain volume [BPF], number of microbleeds). The Bayesian information criterion (BIC) and the coefficient of determination (R2) were used to determine models with the highest predictive ability and the lowest numbers of predictors. -RESULTS: We obtained validated models with a demonstrated ability to predict, for a given patient, 3-year changes in MMSE, MDRS, TMTB, and mRS (R2 on independent samples: 0.22, 0.12, 0.09, and 0.17, respectively). In all cases, the best models according to R2 and BIC values included only the baseline values of the outcome, of BPF, and of LLV. Inclusion of other potential predictors always led to a loss of generalizability. -CONCLUSIONS: The prediction of 3-year changes in MMSE, MDRS, TMTB, and mRS for a given patient with CADASIL can be obtained using simple models relying only on the initial values of the considered score, BPF, and LLV.}, - language = {eng}, - number = {17}, - journal = {Neurology}, - author = {Jouvent, Eric and Duchesnay, Edouard and Hadj-Selem, Foued and De Guio, François and Mangin, Jean-François and Hervé, Dominique and Duering, Marco and Ropele, Stefan and Schmidt, Reinhold and Dichgans, Martin and Chabriat, Hugues}, - month = oct, - year = {2016}, - pmid = {27694265}, - pmcid = {PMC5089530}, - keywords = {Humans, Magnetic Resonance Imaging, Adult, Female, Male, Neuropsychological Tests, Predictive Value of Tests, Young Adult, Middle Aged, Linear Models, Aged, CADASIL, Disease Progression, Longitudinal Studies, Retrospective Studies, Severity of Illness Index, Bayes Theorem, France, Germany, Mental Status Schedule}, - pages = {1787--1795}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DE3KY35Q/Jouvent et al. - 2016 - Prediction of 3-year clinical course in CADASIL.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/CEUKXX7Z/1787.html:text/html;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EG77RT9X/1787.html:text/html}, -} - -@article{pirpamer_determinants_2016, - title = {Determinants of iron accumulation in the normal aging brain}, - volume = {43}, - issn = {1558-1497}, - doi = {10.1016/j.neurobiolaging.2016.04.002}, - abstract = {In a recent postmortem study, R2* relaxometry in gray matter (GM) of the brain has been validated as a noninvasive measure for iron content in brain tissue. Iron accumulation in the normal aging brain is a common finding and relates to brain maturation and degeneration. The goal of this study was to assess the determinants of iron accumulation during brain aging. The study cohort consisted of 314 healthy community-dwelling participants of the Austrian Stroke Prevention Study. Their age ranged from 38-82 years. Quantitative magnetic resonance imaging was performed on 3T and included R2* mapping, based on a 3D multi-echo gradient echo sequence. The median of R2* values was measured in all GM regions, which were segmented automatically using FreeSurfer. We investigated 25 possible determinants for cerebral iron deposition. These included demographics, brain volume, lifestyle factors, cerebrovascular risk factors, serum levels of iron, and single nucleotide polymorphisms related to iron regulating genes (rs1800562, rs3811647, rs1799945, and rs1049296). The body mass index (BMI) was significantly related to R2* in 15/32 analyzed brain regions with the strongest correlations found in the amygdala (p = 0.0091), medial temporal lobe (p = 0.0002), and hippocampus (p ≤ 0.0001). Further associations to R2* values were found in deep GM for age and smoking. No significant associations were found for gender, GM volume, serum levels of iron, or iron-associated genetic polymorphisms. In conclusion, besides age, the BMI and smoking are the only significant determinants of brain iron accumulation in normally aging subjects. Smoking relates to iron deposition in the basal ganglia, whereas higher BMI is associated with iron content in the neocortex following an Alzheimer-like distribution.}, - language = {eng}, - journal = {Neurobiology of Aging}, - author = {Pirpamer, Lukas and Hofer, Edith and Gesierich, Benno and De Guio, François and Freudenberger, Paul and Seiler, Stephan and Duering, Marco and Jouvent, Eric and Duchesnay, Edouard and Dichgans, Martin and Ropele, Stefan and Schmidt, Reinhold}, - year = {2016}, - pmid = {27255824}, - keywords = {Brain, Humans, Magnetic Resonance Imaging, Adult, Female, Male, Middle Aged, Aging, Aged, Aged, 80 and over, Cohort Studies, Magnetic resonance imaging, Iron, Smoking, Body Mass Index, Determinants for iron accumulation, Neocortex, Normal aging brain, R(2)* brain iron mapping}, - pages = {149--155}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/4MJG5PDW/S019745801630029X.html:text/html}, -} - -@article{de_pierrefeu_structured_2018, - title = {Structured {Sparse} {Principal} {Components} {Analysis} {With} the {TV}-{Elastic} {Net} {Penalty}}, - volume = {37}, - issn = {1558-254X}, - doi = {10.1109/TMI.2017.2749140}, - abstract = {Principal component analysis (PCA) is an exploratory tool widely used in data analysis to uncover the dominant patterns of variability within a population. Despite its ability to represent a data set in a low-dimensional space, PCA's interpretability remains limited. Indeed, the components produced by PCA are often noisy or exhibit no visually meaningful patterns. Furthermore, the fact that the components are usually non-sparse may also impede interpretation, unless arbitrary thresholding is applied. However, in neuroimaging, it is essential to uncover clinically interpretable phenotypic markers that would account for the main variability in the brain images of a population. Recently, some alternatives to the standard PCA approach, such as sparse PCA (SPCA), have been proposed, their aim being to limit the density of the components. Nonetheless, sparsity alone does not entirely solve the interpretability problem in neuroimaging, since it may yield scattered and unstable components. We hypothesized that the incorporation of prior information regarding the structure of the data may lead to improved relevance and interpretability of brain patterns. We therefore present a simple extension of the popular PCA framework that adds structured sparsity penalties on the loading vectors in order to identify the few stable regions in the brain images that capture most of the variability. Such structured sparsity can be obtained by combining, e.g., and total variation (TV) penalties, where the TV regularization encodes information on the underlying structure of the data. This paper presents the structured SPCA (denoted SPCA-TV) optimization framework and its resolution. We demonstrate SPCA-TV's effectiveness and versatility on three different data sets. It can be applied to any kind of structured data, such as, e.g., -dimensional array images or meshes of cortical surfaces. The gains of SPCA-TV over unstructured approaches (such as SPCA and ElasticNet PCA) or structured approach (such as GraphNet PCA) are significant, since SPCA-TV reveals the variability within a data set in the form of intelligible brain patterns that are easier to interpret and more stable across different samples.}, - language = {eng}, - number = {2}, - journal = {IEEE Transactions on Medical Imaging}, - author = {de Pierrefeu, Amicie and Lofstedt, Tommy and Hadj-Selem, Fouad and Dubois, Mathieu and Jardri, Renaud and Fovet, Thomas and Ciuciu, Philippe and Frouin, Vincent and Duchesnay, Edouard}, - year = {2018}, - pmid = {28880163}, - keywords = {Loading, Minimization, MRI, Optimization, PCA, Principal Component Analysis, Sociology, total variation, TV, unsupervisedmachine learning}, - pages = {396--407}, - annote = {WOS:000424467000006}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/VFGT57HH/de Pierrefeu et al. - 2018 - Structured Sparse Principal Components Analysis Wi.pdf:application/pdf;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BPA4ESHX/8025614.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TIGGBPKW/Pierrefeu et al. - 2018 - Structured Sparse Principal Components Analysis Wi.pdf:application/pdf}, -} - -@article{hadj-selem_continuation_2018, - title = {Continuation of {Nesterov}'s {Smoothing} for {Regression} {With} {Structured} {Sparsity} in {High}-{Dimensional} {Neuroimaging}}, - volume = {37}, - issn = {1558-254X}, - doi = {10.1109/TMI.2018.2829802}, - abstract = {Predictive models can be used on high-dimensional brain images to decode cognitive states or diagnosis/prognosis of a clinical condition/evolution. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total variation (TV) is a promising candidate for structured penalization: it enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties. However, reasonable precision requires a small smoothing parameter, which slows down the convergence speed to unacceptable levels. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed toward any globally desired precision. Our main contributions are: gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the To propose an expression of the duality convergence speed. This expression is applicable to many penalties and can be used with other solvers than CONESTA. We also propose an expression for the particular smoothing parameter that minimizes the number of iterations required to reach a given precision. Furthermore, we provide a convergence proof and its rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.}, - language = {eng}, - number = {11}, - journal = {IEEE Transactions on Medical Imaging}, - author = {Hadj-Selem, Fouad and Lofstedt, Tommy and Dohmatob, Elvis and Frouin, Vincent and Dubois, Mathieu and Guillemot, Vincent and Duchesnay, Edouard}, - month = nov, - year = {2018}, - pmid = {29993684}, - keywords = {TV, Prediction, Statistics - Machine Learning, Machine Learning, Convergence, Smoothing methods, Convex Optimization, Signature, Structured Sparsity, Three-dimensional displays}, - pages = {2403--2413}, - annote = {arXiv: 1605.09658}, - annote = {Comment: 11 pages, 6 figures, preprint}, - annote = {Comment: 34 pages, 4 figures, preprint}, - file = {arXiv\:1605.09658 PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7HU2Q2HU/Hadj-Selem et al. - 2016 - Iterative Smoothing Proximal Gradient for Regressi.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BM7TDIAZ/1605.html:text/html;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/GY6AU69K/1605.html:text/html;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7PKLCQVW/8345691.html:text/html;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ULK3JG9T/Hadj-Selem et al. - 2018 - Continuation of Nesterov's Smoothing for Regressio.pdf:application/pdf}, -} - -@article{de_pierrefeu_identifying_2018, - title = {Identifying a neuroanatomical signature of schizophrenia, reproducible across sites and stages, using machine learning with structured sparsity}, - volume = {138}, - issn = {1600-0447}, - doi = {10.1111/acps.12964}, - abstract = {OBJECTIVE: Structural MRI (sMRI) increasingly offers insight into abnormalities inherent to schizophrenia. Previous machine learning applications suggest that individual classification is feasible and reliable and, however, is focused on the predictive performance of the clinical status in cross-sectional designs, which has limited biological perspectives. Moreover, most studies depend on relatively small cohorts or single recruiting site. Finally, no study controlled for disease stage or medication's effect. These elements cast doubt on previous findings' reproducibility. -METHOD: We propose a machine learning algorithm that provides an interpretable brain signature. Using large datasets collected from 4 sites (276 schizophrenia patients, 330 controls), we assessed cross-site prediction reproducibility and associated predictive signature. For the first time, we evaluated the predictive signature regarding medication and illness duration using an independent dataset of first-episode patients. -RESULTS: Machine learning classifiers based on neuroanatomical features yield significant intersite prediction accuracies (72\%) together with an excellent predictive signature stability. This signature provides a neural score significantly correlated with symptom severity and the extent of cognitive impairments. Moreover, this signature demonstrates its efficiency on first-episode psychosis patients (73\% accuracy). -CONCLUSION: These results highlight the existence of a common neuroanatomical signature for schizophrenia, shared by a majority of patients even from an early stage of the disorder.}, - language = {eng}, - number = {6}, - journal = {Acta Psychiatrica Scandinavica}, - author = {de Pierrefeu, A. and Löfstedt, T. and Laidi, C. and Hadj-Selem, F. and Bourgin, J. and Hajek, T. and Spaniel, F. and Kolenic, M. and Ciuciu, P. and Hamdani, N. and Leboyer, M. and Fovet, T. and Jardri, R. and Houenou, J. and Duchesnay, E.}, - month = dec, - year = {2018}, - pmid = {30242828}, - keywords = {structural MRI, schizophrenia, classification, first-episode psychosis, psychoradiology}, - pages = {571--580}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/V6MET7X7/de Pierrefeu et al. - 2018 - Identifying a neuroanatomical signature of schizop.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/7QP5YXYL/acps.html:text/html}, -} - -@article{reiner_sulcal_2012, - title = {Sulcal span in {Azheimer}'s disease, amnestic mild cognitive impairment, and healthy controls}, - volume = {29}, - issn = {1875-8908}, - doi = {10.3233/JAD-2012-111622}, - abstract = {Differences of cortical morphology between healthy controls (HC), amnestic mild cognitive impairment (MCI), and Alzheimer's disease (AD) have been repeatedly investigated using voxel-based morphometry (VBM). However, the results obtained using mainly VBM remain difficult to interpret as they can be explained by various mechanisms. The aim of the present study was to evaluate the differences of cortical morphology between HC, MCI, and AD patients using a new post-processing method based on reconstruction and identification of cortical sulci. Thirty HC, 33 MCI, and 30 AD patients were randomly selected from the ADNI database. For each subject, cortical sulci were reconstructed and automatically identified using Brainvisa software. Depth and fold opening of nine large sulci were compared between HC, MCI, and AD patients. Fold opening of parietaloccipital fissure and intraparietal sulcus on both sides strongly differed between the 3 groups, with gradual increase from HC to MCI of about 1 mm and from MCI to AD of about 2 mm (right intraparietal: p = 0.005; left intraparietal: p = 0.004; right parietaloccipital: p = 0.003; left parietaloccipital: p = 0.0009). Results were left unchanged after adjustment for age, gender, and level of education. These variables were also strongly linked to neuropsychological scores, independent of age, gender, and level of education. In the present study, we found important regional differences of cortical morphology with gradual deterioration from HC to MCI to AD. The most important differences were found in parietaloccipital fissure and intraparietal sulcus. Further studies are needed to understand the involved underlying mechanisms.}, - language = {eng}, - number = {3}, - journal = {Journal of Alzheimer's disease: JAD}, - author = {Reiner, Peggy and Jouvent, Eric and Duchesnay, Edouard and Cuingnet, Rémi and Mangin, Jean-François and Chabriat, Hugues and {Alzheimer's Disease Neuroimaging Initiative}}, - year = {2012}, - pmid = {22297645}, - keywords = {Humans, Magnetic Resonance Imaging, Brain Mapping, Image Processing, Computer-Assisted, Alzheimer Disease, Female, Male, Neuropsychological Tests, Cerebral Cortex, Middle Aged, Aged, Aged, 80 and over, Mild Cognitive Impairment, Educational Status, Cognitive Dysfunction}, - pages = {605--613}, -} - -@article{duering_strategic_2014, - title = {Strategic white matter tracts for processing speed deficits in age-related small vessel disease}, - volume = {82}, - issn = {1526-632X}, - doi = {10.1212/WNL.0000000000000475}, - abstract = {OBJECTIVE: Cerebral small vessel disease is the most common cause of vascular cognitive impairment and typically manifests with slowed processing speed. We investigated the impact of lesion location on processing speed in age-related small vessel disease. -METHODS: A total of 584 community-dwelling elderly underwent brain MRI followed by segmentation of white matter hyperintensities. Processing speed was determined by the timed measure of the Trail Making Test part B. The impact of the location of white matter hyperintensities was assessed by voxel-based lesion-symptom mapping and graph-based statistical models on regional lesion volumes in major white matter tracts. -RESULTS: Voxel-based lesion-symptom mapping identified multiple voxel clusters where the presence of white matter hyperintensities was associated with slower performance on the Trail Making Test part B. Clusters were located bilaterally in the forceps minor and anterior thalamic radiation. Region of interest-based Bayesian network analyses on lesion volumes within major white matter tracts depicted the same tracts as direct predictors for an impaired Trail Making Test part B performance. -CONCLUSIONS: Our findings highlight damage to frontal interhemispheric and thalamic projection fiber tracts harboring frontal-subcortical neuronal circuits as a predictor for processing speed performance in age-related small vessel disease.}, - language = {eng}, - number = {22}, - journal = {Neurology}, - author = {Duering, Marco and Gesierich, Benno and Seiler, Stephan and Pirpamer, Lukas and Gonik, Mariya and Hofer, Edith and Jouvent, Eric and Duchesnay, Edouard and Chabriat, Hugues and Ropele, Stefan and Schmidt, Reinhold and Dichgans, Martin}, - month = jun, - year = {2014}, - pmid = {24793184}, - pmcid = {PMC4105258}, - keywords = {Brain, Humans, Brain Mapping, Female, Male, Middle Aged, Aged, Cognition Disorders, Leukoencephalopathies, Cerebral Small Vessel Diseases, Trail Making Test}, - pages = {1946--1950}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/Z8WWA4LD/Duering et al. - 2014 - Strategic white matter tracts for processing speed.pdf:application/pdf}, -} - -@article{jouvent_shape_2016, - title = {Shape of the {Central} {Sulcus} and {Disability} {After} {Subcortical} {Stroke}: {A} {Motor} {Reserve} {Hypothesis}}, - volume = {47}, - issn = {1524-4628}, - shorttitle = {Shape of the {Central} {Sulcus} and {Disability} {After} {Subcortical} {Stroke}}, - doi = {10.1161/STROKEAHA.115.012562}, - abstract = {BACKGROUND AND PURPOSE: Both brain and cognitive reserves modulate the clinical impact of chronic brain diseases. Whether a motor reserve also modulates the relationships between stroke and disability is unknown. We aimed to determine whether the shape of the central sulcus, a marker of the development of underlying motor connections, is independently associated with disability in patients with a positive history of small subcortical ischemic stroke. -METHODS: Shapes of central sulci were reconstructed from high-resolution magnetic resonance imaging and ordered without supervision according to a validated algorithm in 166 patients with a positive history of small subcortical ischemic stroke caused by CADASIL (Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy), a severe monogenic cerebral small vessel disease affecting young patients. Ordinal logistic regression modeling was used to test the relationships between modified Rankin scale, a disability scale strongly weighted toward motor disability, and sulcal shape. -RESULTS: Modified Rankin scale was strongly associated with sulcal shape, independent of age, sex, and level of education (proportional odds ratio =1.19, 95\% confidence interval =1.06-1.35; P=0.002). Results remained significant after further adjustment for brain atrophy, volume of lacunes, and volume of white matter hyperintensities of presumed vascular origin. -CONCLUSIONS: The severity of disability in patients with a positive history of small subcortical ischemic stroke caused by a severe cerebral small vessel disease is related to the shape of the central sulcus, independently of the main determinants of disability. These results support the concept of a motor reserve that could modulate the clinical severity in patients with a positive history of small subcortical ischemic stroke.}, - language = {eng}, - number = {4}, - journal = {Stroke}, - author = {Jouvent, Eric and Sun, Zhong Yi and De Guio, François and Duchesnay, Edouard and Duering, Marco and Ropele, Stefan and Dichgans, Martin and Mangin, Jean-François and Chabriat, Hugues}, - month = apr, - year = {2016}, - pmid = {26941259}, - keywords = {Algorithms, Humans, Magnetic Resonance Imaging, Brain Mapping, Image Processing, Computer-Assisted, Adult, Female, Male, Cerebral Cortex, Middle Aged, Aged, Atrophy, CADASIL, White Matter, central sulcus, motor reserve, stroke, Stroke, Recovery of Function, cerebral cortex}, - pages = {1023--1029}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/MVY5J3R3/1023.html:text/html}, -} - -@article{duchesnay_different_2018, - title = {Different {Types} of {White} {Matter} {Hyperintensities} in {CADASIL}}, - volume = {9}, - issn = {1664-2295}, - doi = {10.3389/fneur.2018.00526}, - abstract = {Objective: In CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), white matter hyperintensities (WMH) are considered to result from hypoperfusion. We hypothesized that in fact the burden of WMH results from the combination of several regional populations of WMH with different mechanisms and clinical consequences. Methods: To identify regional WMH populations, we used a 4-step approach. First, we used an unsupervised principal component algorithm to determine, without a priori knowledge, the main sources of variation of the global spatial pattern of WMH. Thereafter, to determine whether these sources are likely to include relevant information regarding regional populations of WMH, we tested their relationships with: (1) MRI markers of the disease; (2) the clinical severity assessed by the Mattis Dementia Rating scale (MDRS) (cognitive outcome) and the modified Rankin's score (disability outcome). Finally, through careful interpretation of all the results, we tried to identify different regional populations of WMH. Results: The unsupervised principal component algorithm identified 3 main sources of variation of the global spatial pattern of WMH, which showed significant and sometime inverse relationships with MRI markers and clinical scores. The models predicting clinical severity based on these sources outperformed those evaluating WMH by their volume (MDRS, coefficient of determination of 39.0 vs. 35.3\%, p = 0.01; modified Rankin's score, 43.7 vs. 38.1\%, p = 0.001). By carefully interpreting the visual aspect of these sources as well as their relationships with MRI markers and clinical severity, we found strong arguments supporting the existence of different regional populations of WMH. For instance, in multivariate analyses, larger extents of WMH in anterior temporal poles and superior frontal gyri were associated with better outcomes, while larger extents of WMH in pyramidal tracts were associated with worse outcomes, which could not be explained if WMH in these different areas shared the same mechanisms. Conclusion: The results of the present study support the hypothesis that the whole extent of WMH results from a combination of different regional populations of WMH, some of which are associated, for yet undetermined reasons, with milder forms of the disease.}, - language = {eng}, - journal = {Frontiers in Neurology}, - author = {Duchesnay, Edouard and Hadj Selem, Fouad and De Guio, François and Dubois, Mathieu and Mangin, Jean-François and Duering, Marco and Ropele, Stefan and Schmidt, Reinhold and Dichgans, Martin and Chabriat, Hugues and Jouvent, Eric}, - year = {2018}, - pmid = {30042721}, - pmcid = {PMC6048276}, - keywords = {CADASIL, cerebral small vessel disease, white matter hyperintensities, Cerebral Small Vessel Diseases, brain atrophy, lacunes, white matter hyperintensities (WMH), White Matter Integrity, clinical severity, white matter changes}, - pages = {526}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YCRAGYJM/Duchesnay et al. - 2018 - Different Types of White Matter Hyperintensities i.pdf:application/pdf}, -} - -@article{scott_prospective_2019, - title = {Prospective cohort study of early biosignatures of response to lithium in bipolar-{I}-disorders: overview of the {H2020}-funded {R}-{LiNK} initiative}, - volume = {7}, - issn = {2194-7511}, - shorttitle = {Prospective cohort study of early biosignatures of response to lithium in bipolar-{I}-disorders}, - url = {https://journalbipolardisorders.springeropen.com/articles/10.1186/s40345-019-0156-x}, - doi = {10.1186/s40345-019-0156-x}, - language = {en}, - number = {1}, - urldate = {2020-10-15}, - journal = {International Journal of Bipolar Disorders}, - author = {Scott, Jan and Hidalgo-Mazzei, Diego and Strawbridge, Rebecca and Young, Allan and Resche-Rigon, Matthieu and Etain, Bruno and Andreassen, Ole A. and Bauer, Michael and Bennabi, Djamila and Blamire, Andrew M. and Boumezbeur, Fawzi and Brambilla, Paolo and Cattane, Nadia and Cattaneo, Annamaria and Chupin, Marie and Coello, Klara and Cointepas, Yann and Colom, Francesc and Cousins, David A. and Dubertret, Caroline and Duchesnay, Edouard and Ferro, Adele and Garcia-Estela, Aitana and Goikolea, Jose and Grigis, Antoine and Haffen, Emmanuel and Høegh, Margrethe C. and Jakobsen, Petter and Kalman, Janos L. and Kessing, Lars V. and Klohn-Saghatolislam, Farah and Lagerberg, Trine V. and Landén, Mikael and Lewitzka, Ute and Lutticke, Ashley and Mazer, Nicolas and Mazzelli, Monica and Mora, Cristina and Muller, Thorsten and Mur-Mila, Estanislao and Oedegaard, Ketil Joachim and Oltedal, Leif and Pålsson, Erik and Papadopoulos Orfanos, Dimitri and Papiol, Sergi and Perez-Sola, Victor and Reif, Andreas and Ritter, Philipp and Rossi, Roberto and Schulze, Thomas and Senner, Fanny and Smith, Fiona E. and Squarcina, Letizia and Steen, Nils Eiel and Thelwall, Pete E. and Varo, Cristina and Vieta, Eduard and Vinberg, Maj and Wessa, Michele and Westlye, Lars T. and Bellivier, Frank}, - month = dec, - year = {2019}, - keywords = {Neuroimaging, Phenotype, Lithium, Response, Actigraphy, Bipolar, Digital, Omics, Personalization, Precision}, - file = {Springer Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/TIHK9QC7/Scott et al. - 2019 - Prospective cohort study of early biosignatures of.pdf:application/pdf}, -} - -@inproceedings{ambroise_multi-view_2023, - title = {Multi-{View} {Variational} {Autoencoders} {Allow} for {Interpretability} {Leveraging} {Digital} {Avatars}: {Application} to the {HBN} {Cohort}}, - copyright = {All rights reserved}, - shorttitle = {Multi-{View} {Variational} {Autoencoders} {Allow} for {Interpretability} {Leveraging} {Digital} {Avatars}}, - doi = {10.1109/ISBI53787.2023.10230552}, - booktitle = {{IEEE} 20th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI}) 2023}, - author = {Ambroise, Corentin and Grigis, Antoine and Duchesnay, Edouard and Frouin, Vincent}, - month = apr, - year = {2023}, -} - -@inproceedings{barbano_contrastive_2023, - title = {Contrastive learning for regression in multi-site brain age prediction}, - copyright = {All rights reserved}, - url = {http://arxiv.org/abs/2211.08326}, - doi = {10.48550/arXiv.2211.08326}, - abstract = {Building accurate Deep Learning (DL) models for brain age prediction is a very relevant topic in neuroimaging, as it could help better understand neurodegenerative disorders and find new biomarkers. To estimate accurate and generalizable models, large datasets have been collected, which are often multi-site and multi-scanner. This large heterogeneity negatively affects the generalization performance of DL models since they are prone to overfit site-related noise. Recently, contrastive learning approaches have been shown to be more robust against noise in data or labels. For this reason, we propose a novel contrastive learning regression loss for robust brain age prediction using MRI scans. Our method achieves state-of-the-art performance on the OpenBHB challenge, yielding the best generalization capability and robustness to site-related noise.}, - urldate = {2024-01-26}, - booktitle = {{IEEE} 20th {International} {Symposium} on {Biomedical} {Imaging} ({ISBI}) 2023}, - publisher = {arXiv}, - author = {Barbano, Carlo Alberto and Dufumier, Benoit and Duchesnay, Edouard and Grangetto, Marco and Gori, Pietro}, - month = mar, - year = {2023}, - note = {arXiv:2211.08326 [cs, eess]}, - keywords = {Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing}, - annote = {Comment: 5 pages}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/E9KWINXZ/Barbano et al. - 2023 - Contrastive learning for regression in multi-site .pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/J4HGPUI4/2211.html:text/html}, -} - -@inproceedings{cachia_sulcus-based_2005, - address = {Toronto, Canada}, - title = {Sulcus-based morphometry of heteromodal cortex in schizophrenia patients with resistant auditory hallucinations.}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {Proc. 11th {HBM} {CD}-{Rom} {Neuroimage} vol 26 (1)}, - author = {Cachia, A. and Duchesnay, E. and Plaze, M. and Paillère-Martinot, M.-L. and Januel, D. and Bellivier, F. and Galinowski, A. and Andoh, J. and Bartrés-Faz, D. and De Beaurepaire, R. and Artiges, E. and Rivière, D. and Mangin, J.-F. and Martinot, J.-L.}, - year = {2005}, - keywords = {anatomy, conference, Anatomy, Sulci, sulci}, -} - -@inproceedings{da_mota_calcul_2014, - title = {Le calcul haute performance pour l'analyse de données de neuroimagerie-génétique en grandes dimensions}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - abstract = {Les progrès technologiques en génotypage et en neuroimagerie offrent désormais la perspective d’une analyse jointe afin de mieux comprendre les liens entre des mutations génétiques et des pathologies cérébrales neurologiques ou psychiatriques. Ces études d'associations permettent la découverte de biomarqueurs pour le diagnostic et le suivi de l'évolution de ces pathologies et contribuent à l'identification de cibles pour des thérapies personnalisées. De telles analyses s’appuient sur des données biologiques de très grandes dimensions (millions de nucléotides en génétique, millions de pixels en imagerie). La dimension des données et le volume de calculs imposent l’utilisation de cluster de calcul haute performance (HPC). Dans cet exposé nous présenterons les enjeux scientifiques, les solutions identifiées, et les résultats obtenus sur le supercalculateur Curie dans le cadre d’une étude cerveau complet / génome complet.}, - author = {Da Mota, Benoit and Duchesnay, Edouard}, - year = {2014}, -} - -@inproceedings{damon_structured_2011, - title = {Structured {Multivariate} {Pattern} {Classification} to {Detect} {MRI} {Markers} for an {Early} {Diagnosis} of {Alzheimer}'s {Disease}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-1-4577-2134-2}, - url = {http://dl.acm.org/citation.cfm?id=2353108.2353268}, - doi = {10.1109/ICMLA.2011.185}, - booktitle = {2011 10th {International} {Conference} on {Machine} {Learning} and {Applications} and {Workshops}}, - publisher = {IEEE}, - author = {Damon, C. and Duchesnay, E. and Depecker, M.}, - month = dec, - year = {2011}, - keywords = {conference}, - pages = {384--387}, -} - -@inproceedings{dubois_predictive_2014, - title = {Predictive support recovery with {TV}-{Elastic} {Net} penalty and logistic regression: {An} application to structural {MRI}}, - copyright = {All rights reserved}, - shorttitle = {Predictive support recovery with {TV}-{Elastic} {Net} penalty and logistic regression}, - doi = {10.1109/PRNI.2014.6858517}, - abstract = {The use of machine-learning in neuroimaging offers new perspectives in early diagnosis and prognosis of brain diseases. Although such multivariate methods can capture complex relationships in the data, traditional approaches provide irregular (ℓ2 penalty) or scattered (ℓ1 penalty) predictive pattern with a very limited relevance. A penalty like Total Variation (TV) that exploits the natural 3D structure of the images can increase the spatial coherence of the weight map. However, TV penalization leads to non-smooth optimization problems that are hard to minimize. We propose an optimization framework that minimizes any combination of ℓ1, ℓ2, and TV penalties while preserving the exact ℓ1 penalty. This algorithm uses Nesterov's smoothing technique to approximate the TV penalty with a smooth function such that the loss and the penalties are minimized with an exact accelerated proximal gradient algorithm. We propose an original continuation algorithm that uses successively smaller values of the smoothing parameter to reach a prescribed precision while achieving the best possible convergence rate. This algorithm can be used with other losses or penalties. The algorithm is applied on a classification problem on the ADNI dataset. We observe that the TV penalty does not necessarily improve the prediction but provides a major breakthrough in terms of support recovery of the predictive brain regions.}, - author = {Dubois, M. and Hadj-Selem, F. and Löfstedt, T. and Perrot, M. and Fischer, C. and Frouin, V. and Duchesnay, E.}, - month = jun, - year = {2014}, - note = {tex.ids: dubois2014predictive -tex.organization: IEEE}, - keywords = {biomedical MRI, Brain, diseases, image classification, learning (artificial intelligence), Machine learning, medical image processing, structural MRI, machine learning, Neuroimaging, logistic regression, Prognosis, regression analysis, optimisation, Vectors, Approximation algorithms, Prediction algorithms, ADNI dataset, brain, brain diseases, classification problem, complex data relationships, Convergence, diagnosis, exact accelerated proximal gradient algorithm, irregular ℓ2 penalty, irregular ℓ2penalty, Logistics, multivariate methods, natural 3D structure, Nesterov smoothing technique, neuroimaging, neurophysiology, nonsmooth optimization problems, penalty-like total variation, predictive brain regions, predictive support recovery, prognosis, scattered l1 penalty, scattered ℓ1 penalty, scattered ℓ1penalty, smoothing methods, Smoothing methods, spatial coherence, TV-elastic net penalty}, - pages = {1--4}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QXSFJSQN/6858517.html:text/html;IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZHPJBMRV/6858517.html:text/html;IEEE Xplore Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/NZC9QLSH/Dubois et al. - 2014 - Predictive support recovery with TV-Elastic Net pe.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/247ZIIIT/Dubois et al. - 2014 - Predictive support recovery with TV-Elastic Net pe.pdf:application/pdf}, -} - -@inproceedings{duchesnay_irregular_2000, - address = {Nashville, USA}, - title = {Irregular adaptative pyramid of agents for segmentation to interpretation of image}, - volume = {3}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - doi = {10.1109/ICSMC.2000.886246}, - abstract = {The paper presents the main concepts of a machine vision architecture based on a hybrid and a fine granularity multiagent system, that encourages incremental design via modular and hierarchical structuring of knowledge and pattern recognition mechanisms. The objective is not optimality of the image segmentation/interpretation but rather reliability versus unforeseen observation. We then present a first implementation of the architecture that tends to validate the approach and also that shows up a physical distribution of computation}, - booktitle = {2000 {IEEE} {International} {Conference} on {Systems}, {Man}, and {Cybernetics}}, - author = {Duchesnay, E. and Montois, J. J. and Jacquelet, Y. and Kinie, A.}, - year = {2000}, - keywords = {image segmentation, Pattern recognition, adaptive systems, Computer architecture, computer vision, Computer vision, Computerized monitoring, Distributed control, fine granularity multiagent system, hierarchical knowledge structuring, image interpretation, image recognition, Image segmentation, image segmentation/interpretation, incremental design, irregular adaptative agent pyramid, irregular adaptive pyramid, Machine vision, machine vision architecture, Merging, multi-agent systems, Multiagent systems, pattern recognition mechanisms, Physics computing, reliability, unforeseen observation}, - pages = {1574--1580 vol.3}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/H2PKZV3G/886246.html:text/html}, -} - -@inproceedings{duchesnay_architecture_1999, - title = {Architecture intelligente distribuée pour la vision artificielle}, - copyright = {All rights reserved}, - author = {Duchesnay, Edouard and Montois, J.-J.}, - year = {1999}, - pages = {88--95}, -} - -@inproceedings{duchesnay_guessing_2004, - title = {Guessing the {Sex} from the {Shapes} of {Cortical} {Folds}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {{HBM}, {Budapest}}, - author = {Duchesnay, Edouard and Roche, Alexis and Rivière, Denis and Papadopoulos-Orfanos, Dimitri and Cointepas, Yann and Mangin, Jean-Francois}, - year = {2004}, - keywords = {conference}, - pages = {164}, -} - -@inproceedings{duchesnay_population_2004, - address = {Arlington, VA, USA}, - title = {Population {Classification} {Based} on {Structural} {Morphometry} of {Cortical} {Sulci}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {International {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Duchesnay, Edouard and Roche, Alexis and Rivière, Denis and Papadopoulos-Orfanos, Dimitri and Cointepas, Yann and Mangin, Jean-Francois}, - year = {2004}, - keywords = {biomedical MRI, pattern classification, Support vector machine classification, Support vector machines, Neuroimaging, conference, support vector machines, brain, neurophysiology, artificial neuroanatomist, Automatic testing, brains, cortical sulci, Diseases, Image databases, iterative feature selection loop, leave-one-out procedure, medical computing, Performance analysis, population classification, shape measurement, Shape measurement, Spatial databases, structural morphometry, sulcus recognition system, support vector machine classifier, System testing}, - pages = {1276--1279}, - file = {IEEE Xplore Abstract Record:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6F4ZY2VL/1398776.html:text/html}, -} - -@inproceedings{dufumier_integrating_2023, - title = {Integrating {Prior} {Knowledge} in {Contrastive} {Learning} with {Kernel}}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - url = {https://telecom-paris.hal.science/hal-04111825}, - abstract = {Data augmentation is a crucial component in unsupervised contrastive learning (CL). It determines how positive samples are defined and, ultimately, the quality of the learnt representation. In this work, we open the door to new perspectives for CL by integrating prior knowledge, given either by generative models-viewed as prior representations-or weak attributes in the positive and negative sampling. To this end, we use kernel theory to propose a novel loss, called decoupled uniformity, that i) allows the integration of prior knowledge and ii) removes the negative-positive coupling in the original InfoNCE loss. We draw a connection between contrastive learning and conditional mean embedding theory to derive tight bounds on the downstream classification loss. In an unsupervised setting, we empirically demonstrate that CL benefits from generative models to improve its representation both on natural and medical images. In a weakly supervised scenario, our framework outperforms other unconditional and conditional CL approaches. Source code is available at this https URL.}, - language = {en}, - urldate = {2024-02-02}, - booktitle = {40th {International} {Conference} on {Machine} {Learning} ({ICML}) 2023}, - author = {Dufumier, Benoit and Barbano, Carlo Alberto and Louiset, Robin and Duchesnay, Edouard and Gori, Pietro}, - month = jul, - year = {2023}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/ZXEMGR29/Dufumier et al. - 2023 - Integrating Prior Knowledge in Contrastive Learnin.pdf:application/pdf}, -} - -@inproceedings{dufumier_contrastive_2021, - title = {Contrastive {Learning} with {Continuous} {Proxy} {Meta}-{Data} for {3D} {MRI} {Classification}}, - copyright = {All rights reserved}, - url = {https://link.springer.com/chapter/10.1007%2F978-3-030-87196-3_6}, - doi = {10.1007/978-3-030-87196-3_6}, - abstract = {Traditional supervised learning with deep neural networks requires a tremendous amount of labelled data to converge to a good solution. For 3D medical images, it is often impractical to build a large homogeneous annotated dataset for a specific pathology. Self-supervised methods offer a new way to learn a representation of the images in an unsupervised manner with a neural network. In particular, contrastive learning has shown great promises by (almost) matching the performance of fully-supervised CNN on vision tasks. Nonetheless, this method does not take advantage of available meta-data, such as participant's age, viewed as prior knowledge. Here, we propose to leverage continuous proxy metadata, in the contrastive learning framework, by introducing a new loss called y-Aware InfoNCE loss. Specifically, we improve the positive sampling during pre-training by adding more positive examples with similar proxy meta-data with the anchor, assuming they share similar discriminative semantic features.With our method, a 3D CNN model pre-trained on \$10{\textasciicircum}4\$ multi-site healthy brain MRI scans can extract relevant features for three classification tasks: schizophrenia, bipolar diagnosis and Alzheimer's detection. When fine-tuned, it also outperforms 3D CNN trained from scratch on these tasks, as well as state-of-the-art self-supervised methods. Our code is made publicly available here.}, - urldate = {2021-06-17}, - booktitle = {24th {International} {Conference} on {Medical} {Image} {Computing} and {Computer} {Assisted} {Intervention} ({MICCAI}) 2021}, - author = {Dufumier, Benoit and Gori, Pietro and Victor, Julie and Grigis, Antoine and Wessa, Michel and Brambilla, Paolo and Favre, Pauline and Polosan, Mircea and McDonald, Colm and Piguet, Camille Marie and Duchesnay, Edouard}, - month = jun, - year = {2021}, - note = {arXiv: 2106.08808}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition}, - annote = {Comment: MICCAI 2021}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/PEGCWZMR/Dufumier et al. - 2021 - Contrastive Learning with Continuous Proxy Meta-Da.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3NXT9S7C/2106.html:text/html}, -} - -@inproceedings{dufumier_conditional_2021, - title = {Conditional {Alignment} and {Uniformity} for {Contrastive} {Learning} with {Continuous} {Proxy} {Labels}}, - copyright = {All rights reserved}, - url = {https://hal.telecom-paris.fr/hal-03523114}, - abstract = {Contrastive Learning has shown impressive results on natural and medical images, without requiring annotated data. However, a particularity of medical images is the availability of meta-data (such as age or sex) that can be exploited for learning representations. Here, we show that the recently proposed contrastive y-Aware InfoNCE loss, that integrates multi-dimensional meta-data, asymptotically optimizes two properties: conditional alignment and global uniformity. Similarly to [33], conditional alignment means that similar samples should have similar features, but conditionally on the meta-data. Instead, global uniformity means that the (normalized) features should be uniformly distributed on the unit hypersphere, independently of the meta-data. Here, we propose to define conditional uniformity, relying on the meta-data, that repel only samples with dissimilar metadata. We show that direct optimization of both conditional alignment and uniformity improves the representations, in terms of linear evaluation, on both CIFAR-100 and a brain MRI dataset.}, - language = {en}, - urldate = {2022-06-14}, - author = {Dufumier, Benoit and Gori, Pietro and Victor, Julie and Grigis, Antoine and Duchesnay, Edouard}, - month = dec, - year = {2021}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UFCYY32N/hal-03523114v1.html:text/html}, -} - -@inproceedings{fouque_voxelwise_2011, - title = {Voxelwise multivariate statistics and brain-wide machine learning using the full diffusion tensor}, - volume = {14}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - abstract = {In this paper, we propose to use the full diffusion tensor to perform brain-wide score prediction on diffusion tensor imaging (DTI) using the log-Euclidean framework., rather than the commonly used fractional anisotropy (FA). Indeed, scalar values such as the FA do not capture all the information contained in the diffusion tensor. Additionally, full tensor information is included in every step of the pre-processing pipeline: registration, smoothing and feature selection using voxelwise multivariate regression analysis. This approach was tested on data obtained from 30 children and adolescents with autism spectrum disorder and showed some improvement over the FA-only analysis.}, - language = {eng}, - booktitle = {{MICCAI}}, - author = {Fouque, Anne-Laure and Fillard, Pierre and Bargiacchi, Anne and Cachia, Arnaud and Zilbovicius, Monica and Thyreau, Benjamin and Le Floch, Edith and Ciuciu, Philippe and Duchesnay, Edouard}, - year = {2011}, - pmid = {21995007}, - keywords = {Algorithms, Artificial Intelligence, Brain, Humans, Magnetic Resonance Imaging, Software, Brain Mapping, Computer-Assisted, Image Processing, Image Processing, Computer-Assisted, Models, Models, Statistical, Statistical, Brain Mapping: methods, Child, Child Development Disorders, Pervasive, Diffusion Tensor Imaging, conference, Multivariate Analysis, Brain: pathology, Child Development Disorders, Computer-Assisted: methods, Diffusion Tensor Imaging: methods, Magnetic Resonance Imaging: methods, Pervasive, Pervasive: pathology}, - pages = {9--16}, - file = {Attachment:/home/ed203246/snap/zotero-snap/common/Zotero/storage/E6SJHUJJ/MICCAI2011.pdf:application/pdf}, -} - -@inproceedings{fouque_comparison_2013, - title = {Comparison of {Features} for {Voxel}-{Based} {Analysis} and {Classification} of {Anatomical} {Neuroimaging} {Data}}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - isbn = {978-0-7695-5061-9}, - url = {http://dl.acm.org/citation.cfm?id=2552484.2552547}, - doi = {10.1109/PRNI.2013.55}, - booktitle = {2013 {International} {Workshop} on {Pattern} {Recognition} in {Neuroimaging}}, - publisher = {IEEE}, - author = {Fouque, Anne-Laure and Fischer, Clara and Frouin, Vincent and Ciuciu, Philippe and Duchesnay, Edouard}, - month = jun, - year = {2013}, - keywords = {MRI, conference, classification, group analysis}, - pages = {186--189}, -} - -@inproceedings{le_floch_discovering_2012, - title = {Discovering associations in high dimensional imaging-genetics data: {A} comparison study of dimension reduction and regularisation strategies combined with partial least squares}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - booktitle = {International {Symposium} on {Biomedical} {Imaging} ({ISBI})}, - author = {Le Floch, Edith and Pinel, Philippe and Tenenhaus, Arthur and Trinchera, Laura and Poline, Jean-Baptiste and Frouin, Vincent and Duchesnay, Edouard}, - year = {2012}, - keywords = {conference}, - pages = {1503--1506}, -} - -@inproceedings{le_floch_dimension_2013, - address = {New York, NY}, - title = {Dimension {Reduction} and {Regularization} {Combined} with {Partial} {Least} {Squares} in {High} {Dimensional} {Imaging} {Genetics} {Studies}}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - isbn = {978-1-4614-8283-3}, - abstract = {In the imaging genetics field, the classical univariate approach ignores the potential joint effects between genes or the potential covariations between brain regions. In this paper, we propose instead to investigate exploratory multivariate methods, namely partial least squares regression or canonical correlation analysis, in order to identify a set of genetic polymorphisms covarying with a set of neuroimaging phenotypes. However, in high-dimensional settings, such multivariate methods may encounter overfitting issues. Thus, we investigate the use of different strategies of regularization and dimension reduction, combined with PLS or CCA, to face the very high dimensionality of imaging genetics studies. We propose a comparison study of the different strategies on a simulated dataset. We estimate the generalisability of the multivariate association with a cross-validation scheme and assess the capacity of good detection. Univariate selection seems necessary to reduce the dimensionality. However, the best results are obtained by combining univariate filtering and L1-regularized PLS, which suggests that discovering meaningful genetic associations calls for a multivariate approach.}, - booktitle = {New {Perspectives} in {Partial} {Least} {Squares} and {Related} {Methods}}, - publisher = {Springer New York}, - author = {Le Floch, Edith and Trinchera, Laura and Guillemot, Vincent and Tenenhaus, Arthur and Poline, Jean-Baptiste and Frouin, Vincent and Duchesnay, Edouard}, - editor = {Abdi, Herve and Chin, Wynne W. and Esposito Vinzi, Vincenzo and Russolillo, Giorgio and Trinchera, Laura}, - year = {2013}, - pages = {147--158}, -} - -@inproceedings{louiset_sepclr_2024, - title = {{SepCLR}: {Separating} common from salient patterns with {Contrastive} {Representation} {Learning}}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - url = {https://openreview.net/forum?id=30N3bNAiw3}, - abstract = {Contrastive Analysis is a sub-field of Representation Learning that aims at separating 1) salient factors of variation - that only exist in the target dataset (i.e., diseased subjects) in contrast with 2) common factors of variation between target and background (i.e., healthy subjects) datasets. Despite their relevance, current models based on Variational Auto-Encoders have shown poor performance in learning semantically-expressive representations. On the other hand, Contrastive Representation Learning has shown tremendous performance leaps in various applications (classification, clustering, etc.). In this work, we propose to leverage the ability of Contrastive Learning to learn semantically expressive representations when performing Contrastive Analysis. Namely, we reformulate Contrastive Analysis under the lens of the InfoMax Principle and identify two Mutual Information terms to maximize and one to minimize. We decompose the two first terms into an Alignment and a Uniformity term, as commonly done in Contrastive Learning. Then, we motivate a novel Mutual Information minimization strategy to prevent information leakage between common and salient distributions. We validate our method on datasets designed to assess the pattern separation capability in Contrastive Analysis, including MNIST superimposed on CIFAR10, CelebA accessories, dSprites item superimposed on a digit grid, and three medical datasets.}, - language = {en}, - urldate = {2024-01-31}, - booktitle = {The {Twelfth} {International} {Conference} on {Learning} {Representations} ({ICLR}) 2024}, - author = {Louiset, Robin and Duchesnay, Edouard and Dufumier, Benoit and Grigis, Antoine and Gori, Pietro}, - year = {2024}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AIMFTNYG/2023 - Separating common from salient patterns with Contr.pdf:application/pdf}, -} - -@inproceedings{louiset_sepvae_2023, - title = {{SepVAE}: a contrastive {VAE} to separate pathological patterns from healthy ones}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - shorttitle = {{SepVAE}}, - url = {http://arxiv.org/abs/2307.06206}, - doi = {10.48550/arXiv.2307.06206}, - abstract = {Contrastive Analysis VAE (CA-VAEs) is a family of Variational auto-encoders (VAEs) that aims at separating the common factors of variation between a background dataset (BG) (i.e., healthy subjects) and a target dataset (TG) (i.e., patients) from the ones that only exist in the target dataset. To do so, these methods separate the latent space into a set of salient features (i.e., proper to the target dataset) and a set of common features (i.e., exist in both datasets). Currently, all models fail to prevent the sharing of information between latent spaces effectively and to capture all salient factors of variation. To this end, we introduce two crucial regularization losses: a disentangling term between common and salient representations and a classification term between background and target samples in the salient space. We show a better performance than previous CA-VAEs methods on three medical applications and a natural images dataset (CelebA). Code and datasets are available on GitHub https://github.com/neurospin-projects/2023\_rlouiset\_sepvae.}, - urldate = {2024-01-31}, - publisher = {arXiv}, - author = {Louiset, Robin and Duchesnay, Edouard and Grigis, Antoine and Dufumier, Benoit and Gori, Pietro}, - month = jul, - year = {2023}, - note = {arXiv:2307.06206 [cs, stat]}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition}, - annote = {Comment: Workshop on Interpretable ML in Healthcare at International Conference on Machine Learning (ICML), Honolulu, Hawaii, USA. 2023}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HW6TQVV4/Louiset et al. - 2023 - SepVAE a contrastive VAE to separate pathological.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3VTKDE2W/2307.html:text/html}, -} - -@inproceedings{louiset_ucsl_2021, - address = {Bilbao, Spain}, - title = {{UCSL} : {A} {Machine} {Learning} {Expectation}-{Maximization} framework for {Unsupervised} {Clustering} driven by {Supervised} {Learning}}, - copyright = {All rights reserved}, - shorttitle = {{UCSL}}, - url = {http://arxiv.org/abs/2107.01988}, - abstract = {Subtype Discovery consists in finding interpretable and consistent sub-parts of a dataset, which are also relevant to a certain supervised task. From a mathematical point of view, this can be defined as a clustering task driven by supervised learning in order to uncover subgroups in line with the supervised prediction. In this paper, we propose a general Expectation-Maximization ensemble framework entitled UCSL (Unsupervised Clustering driven by Supervised Learning). Our method is generic, it can integrate any clustering method and can be driven by both binary classification and regression. We propose to construct a non-linear model by merging multiple linear estimators, one per cluster. Each hyperplane is estimated so that it correctly discriminates - or predict - only one cluster. We use SVC or Logistic Regression for classification and SVR for regression. Furthermore, to perform cluster analysis within a more suitable space, we also propose a dimension-reduction algorithm that projects the data onto an orthonormal space relevant to the supervised task. We analyze the robustness and generalization capability of our algorithm using synthetic and experimental datasets. In particular, we validate its ability to identify suitable consistent sub-types by conducting a psychiatric-diseases cluster analysis with known ground-truth labels. The gain of the proposed method over previous state-of-the-art techniques is about +1.9 points in terms of balanced accuracy. Finally, we make codes and examples available in a scikit-learn-compatible Python package at https://github.com/neurospin-projects/2021\_rlouiset\_ucsl}, - urldate = {2022-02-01}, - booktitle = {Joint {European} {Conference} on {Machine} {Learning} and {Knowledge} {Discovery} in {Databases} ({ECML}/{PKDD}) 2021}, - author = {Louiset, Robin and Gori, Pietro and Dufumier, Benoit and Houenou, Josselin and Grigis, Antoine and Duchesnay, Edouard}, - year = {2021}, - note = {arXiv: 2107.01988}, - keywords = {Statistics - Machine Learning, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Computer Science - Artificial Intelligence}, - annote = {Comment: ECML/PKDD 2021}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/JX2XAKXU/Louiset et al. - 2021 - UCSL A Machine Learning Expectation-Maximization.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IJHUX3CU/2107.html:text/html}, -} - -@article{bourgin_phenotypes_2014, - title = {Phénotypes cliniques précoces et recherche de biomarqueurs stratégiques : les fondements d'une psychiatrie personnalisée}, - volume = {89}, - copyright = {© John Libbey Eurotext}, - issn = {0020-0204}, - shorttitle = {Phénotypes cliniques précoces et recherche de biomarqueurs stratégiques}, - url = {http://www.cairn.info/article.php?ID_ARTICLE=INPSY_8910_0781}, - doi = {10.1684/ipe.2013.1128}, - language = {fr}, - number = {10}, - urldate = {2014-12-03}, - journal = {L'information psychiatrique}, - author = {Bourgin, Julie and Duchesnay, Edouard}, - month = jan, - year = {2014}, - keywords = {épigénétique, imagerie cérébrale, marqueur biologique, médecine prédictive, prodrome, schizophrénie, stress}, - pages = {781--789}, - file = {Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YYHU4566/resume.html:text/html}, -} - -@article{bourgin_predicting_2019, - title = {Predicting the individual risk of psychosis conversion in at-risk mental state ({ARMS}): a multivariate model reveals the influence of nonpsychotic prodromal symptoms}, - copyright = {All rights reserved}, - issn = {1435-165X}, - shorttitle = {Predicting the individual risk of psychosis conversion in at-risk mental state ({ARMS})}, - doi = {10.1007/s00787-019-01461-y}, - abstract = {To improve the prediction of the individual risk of conversion to psychosis in UHR subjects, by considering all CAARMS' symptoms at first presentation and using a multivariate machine learning method known as logistic regression with Elastic-net shrinkage. 46 young individuals who sought help from the specialized outpatient unit at Sainte-Anne hospital and who met CAARMS criteria for UHR were assessed, among whom 27 were reassessed at follow-up (22.4 ± 6.54 months) and included in the analysis. Elastic net logistic regression was trained, using CAARMS items at baseline to predict individual evolution between converters (UHR-P) and non-converters (UHR-NP). Elastic-net was used to select the few CAARMS items that best predict the clinical evolution. All validations and significances of predictive models were computed with non-parametric re-sampling strategies that provide robust estimators even when the distributional assumption cannot be guaranteed. Among the 25 CAARMS items, the Elastic net selected 'obsessive-compulsive symptoms' and 'aggression/dangerous behavior' as risk factors for conversion while 'anhedonia' and 'mood swings/lability' were associated with non-conversion at follow-up. In the ten-fold stratified cross-validation, the classification achieved 81.8\% of sensitivity (P = 0.035) and 93.7\% of specificity (P = 0.0016). Non-psychotic prodromal symptoms bring valuable information to improve the prediction of conversion to psychosis. Elastic net logistic regression applied to clinical data is a promising way to switch from group prediction to an individualized prediction.}, - language = {eng}, - journal = {European Child \& Adolescent Psychiatry}, - author = {Bourgin, Julie and Duchesnay, Edouard and Magaud, Emilie and Gaillard, Raphaël and Kazes, Mathilde and Krebs, Marie-Odile}, - month = dec, - year = {2019}, - pmid = {31872289}, - keywords = {Schizophrenia, Early detection, Impulsivity, Machine learning algorithms, Obsessive compulsive symptoms}, - file = {Bourgin et al. - 2019 - Predicting the individual risk of psychosis conver.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/KUW2Y9ZY/Bourgin et al. - 2019 - Predicting the individual risk of psychosis conver.pdf:application/pdf}, -} - -@article{cachia_cortical_2008, - title = {Cortical folding abnormalities in schizophrenia patients with resistant auditory hallucinations}, - volume = {39}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2007.08.049}, - abstract = {Gray matter volume and functional abnormalities have been reported in language-related cortex in schizophrenia patients with auditory hallucinations. Such abnormalities might denote abnormal cortical folding development, which can now be investigated using gyrification measures. Anatomic magnetic resonance images (MRIs) were obtained from 30 schizophrenia patients screened for resistant auditory hallucinations and 28 control subjects. We searched for overall gyrification abnormalities in the whole cortex as well as localized abnormalities in language-related cortex, assuming that gyrification is associated with brain sulcation. A fully automated method was applied to MRIs to extract, label and measure the sulcus area in the whole cortex. Gyrification was assessed using both global and local sulcal indices, respectively the ratio between total sulcal area, or area of each labeled sulcus, and outer cortex area. For both hemispheres, the patients had a lower global sulcal index. The local sulcal index decrease was not homogeneous across the whole cortex. It was more significant in the superior temporal sulcus bilaterally, in the left middle frontal sulcus and in the diagonal branch of left sylvian fissure (Broca's area). Findings suggest abnormalities in cortical gyrification in these patients. Sulcal abnormalities in language-related cortex might underlie these patients' particular vulnerability to hallucinations.}, - language = {eng}, - number = {3}, - journal = {NeuroImage}, - author = {Cachia, Arnaud and Paillère-Martinot, Marie-Laure and Galinowski, André and Januel, Dominique and de Beaurepaire, Renaud and Bellivier, Frank and Artiges, Eric and Andoh, Jamila and Bartrés-Faz, David and Duchesnay, Edouard and Rivière, Denis and Plaze, Marion and Mangin, Jean-Francois and Martinot, Jean-Luc}, - month = feb, - year = {2008}, - pmid = {17988891}, - keywords = {Humans, Magnetic Resonance Imaging, Schizophrenia, Image Processing, Computer-Assisted, Adult, Female, Male, Cerebral Cortex, Middle Aged, Linear Models, Functional Laterality, Antipsychotic Agents, Hallucinations, Psychiatric Status Rating Scales, Sulci,Anatomy,brainvisa}, - pages = {927--935}, - annote = {The following values have no corresponding Zotero field:number: 3label: ACLcustom1: NeuroSpin}, - annote = {Unati - Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/Cachia-NI08.pdf}, -} - -@article{ching_what_2020, - title = {What we learn about bipolar disorder from large-scale neuroimaging: {Findings} and future directions from the {ENIGMA} {Bipolar} {Disorder} {Working} {Group}}, - copyright = {All rights reserved}, - issn = {1097-0193}, - shorttitle = {What we learn about bipolar disorder from large-scale neuroimaging}, - doi = {10.1002/hbm.25098}, - abstract = {MRI-derived brain measures offer a link between genes, the environment and behavior and have been widely studied in bipolar disorder (BD). However, many neuroimaging studies of BD have been underpowered, leading to varied results and uncertainty regarding effects. The Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Bipolar Disorder Working Group was formed in 2012 to empower discoveries, generate consensus findings and inform future hypothesis-driven studies of BD. Through this effort, over 150 researchers from 20 countries and 55 institutions pool data and resources to produce the largest neuroimaging studies of BD ever conducted. The ENIGMA Bipolar Disorder Working Group applies standardized processing and analysis techniques to empower large-scale meta- and mega-analyses of multimodal brain MRI and improve the replicability of studies relating brain variation to clinical and genetic data. Initial BD Working Group studies reveal widespread patterns of lower cortical thickness, subcortical volume and disrupted white matter integrity associated with BD. Findings also include mapping brain alterations of common medications like lithium, symptom patterns and clinical risk profiles and have provided further insights into the pathophysiological mechanisms of BD. Here we discuss key findings from the BD working group, its ongoing projects and future directions for large-scale, collaborative studies of mental illness.}, - language = {eng}, - journal = {Human Brain Mapping}, - author = {Ching, Christopher R. K. and Hibar, Derrek P. and Gurholt, Tiril P. and Nunes, Abraham and Thomopoulos, Sophia I. and Abé, Christoph and Agartz, Ingrid and Brouwer, Rachel M. and Cannon, Dara M. and de Zwarte, Sonja M. C. and Eyler, Lisa T. and Favre, Pauline and Hajek, Tomas and Haukvik, Unn K. and Houenou, Josselin and Landén, Mikael and Lett, Tristram A. and McDonald, Colm and Nabulsi, Leila and Patel, Yash and Pauling, Melissa E. and Paus, Tomas and Radua, Joaquim and Soeiro-de-Souza, Marcio G. and Tronchin, Giulia and van Haren, Neeltje E. M. and Vieta, Eduard and Walter, Henrik and Zeng, Ling-Li and Alda, Martin and Almeida, Jorge and Alnaes, Dag and Alonso-Lana, Silvia and Altimus, Cara and Bauer, Michael and Baune, Bernhard T. and Bearden, Carrie E. and Bellani, Marcella and Benedetti, Francesco and Berk, Michael and Bilderbeck, Amy C. and Blumberg, Hilary P. and Bøen, Erlend and Bollettini, Irene and Del Mar Bonnin, Caterina and Brambilla, Paolo and Canales-Rodríguez, Erick J. and Caseras, Xavier and Dandash, Orwa and Dannlowski, Udo and Delvecchio, Giuseppe and Díaz-Zuluaga, Ana M. and Dima, Danai and Duchesnay, Edouard and Elvsåshagen, Torbjørn and Fears, Scott C. and Frangou, Sophia and Fullerton, Janice M. and Glahn, David C. and Goikolea, Jose M. and Green, Melissa J. and Grotegerd, Dominik and Gruber, Oliver and Haarman, Bartholomeus C. M. and Henry, Chantal and Howells, Fleur M. and Ives-Deliperi, Victoria and Jansen, Andreas and Kircher, Tilo T. J. and Knöchel, Christian and Kramer, Bernd and Lafer, Beny and López-Jaramillo, Carlos and Machado-Vieira, Rodrigo and MacIntosh, Bradley J. and Melloni, Elisa M. T. and Mitchell, Philip B. and Nenadic, Igor and Nery, Fabiano and Nugent, Allison C. and Oertel, Viola and Ophoff, Roel A. and Ota, Miho and Overs, Bronwyn J. and Pham, Daniel L. and Phillips, Mary L. and Pineda-Zapata, Julian A. and Poletti, Sara and Polosan, Mircea and Pomarol-Clotet, Edith and Pouchon, Arnaud and Quidé, Yann and Rive, Maria M. and Roberts, Gloria and Ruhe, Henricus G. and Salvador, Raymond and Sarró, Salvador and Satterthwaite, Theodore D. and Schene, Aart H. and Sim, Kang and Soares, Jair C. and Stäblein, Michael and Stein, Dan J. and Tamnes, Christian K. and Thomaidis, Georgios V. and Upegui, Cristian Vargas and Veltman, Dick J. and Wessa, Michèle and Westlye, Lars T. and Whalley, Heather C. and Wolf, Daniel H. and Wu, Mon-Ju and Yatham, Lakshmi N. and Zarate, Carlos A. and Thompson, Paul M. and Andreassen, Ole A. and {ENIGMA Bipolar Disorder Working Group}}, - month = jul, - year = {2020}, - pmid = {32725849}, - keywords = {MRI, neuroimaging, bipolar disorder, cortical surface area, cortical thickness, ENIGMA, mega-analysis, meta-analysis, psychiatry, volume}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UKP5I362/Ching et al. - 2020 - What we learn about bipolar disorder from large-sc.pdf:application/pdf}, -} - -@article{claude_will_2020, - title = {Will machine learning applied to neuroimaging in bipolar disorder help the clinician? {A} critical review and methodological suggestions}, - copyright = {All rights reserved}, - issn = {1399-5618}, - shorttitle = {Will machine learning applied to neuroimaging in bipolar disorder help the clinician?}, - doi = {10.1111/bdi.12895}, - abstract = {OBJECTIVES: The existence of anatomo-functional brain abnormalities in Bipolar Disorder (BD) is now well established by magnetic resonance imaging (MRI) studies. To create diagnostic and prognostic tools, as well as identifying biologically valid subtypes of BD, research has recently turned towards the use of machine learning (ML) techniques. We assessed both supervised ML and unsupervised ML studies in BD to evaluate their robustness, reproducibility and the potential need for improvement. -METHOD: We systematically searched for studies using ML algorithms based on MRI data of patients with BD until February 2019. -RESULT: We identified 47 studies, 45 using supervised ML techniques and 2 including unsupervised ML analyses. Among supervised studies, 43 focused on diagnostic classification. The reported accuracies for classification of BD ranged between i) 57\% and 100\%, for BD vs. healthy controls (HC); ii) 49.5\% and 93.1\% for BD vs. patients with major depressive disorder (MDD); iii) 50\% and 96.2\% for BD vs. patients with schizophrenia. Reported accuracies for discriminating subjects genetically at risk for BD (either from control or from patients with BD) ranged between 64.3\% and 88.93\%. -CONCLUSIONS: Although there are strong methodological limitations in previous studies and an important need for replication in large multicentric samples, the conclusions of our review bring hope of future computer aided diagnosis of BD and pave the way for other applications, such as treatment response prediction. To reinforce the reliability of future results we provide methodological suggestions for good practice in conducting and reporting MRI-based ML studies in BD.}, - language = {eng}, - journal = {Bipolar Disorders}, - author = {Claude, Laurie-Anne and Houenou, Josselin and Duchesnay, Edouard and Favre, Pauline}, - month = feb, - year = {2020}, - pmid = {32108409}, - keywords = {Magnetic Resonance Imaging, Machine Learning, Bipolar Disorders, Precision Medicine}, -} - -@article{dubois_automated_2007, - title = {Automated three-dimensional analysis of histological and autoradiographic rat brain sections: application to an activation study}, - volume = {27}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {0271-678X}, - shorttitle = {Automated three-dimensional analysis of histological and autoradiographic rat brain sections}, - doi = {10.1038/sj.jcbfm.9600470}, - abstract = {Besides the newly developed positron emission tomography scanners (microPET) dedicated to the in vivo functional study of small animals, autoradiography remains the reference technique widely used for functional brain imaging and the gold standard for the validation of in vivo results. The analysis of autoradiographic data is classically achieved in two dimensions (2D) using a section-by-section approach, is often limited to few sections and the delineation of the regions of interest to be analysed is directly performed on autoradiographic sections. In addition, such approach of analysis does not accommodate the possible anatomical shifts linked to dissymmetry associated with the sectioning process. This classic analysis is time-consuming, operator-dependent and can therefore lead to non-objective and non-reproducible results. In this paper, we have developed an automated and generic toolbox for processing of autoradiographic and corresponding histological rat brain sections based on a three-step approach, which involves: (1) an optimized digitization dealing with hundreds of autoradiographic and histological sections; (2) a robust reconstruction of the volumes based on a reliable registration method; and (3) an original 3D-geometry-based approach to analysis of anatomical and functional post-mortem data. The integration of the toolbox under a unified environment (in-house software BrainVISA, http://brainvisa.info) with a graphic interface enabled a robust and operator-independent exploitation of the overall anatomical and functional information. We illustrated the substantial qualitative and quantitative benefits obtained by applying our methodology to an activation study (rats, n=5, under unilateral visual stimulation).}, - language = {eng}, - number = {10}, - journal = {Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism}, - author = {Dubois, Albertine and Dauguet, Julien and Herard, Anne-Sophie and Besret, Laurent and Duchesnay, Edouard and Frouin, Vincent and Hantraye, Philippe and Bonvento, Gilles and Delzescaux, Thierry}, - month = oct, - year = {2007}, - pmid = {17377517}, - keywords = {Brain, Imaging, Three-Dimensional, Animals, Autoradiography, Rats}, - pages = {1742--1755}, - annote = {The following values have no corresponding Zotero field:number: 10label: ACLcustom1: NeuroSpin}, - annote = {Unati - ftp://ftp.cea.fr/pub/dsv/anatomist/papers/ADubois-JCBFM07.pdfarticle}, -} - -@article{duchesnay_feature_2011, - series = {Special {Issue}: {Educational} {Neuroscience}}, - title = {Feature selection and classification of imbalanced datasets: {Application} to {PET} images of children with autistic spectrum disorders}, - volume = {57}, - copyright = {All rights reserved}, - issn = {1053-8119}, - shorttitle = {Feature selection and classification of imbalanced datasets}, - url = {http://www.sciencedirect.com/science/article/pii/S105381191100499X}, - doi = {10.1016/j.neuroimage.2011.05.011}, - abstract = {Learning with discriminative methods is generally based on minimizing the misclassification of training samples, which may be unsuitable for imbalanced datasets where the recognition might be biased in favor of the most numerous class. This problem can be addressed with a generative approach, which typically requires more parameters to be determined leading to reduced performances in high dimension. In such situations, dimension reduction becomes a crucial issue. We propose a feature selection/classification algorithm based on generative methods in order to predict the clinical status of a highly imbalanced dataset made of PET scans of forty-five low-functioning children with autism spectrum disorders (ASD) and thirteen non-ASD low functioning children. ASDs are typically characterized by impaired social interaction, narrow interests, and repetitive behaviors, with a high variability in expression and severity. The numerous findings revealed by brain imaging studies suggest that ASD is associated with a complex and distributed pattern of abnormalities that makes the identification of a shared and common neuroimaging profile a difficult task. In this context, our goal is to identify the rest functional brain imaging abnormalities pattern associated with ASD and to validate its efficiency in individual classification. The proposed feature selection algorithm detected a characteristic pattern in the ASD group that included a hypoperfusion in the right Superior Temporal Sulcus (STS) and a hyperperfusion in the contralateral postcentral area. Our algorithm allowed for a significantly accurate (88\%), sensitive (91\%) and specific (77\%) prediction of clinical category. For this imbalanced dataset, with only 13 control scans, the proposed generative algorithm outperformed other state-of-the-art discriminant methods. The high predictive power of the characteristic pattern, which has been automatically identified on whole brains without any priors, confirms previous findings concerning the role of STS in ASD. This work offers exciting possibilities for early autism detection and/or the evaluation of treatment response in individual patients.}, - language = {en}, - number = {3}, - urldate = {2021-01-04}, - journal = {NeuroImage}, - author = {Duchesnay, Edouard and Cachia, Arnaud and Boddaert, Nathalie and Chabane, Nadia and Mangin, Jean-Franois and Martinot, Jean-Luc and Brunelle, Francis and Zilbovicius, Monica}, - month = aug, - year = {2011}, - keywords = {Feature selection, Autism, Dimension reduction, Multivariate classification}, - pages = {1003--1014}, - annote = {The following values have no corresponding Zotero field:number: 3accession-num: WOS:000292717900034label: ACLcustom1: Neurospin}, - annote = {Unati1053-8119SI}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B36T2GS2/S105381191100499X.html:text/html}, -} - -@article{duchesnay_cooperative_2003, - title = {Cooperative agents society organized as an irregular pyramid: {A} mammography segmentation application}, - volume = {24}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - shorttitle = {Cooperative agents society organized as an irregular pyramid}, - url = {http://www.sciencedirect.com/science/article/pii/S0167865503000771}, - number = {14}, - urldate = {2017-01-10}, - journal = {Pattern Recognition Letters}, - author = {Duchesnay, Edouard and Montois, Jean-Jacques and Jacquelet, Yann}, - year = {2003}, - pages = {2435--2445}, - file = {[PDF] à partir de researchgate.net:/home/ed203246/snap/zotero-snap/common/Zotero/storage/FWVSIDWF/Duchesnay et al. - 2003 - Cooperative agents society organized as an irregul.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/587TH2Z2/S0167865503000771.html:text/html}, -} - -@article{dufumier_openbhb_2022, - title = {{OpenBHB}: a {Large}-{Scale} {Multi}-{Site} {Brain} {MRI} {Data}-set for {Age} {Prediction} and {Debiasing}}, - copyright = {All rights reserved}, - issn = {1053-8119}, - shorttitle = {{OpenBHB}}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811922007522}, - doi = {10.1016/j.neuroimage.2022.119637}, - abstract = {Prediction of chronological age from neuroimaging in the healthy population is an important issue because the deviations from normal brain age may highlight abnormal trajectories towards brain disorders. As a first step, ML models have emerged to predict chronological age from brain MRI, as a proxy measure of biological age. However, there is currently no consensus w.r.t which Machine Learning (ML) model is best suited for this task, largely because of a lack of public benchmark. Furthermore, new large emerging population neuroimaging datasets are often biased by the acquisition center images are coming from. This bias heavily deteriorates models generalization capacities, especially for Deep Learning (DL) algorithms that are known to overfit rapidly on the simplest features (known as simplicity bias). Here we propose a new public benchmarking resource, namely Open Big Healthy Brains (OpenBHB), along with a challenge for both brain age prediction and site-effect removal through a representation learning framework. OpenBHB is large-scale, gathering {\textgreater}5K 3D T1 brain MRI from Healthy Controls (HC) and highly multi-sites, aggregating {\textgreater}60 centers worldwide and 10 studies. OpenBHB is expected to grow both in terms of available modalities and number of subjects. All OpenBHB datasets are uniformly preprocessed, including quality check, with container technologies that consist in: 3D Voxel-Based Morphometry maps (VBM from CAT12), quasi-raw (simple linear alignment of images), and Surface-Based Morphometry indices (SBM, from FreeSurfer). The OpenBHB challenge is permanent and we provide all tools, materials and tutorials for participants to easily submit and benchmark their model against each other on a public leaderboard.}, - language = {en}, - urldate = {2022-09-20}, - journal = {NeuroImage}, - author = {Dufumier, Benoit and Grigis, Antoine and Victor, Julie and Ambroise, Corentin and Frouin, Vincent and Duchesnay, Edouard}, - month = sep, - year = {2022}, - pages = {119637}, - file = {ScienceDirect Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/XSKTP76F/Dufumier et al. - 2022 - OpenBHB a Large-Scale Multi-Site Brain MRI Data-s.pdf:application/pdf;ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/RWBG5P8M/S1053811922007522.html:text/html}, -} - -@article{dupont_prediction_2024, - title = {Prediction of post-traumatic stress disorder in family members of {ICU} patients: a machine learning approach}, - volume = {50}, - copyright = {CC0 1.0 Universal Public Domain Dedication}, - issn = {1432-1238}, - shorttitle = {Prediction of post-traumatic stress disorder in family members of {ICU} patients}, - url = {https://doi.org/10.1007/s00134-023-07288-1}, - doi = {10.1007/s00134-023-07288-1}, - abstract = {Post-traumatic stress disorder (PTSD) can affect family members of patients admitted to the intensive care unit (ICU). Easily accessible patient’s and relative’s information may help develop accurate risk stratification tools to direct relatives at higher risk of PTSD toward appropriate management.}, - language = {en}, - number = {1}, - urldate = {2024-01-26}, - journal = {Intensive Care Medicine}, - author = {Dupont, Thibault and Kentish-Barnes, Nancy and Pochard, Frédéric and Duchesnay, Edouard and Azoulay, Elie}, - month = jan, - year = {2024}, - keywords = {Machine learning, Prediction, Algorithm, Mechanical ventilation, Post-ICU burden}, - pages = {114--124}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/AW94FYLA/Dupont et al. - 2024 - Prediction of post-traumatic stress disorder in fa.pdf:application/pdf}, -} - -@article{elandaloussi_understanding_2023, - title = {Understanding the relationship between cerebellar structure and social abilities}, - volume = {14}, - copyright = {All rights reserved}, - issn = {2040-2392}, - url = {https://doi.org/10.1186/s13229-023-00551-8}, - doi = {10.1186/s13229-023-00551-8}, - abstract = {The cerebellum contains more than 50\% of all neurons in the brain and is involved in a broad range of cognitive functions, including social communication and social cognition. Inconsistent atypicalities in the cerebellum have been reported in individuals with autism compared to controls suggesting the limits of categorical case control comparisons. Alternatively, investigating how clinical dimensions are related to neuroanatomical features, in line with the Research Domain Criteria approach, might be more relevant. We hypothesized that the volume of the “cognitive” lobules of the cerebellum would be associated with social difficulties.}, - number = {1}, - urldate = {2023-11-25}, - journal = {Molecular Autism}, - author = {Elandaloussi, Yannis and Floris, Dorothea L. and Coupé, Pierrick and Duchesnay, Edouard and Mihailov, Angeline and Grigis, Antoine and Bègue, Indrit and Victor, Julie and Frouin, Vincent and Leboyer, Marion and Houenou, Josselin and Laidi, Charles}, - month = may, - year = {2023}, - keywords = {MRI, Cerebellum, Autism, Parcellation, Social communication, Volumetry}, - pages = {18}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/37DCRVAS/Elandaloussi et al. - 2023 - Understanding the relationship between cerebellar .pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WRK99LKT/s13229-023-00551-8.html:text/html}, -} - -@article{favre_widespread_2019, - title = {Widespread white matter microstructural abnormalities in bipolar disorder: evidence from mega- and meta-analyses across 3033 individuals}, - copyright = {2019 The Author(s), under exclusive licence to American College of Neuropsychopharmacology}, - issn = {1740-634X}, - shorttitle = {Widespread white matter microstructural abnormalities in bipolar disorder}, - url = {https://www.nature.com/articles/s41386-019-0485-6}, - doi = {10.1038/s41386-019-0485-6}, - abstract = {Fronto-limbic white matter (WM) abnormalities are assumed to lie at the heart of the pathophysiology of bipolar disorder (BD); however, diffusion tensor imaging (DTI) studies have reported heterogeneous results and it is not clear how the clinical heterogeneity is related to the observed differences. This study aimed to identify WM abnormalities that differentiate patients with BD from healthy controls (HC) in the largest DTI dataset of patients with BD to date, collected via the ENIGMA network. We gathered individual tensor-derived regional metrics from 26 cohorts leading to a sample size of N = 3033 (1482 BD and 1551 HC). Mean fractional anisotropy (FA) from 43 regions of interest (ROI) and average whole-brain FA were entered into univariate mega- and meta-analyses to differentiate patients with BD from HC. Mega-analysis revealed significantly lower FA in patients with BD compared with HC in 29 regions, with the highest effect sizes observed within the corpus callosum (R2 = 0.041, Pcorr {\textless} 0.001) and cingulum (right: R2 = 0.041, left: R2 = 0.040, Pcorr {\textless} 0.001). Lithium medication, later onset and short disease duration were related to higher FA along multiple ROIs. Results of the meta-analysis showed similar effects. We demonstrated widespread WM abnormalities in BD and highlighted that altered WM connectivity within the corpus callosum and the cingulum are strongly associated with BD. These brain abnormalities could represent a biomarker for use in the diagnosis of BD. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.}, - language = {en}, - urldate = {2019-08-21}, - journal = {Neuropsychopharmacology}, - author = {Favre, Pauline and Pauling, Melissa and Stout, Jacques and Hozer, Franz and Sarrazin, Samuel and Abé, Christoph and Alda, Martin and Alloza, Clara and Alonso-Lana, Silvia and Andreassen, Ole A. and Baune, Bernhard T. and Benedetti, Francesco and Busatto, Geraldo F. and Canales-Rodríguez, Erick J. and Caseras, Xavier and Chaim-Avancini, Tiffany Moukbel and Ching, Christopher R. K. and Dannlowski, Udo and Deppe, Michael and Eyler, Lisa T. and Fatjo-Vilas, Mar and Foley, Sonya F. and Grotegerd, Dominik and Hajek, Tomas and Haukvik, Unn K. and Howells, Fleur M. and Jahanshad, Neda and Kugel, Harald and Lagerberg, Trine V. and Lawrie, Stephen M. and Linke, Julia O. and McIntosh, Andrew and Melloni, Elisa M. T. and Mitchell, Philip B. and Polosan, Mircea and Pomarol-Clotet, Edith and Repple, Jonathan and Roberts, Gloria and Roos, Annerine and Rosa, Pedro G. P. and Salvador, Raymond and Sarró, Salvador and Schofield, Peter R. and Serpa, Mauricio H. and Sim, Kang and Stein, Dan J. and Sussmann, Jess E. and Temmingh, Henk S. and Thompson, Paul M. and Verdolini, Norma and Vieta, Eduard and Wessa, Michele and Whalley, Heather C. and Zanetti, Marcus V. and Leboyer, Marion and Mangin, Jean-François and Henry, Chantal and Duchesnay, Edouard and Houenou, Josselin}, - month = aug, - year = {2019}, - pmid = {31527792}, - note = {tex.ids: favre\_correction\_2019}, - keywords = {Translational research, Diagnostic markers}, - pages = {1--11}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UCEC66DU/Favre et al. - 2019 - Correction Widespread white matter microstructura.pdf:application/pdf;Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/BCH8G2RS/Favre et al. - 2019 - Widespread white matter microstructural abnormalit.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/44P2C76Q/s41386-019-0485-6.html:text/html}, -} - -@article{fovet_decoding_2022, - series = {Biomarkers of {Psychosis}}, - title = {Decoding {Activity} in {Broca}'s {Area} {Predicts} the {Occurrence} of {Auditory} {Hallucinations} {Across} {Subjects}}, - volume = {91}, - copyright = {All rights reserved}, - issn = {0006-3223}, - url = {https://www.sciencedirect.com/science/article/pii/S0006322321015699}, - doi = {10.1016/j.biopsych.2021.08.024}, - abstract = {Background -Functional magnetic resonance imaging (fMRI) capture aims at detecting auditory-verbal hallucinations (AVHs) from continuously recorded brain activity. Establishing efficient capture methods with low computational cost that easily generalize between patients remains a key objective in precision psychiatry. To address this issue, we developed a novel automatized fMRI-capture procedure for AVHs in patients with schizophrenia (SCZ). -Methods -We used a previously validated but labor-intensive personalized fMRI-capture method to train a linear classifier using machine learning techniques. We benchmarked the performances of this classifier on 2320 AVH periods versus resting-state periods obtained from SCZ patients with frequent symptoms (n = 23). We characterized patterns of blood oxygen level–dependent activity that were predictive of AVH both within and between subjects. Generalizability was assessed with a second independent sample gathering 2000 AVH labels (n = 34 patients with SCZ), while specificity was tested with a nonclinical control sample performing an auditory imagery task (840 labels, n = 20). -Results -Our between-subject classifier achieved high decoding accuracy (area under the curve = 0.85) and discriminated AVH from rest and verbal imagery. Optimizing the parameters on the first schizophrenia dataset and testing its performance on the second dataset led to an out-of-sample area under the curve of 0.85 (0.88 for the converse test). We showed that AVH detection critically depends on local blood oxygen level–dependent activity patterns within Broca's area. -Conclusions -Our results demonstrate that it is possible to reliably detect AVH states from fMRI blood oxygen level–dependent signals in patients with SCZ using a multivariate decoder without performing complex preprocessing steps. These findings constitute a crucial step toward brain-based treatments for severe drug-resistant hallucinations.}, - language = {en}, - number = {2}, - urldate = {2022-10-04}, - journal = {Biological Psychiatry}, - author = {Fovet, Thomas and Yger, Pierre and Lopes, Renaud and de Pierrefeu, Amicie and Duchesnay, Edouard and Houenou, Josselin and Thomas, Pierre and Szaffarczyk, Sébastien and Domenech, Philippe and Jardri, Renaud}, - month = jan, - year = {2022}, - keywords = {Hallucinations, Biomarker, fMRI, Detection, Inferior frontal gyrus, Multivoxel pattern analysis (MVPA), Voice hearing}, - pages = {194--201}, - file = {Fovet et al. - 2021 - Decoding Activity in Broca's Area Predicts the Occ.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/DTBXLFDK/Fovet et al. - 2021 - Decoding Activity in Broca's Area Predicts the Occ.pdf:application/pdf;ScienceDirect Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/SZC92ANC/Fovet et al. - 2022 - Decoding Activity in Broca's Area Predicts the Occ.pdf:application/pdf;ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QFIPUM8M/S0006322321015699.html:text/html;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/HLSE6U8Q/Fovet et al. - 2021 - Decoding Activity in Broca's Area Predicts the Occ.pdf:application/pdf}, -} - -@article{fraize_enhancing_2023, - title = {Enhancing fetal alcohol spectrum disorders diagnosis with a classifier based on the intracerebellar gradient of volumetric undersizing}, - volume = {44}, - copyright = {© 2023 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.}, - issn = {1097-0193}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/hbm.26348}, - doi = {10.1002/hbm.26348}, - abstract = {In fetal alcohol spectrum disorders (FASD), brain growth deficiency is a hallmark of subjects both with fetal alcohol syndrome (FAS) and with non-syndromic FASD (NS-FASD, i.e., those without specific diagnostic features). However, although the cerebellum was suggested to be more severely undersized than the rest of the brain, it has not yet been given a specific place in the FASD diagnostic criteria where neuroanatomical features still count for little if anything in diagnostic specificity. We applied a combination of cerebellar segmentation tools on a 1.5 T 3DT1 brain MRI dataset from a monocentric population of 89 FASD (52 FAS, 37 NS-FASD) and 126 typically developing controls (6–20 years old), providing 8 volumes: cerebellum, vermis and 3 lobes (anterior, posterior, inferior), plus total brain volume. After adjustment of confounders, the allometric scaling relationship between these cerebellar volumes (Vi) and the total brain or cerebellum volume (Vt) was fitted (Vi = bVta), and the effect of group (FAS, control) on allometric scaling was evaluated. We then estimated for each cerebellar volume in the FAS population the deviation from the typical scaling (vDTS) learned in the controls. Lastly, we trained and tested two classifiers to discriminate FAS from controls, one based on the total cerebellum vDTS only, the other based on all the cerebellar vDTS, comparing their performance both in the FAS and the NS-FASD group. Allometric scaling was significantly different between FAS and control group for all the cerebellar volumes (p {\textless} .001). We confirmed the excess of total cerebellum volume deficit (vDTS = −10.6\%) and revealed an antero-inferior-posterior gradient of volumetric undersizing in the hemispheres (−12.4\%, 1.1\%, 2.0\%, respectively) and the vermis (−16.7\%, −9.2\%, −8.6\%, repectively). The classifier based on the intracerebellar gradient of vDTS performed more efficiently than the one based on total cerebellum vDTS only (AUC = 92\% vs. 82\%, p = .001). Setting a high probability threshold for {\textgreater}95\% specificity of the classifiers, the gradient-based classifier identified 35\% of the NS-FASD to have a FAS cerebellar phenotype, compared to 11\% with the cerebellum-only classifier (pFISHER = 0.027). In a large series of FASD, this study details the volumetric undersizing within the cerebellum at the lobar and vermian level using allometric scaling, revealing an anterior-inferior-posterior gradient of vulnerability to prenatal alcohol exposure. It also strongly suggests that this intracerebellar gradient of volumetric undersizing may be a reliable neuroanatomical signature of FAS that could be used to improve the specificity of the diagnosis of NS-FASD.}, - language = {en}, - number = {11}, - urldate = {2023-07-04}, - journal = {Human Brain Mapping}, - author = {Fraize, Justine and Fischer, Clara and Elmaleh-Bergès, Monique and Kerdreux, Eliot and Beggiato, Anita and Ntorkou, Alexandra and Duchesnay, Edouard and Bekha, Dhaif and Boespflug-Tanguy, Odile and Delorme, Richard and Hertz-Pannier, Lucie and Germanaud, David}, - year = {2023}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.26348}, - keywords = {cerebellum morphometry, diagnostic imaging, fetal alcohol spectrum disorders, fetal alcohol syndrome, microcephaly, prenatal alcohol exposure, scaling analysis}, - pages = {4321--4336}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/76744Z3U/Fraize et al. - 2023 - Enhancing fetal alcohol spectrum disorders diagnos.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/T5R6NUTY/hbm.html:text/html}, -} - -@article{iftimovici_asynchronous_2023, - title = {Asynchronous neural maturation predicts transition to psychosis}, - copyright = {All rights reserved}, - issn = {1440-1819}, - doi = {10.1111/pcn.13612}, - abstract = {AIM: Neuroimaging-based machine-learning predictions of psychosis onset rely on the hypothesis that structural brain anomalies may reflect the underlying pathophysiology. Yet, current predictors remain difficult to interpret in light of brain structure. Here, we combined an advanced interpretable supervised algorithm and a model of neuroanatomical age to identify the level of brain maturation of the regions most predictive of psychosis. -METHODS: We used the voxel-based morphometry of a healthy control dataset (N = 2024) and a prospective longitudinal UHR cohort (N = 82), of which 27 developed psychosis after one year. In UHR, psychosis was predicted at one year using Elastic-Net-Total-Variation (Enet-TV) penalties within a five-fold cross-validation, providing an interpretable map of distinct predictive regions. Using both the whole brain and each predictive region separately, a brain age predictor was then built and validated in 1605 controls, externally tested in 419 controls from an independent cohort, and applied in UHR. Brain age gaps were computed as the difference between chronological and predicted age, providing a proxy of whole-brain and regional brain maturation. -RESULTS: Psychosis prediction was performant with 80 ± 4\% of area-under-curve and 69 ± 5\% of balanced accuracy (p {\textless} 0.001), and mainly leveraged volumetric increases in the ventromedial prefrontal cortex and decreases in the left precentral gyrus and the right orbitofrontal cortex. These regions were predicted to have, respectively, delayed and accelerated maturational patterns. -CONCLUSION: By combining an interpretable supervised model of conversion to psychosis with a brain age predictor, we showed that inter-regional asynchronous brain maturation underlines the predictive signature of psychosis. This article is protected by copyright. All rights reserved.}, - language = {eng}, - journal = {Psychiatry and Clinical Neurosciences}, - author = {Iftimovici, Anton and Bourgin, Julie and Houenou, Josselin and Gay, Olivier and Grigis, Antoine and Victor, Julie and Chaumette, Boris and Krebs, Marie-Odile and Duchesnay, Edouard and {ICAAR-plus Study Group.}}, - month = oct, - year = {2023}, - pmid = {37904327}, - keywords = {neurodevelopment, psychosis, brain age, machine-learning, voxel-based morphometry}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/EXWGEDSW/Iftimovici et al. - 2023 - Asynchronous neural maturation predicts transition.pdf:application/pdf}, -} - -@article{iftimovici_brain_2022, - title = {Brain anomalies in early psychosis: {From} secondary to primary psychosis}, - copyright = {All rights reserved}, - issn = {0149-7634}, - shorttitle = {{BRAIN} {ANOMALIES} {IN} {EARLY} {PSYCHOSIS}}, - url = {https://www.sciencedirect.com/science/article/pii/S0149763422002056}, - doi = {10.1016/j.neubiorev.2022.104716}, - abstract = {Brain anomalies are frequently found in early psychoses. Although they may remain undetected for many years, their interpretation is critical for differential diagnosis. In secondary psychoses, their identification may allow specific management. They may also shed light on various pathophysiological aspects of primary psychoses. Here we reviewed cases of secondary psychoses associated with brain anomalies, reported over a 20-year period in adolescents and young adults aged 13 to 30 years old. We considered age at first psychotic symptoms, relevant medical history, the nature of psychiatric symptoms, clinical red flags, the nature of the brain anomaly reported, and the underlying disease. We discuss the relevance of each brain area in light of normal brain function, recent case-control studies, and postulated pathophysiology. We show that anomalies in all regions, whether diffuse, multifocal, or highly localized, may lead to psychosis, without necessarily being associated with non-psychiatric symptoms. This underlines the interest of neuroimaging in the initial workup, and supports the hypothesis of psychosis as a global network dysfunction that involves many different regions.}, - language = {en}, - urldate = {2022-06-06}, - journal = {Neuroscience \& Biobehavioral Reviews}, - author = {Iftimovici, Anton and Chaumette, Boris and Duchesnay, Edouard and Krebs, Marie-Odile}, - month = jun, - year = {2022}, - keywords = {Neuroimaging, Brain anomalies, Pathophysiology, Primary and secondary early psychoses}, - pages = {104716}, - file = {Iftimovici et al. - 2022 - BRAIN ANOMALIES IN EARLY PSYCHOSIS FROM SECONDARY.pdf:/home/ed203246/snap/zotero-snap/common/Zotero/storage/WNBHGW9Y/Iftimovici et al. - 2022 - BRAIN ANOMALIES IN EARLY PSYCHOSIS FROM SECONDARY.pdf:application/pdf;ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/W42PI5EE/S0149763422002056.html:text/html}, -} - -@article{iftimovici_longitudinal_2023, - title = {Longitudinal {MicroRNA} {Signature} of {Conversion} to {Psychosis}}, - copyright = {All rights reserved}, - issn = {1745-1701}, - doi = {10.1093/schbul/sbad080}, - abstract = {BACKGROUND AND HYPOTHESIS: The emergence of psychosis in ultra-high-risk subjects (UHR) is influenced by gene-environment interactions that rely on epigenetic mechanisms such as microRNAs. However, whether they can be relevant pathophysiological biomarkers of psychosis' onset remains unknown. -STUDY DESIGN: We present a longitudinal study of microRNA expression, measured in plasma by high-throughput sequencing at baseline and follow-up, in a prospective cohort of 81 UHR, 35 of whom developed psychosis at follow-up (converters). We combined supervised machine learning and differential graph analysis to assess the relative weighted contribution of each microRNA variation to the difference in outcome and identify outcome-specific networks. We then applied univariate models to the resulting microRNA variations common to both strategies, to interpret them as a function of demographic and clinical covariates. -STUDY RESULTS: We identified 207 microRNA variations that significantly contributed to the classification. The differential network analysis found 276 network-specific correlations of microRNA variations. The combination of both strategies identified 25 microRNAs, whose gene targets were overrepresented in cognition and schizophrenia genome-wide association studies findings. Interpretable univariate models further supported the relevance of miR-150-5p and miR-3191-5p variations in psychosis onset, independent of age, sex, cannabis use, and medication. -CONCLUSIONS: In this first longitudinal study of microRNA variation during conversion to psychosis, we combined 2 methodologically independent data-driven strategies to identify a dynamic epigenetic signature of the emergence of psychosis that is pathophysiologically relevant.}, - language = {eng}, - journal = {Schizophrenia Bulletin}, - author = {Iftimovici, Anton and He, Qin and Jiao, Chuan and Duchesnay, Edouard and Krebs, Marie-Odile and Kebir, Oussama and Chaumette, Boris}, - month = aug, - year = {2023}, - pmid = {37607340}, - pages = {sbad080}, -} - -@article{jouvent_longitudinal_2012, - title = {Longitudinal changes of cortical morphology in {CADASIL}}, - volume = {33}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1558-1497}, - doi = {10.1016/j.neurobiolaging.2011.09.013}, - abstract = {In CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leucoencephalopathy), a genetic model of subcortical ischemic vascular dementia (SIVD), clinical status was previously found related to cortex morphology. In the present report, alterations of cortex morphology and their links to clinical worsening were investigated in 190 CADASIL patients followed during 24.4 months. Linear models were used to test relationships between: (1) clinical worsening and changes of depth of cortical sulci and of cortical thickness; (2) alterations of cortical morphology and changes of volume of white matter hyperintensities (WMH(v)) and of lacunar lesions (LL(v)). Reduction of sulcal depth was independently associated with increased time to complete trail making test A and B (p {\textless} 0.0001 and p = 0.004) and that of cortical thickness to increased disability (modified Rankin's scale, p = 0.008), while brain atrophy was only related to global cognitive worsening (Mattis dementia rating scale, p = 0.002). The impact of volume of lacunar lesions on cortical alterations was larger than that of volume of white matter hyperintensities. Cortical alterations, mainly related to lacunar lesions, evolve parallel to clinical worsening. These results further support the eventual role of cortical alterations in subcortical ischemic vascular dementia.}, - language = {eng}, - number = {5}, - journal = {Neurobiology of Aging}, - author = {Jouvent, Eric and Mangin, Jean-François and Duchesnay, Edouard and Porcher, Raphael and Düring, Marco and Mewald, Yvonne and Guichard, Jean-Pierre and Hervé, Dominique and Reyes, Sonia and Zieren, Nikola and Dichgans, Martin and Chabriat, Hugues}, - month = may, - year = {2012}, - pmid = {22000857}, - keywords = {Humans, Magnetic Resonance Imaging, Models, Neurological, Adult, Female, Male, Cerebral Cortex, Middle Aged, Nerve Fibers, Myelinated, Aged, Aged, 80 and over, Atrophy, CADASIL, Dementia, Vascular, Disease Progression, Follow-Up Studies, Longitudinal Studies}, - pages = {1002.e29--36}, - annote = {Times Cited: 0}, -} - -@article{laidi_decreased_2019, - title = {Decreased {Cortical} {Thickness} in the {Anterior} {Cingulate} {Cortex} in {Adults} with {Autism}}, - volume = {49}, - copyright = {All rights reserved}, - issn = {1573-3432}, - doi = {10.1007/s10803-018-3807-3}, - abstract = {Autism spectrum disorder (ASD) is a developmental disorder underdiagnosed in adults. To date, no consistent evidence of alterations in brain structure has been reported in adults with ASD and few studies were conducted at that age. We analyzed structural magnetic resonance imaging data from 167 high functioning adults with ASD and 195 controls. We ran our analyses on a discovery (n = 301) and a replication sample (n = 61). The right caudal anterior cingulate cortical thickness was significantly thinner in adults with ASD compared to controls in both the discovery and the replication sample. Our work underlines the relevance of studying the brain anatomy of an adult ASD population.}, - language = {eng}, - number = {4}, - journal = {Journal of Autism and Developmental Disorders}, - author = {Laidi, Charles and Boisgontier, Jennifer and de Pierrefeu, Amicie and Duchesnay, Edouard and Hotier, Sevan and d'Albis, Marc-Antoine and Delorme, Richard and Bolognani, Federico and Czech, Christian and Bouquet, Céline and Amestoy, Anouck and Petit, Julie and Holiga, Štefan and Dukart, Juergen and Gaman, Alexandru and Toledano, Elie and Ly-Le Moal, Myriam and Scheid, Isabelle and Leboyer, Marion and Houenou, Josselin}, - month = apr, - year = {2019}, - pmid = {30511125}, - keywords = {Humans, Magnetic Resonance Imaging, MRI, Adult, Adolescent, Female, Male, Autistic Disorder, Cerebral Cortex, Autism, Case-Control Studies, Anterior cingulate cortex, Adults}, - pages = {1402--1409}, -} - -@article{laidi_cerebellar_2022, - title = {Cerebellar atypicalities in autism?}, - copyright = {All rights reserved}, - issn = {0006-3223}, - url = {https://www.sciencedirect.com/science/article/pii/S0006322322012781}, - doi = {10.1016/j.biopsych.2022.05.020}, - abstract = {Background -The cerebellum contains more than 50\% of the brain neurons and is involved in social cognition. Cerebellar anatomical atypicalities have repeatedly been reported in individuals with autism. However, studies have yielded inconsistent findings, likely because of a lack of statistical power, and did not capture the clinical and neuroanatomical diversity of autism. Our aim was to better understand cerebellar anatomy and its diversity in autism. -Methods -We studied the cerebellar grey matter morphology in 274 individuals with autism and 219 controls of a multicenter European cohort (EU-AIMS LEAP). To ensure the robustness of our results, we conducted lobular parcellation of the cerebellum with two different pipelines in addition to voxel-based morphometry. We performed statistical analyses with linear, multivariate - including normative modeling - and a meta-analytic approach to capture the diversity of cerebellar anatomy in individuals with autism and controls. Last, we performed a dimensional analysis of cerebellar anatomy in an independent cohort of 352 individuals with autism-related symptoms. -Results -We did not find any significant difference in the cerebellum when comparing individuals with autism and controls using linear models. In addition, there were no significant deviations in our normative models in the cerebellum in individuals with autism. Finally, we found no evidence of cerebellar atypicalities related either to age, IQ, sex or social functioning in individuals with autism. -Conclusions -Despite positive results published in the last decade from relatively small samples, our results suggest that there is no striking difference in cerebellar anatomy of individuals with autism.}, - language = {en}, - urldate = {2022-05-30}, - journal = {Biological Psychiatry}, - author = {Laidi, Charles and Floris, Dorothea L. and Tillmann, Julian and Elandaloussi, Yannis and Zabihi, Mariam and Charman, Tony and Wolfers, Thomas and Durston, Sarah and Moessnang, Caroline and Dell’Acqua, Flavio and Ecker, Christine and Loth, Eva and Murphy, Declan and Baron-Cohen, Simon and Buitelaar, Jan K. and Marquand, Andre F. and Beckmann, Christian F. and Frouin, Vincent and Leboyer, Marion and Duchesnay, Edouard and Coupé, Pierrick and Houenou, Josselin}, - month = may, - year = {2022}, - keywords = {MRI, Cerebellum, Autism, Parcellation, Volumetry, Normative Modelling}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/MCF564BJ/S0006322322012781.html:text/html}, -} - -@article{mangin_brain_2004, - title = {Brain morphometry using {3D} moment invariants}, - volume = {8}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1361-8415}, - doi = {10.1016/j.media.2004.06.016}, - abstract = {This paper advocates the use of shape descriptors based on moments of 3D coordinates for morphometry of the cortical sulci. These descriptors, which have been introduced more than a decade ago, are invariant relatively to rotations, translations and scale and can be computed for any topology. A rapid insight into the derivation of these invariants is proposed first. Then, their potential to characterize shapes is shown from a principal component analysis of the 12 first invariants computed for 12 different deep brain structures manually drawn for 7 different brains. Finally, these invariants are used to find some correlates of handedness and sex among the shapes of 116 different cortical sulci automatically identified in each of 142 brains of the ICBM database.}, - language = {eng}, - number = {3}, - journal = {Medical Image Analysis}, - author = {Mangin, J.-F. and Poupon, F. and Duchesnay, E. and Rivière, D. and Cachia, A. and Collins, D. L. and Evans, A. C. and Régis, J.}, - month = sep, - year = {2004}, - pmid = {15450214}, - keywords = {Algorithms, Humans, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Pattern Recognition, Automated, Female, Male, Cerebral Cortex, Computer Simulation, Functional Laterality, Models, Biological}, - pages = {187--196}, -} - -@article{mangin_framework_2004, - title = {A framework to study the cortical folding patterns}, - volume = {23 Suppl 1}, - copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)}, - issn = {1053-8119}, - doi = {10.1016/j.neuroimage.2004.07.019}, - abstract = {This paper describes a decade-long research program focused on the variability of the cortical folding patterns. The program has developed a framework of using artificial neuroanatomists that are trained to identify sulci from a database. The framework relies on a renormalization of the brain warping problem, which consists in matching the cortices at the scale of the folds. Another component of the program is the search for the alphabet of the folding patterns, namely, a list of indivisible elementary sulci. The search relies on the study of the cortical folding process using antenatal imaging and on backward simulations of morphogenesis aimed at revealing traces of the embryologic dimples in the mature cortical surface. The importance of sulcal-based morphometry is illustrated by a simple study of the correlates of handedness on asymmetry indices. The study shows for instance that the central sulcus is larger in the dominant hemisphere.}, - language = {eng}, - journal = {NeuroImage}, - author = {Mangin, J.-F. and Rivière, D. and Cachia, A. and Duchesnay, E. and Cointepas, Y. and Papadopoulos-Orfanos, D. and Scifo, P. and Ochiai, T. and Brunelle, F. and Régis, J.}, - year = {2004}, - pmid = {15501082}, - keywords = {Humans, Brain Mapping, Image Processing, Computer-Assisted, Female, Cerebral Cortex, Computer Simulation, Databases, Factual, Dominance, Cerebral, Pregnancy, Terminology as Topic}, - pages = {S129--138}, -} - -@article{piguet_irritability_2021, - title = {Irritability {Is} {Associated} {With} {Decreased} {Cortical} {Surface} {Area} and {Anxiety} {With} {Decreased} {Gyrification} {During} {Brain} {Development}}, - volume = {12}, - copyright = {All rights reserved}, - issn = {1664-0640}, - doi = {10.3389/fpsyt.2021.744419}, - abstract = {Background: Brain development is of utmost importance for the emergence of psychiatric disorders, as the most severe of them arise before 25 years old. However, little is known regarding how early transdiagnostic symptoms, in a dimensional framework, are associated with cortical development. Anxiety and irritability are central vulnerability traits for subsequent mood and anxiety disorders. In this study, we investigate how these dimensions are related to structural changes in the brain to understand how they may increase the transition risk to full-blown disorders. Methods: We used the opportunity of an open access developmental cohort, the Healthy Brain Network, to investigate associations between cortical surface markers and irritability and anxiety scores as measured by parents and self-reports. Results: We found that in 658 young people (with a mean age of 11.6) the parental report of irritability is associated with decreased surface area in the bilateral rostral prefrontal cortex and the precuneus. Furthermore, parental reports of anxiety were associated with decreased local gyrification index in the anterior cingulate cortex and dorsomedial prefrontal cortex. Conclusions: These results are consistent with current models of emotion regulation network maturation, showing decreased surface area or gyrification index in regions associated with impaired affective control in mood and anxiety disorders. Our results highlight how dimensional traits may increase vulnerability for these disorders.}, - language = {eng}, - journal = {Frontiers in Psychiatry}, - author = {Piguet, Camille and Mihailov, Angeline and Grigis, Antoine and Laidi, Charles and Duchesnay, Edouard and Houenou, Josselin}, - year = {2021}, - pmid = {34630188}, - pmcid = {PMC8492928}, - keywords = {MRI, anxiety, development, dimensional model, gyrification index, irritability}, - pages = {744419}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/6S2MLA6N/Piguet et al. - 2021 - Irritability Is Associated With Decreased Cortical.pdf:application/pdf}, -} - -@article{poiret_fast_2023, - title = {A fast and robust hippocampal subfields segmentation: {HSF} revealing lifespan volumetric dynamics}, - volume = {17}, - copyright = {All rights reserved}, - issn = {1662-5196}, - shorttitle = {A fast and robust hippocampal subfields segmentation}, - url = {https://www.frontiersin.org/articles/10.3389/fninf.2023.1130845}, - abstract = {The hippocampal subfields, pivotal to episodic memory, are distinct both in terms of cyto- and myeloarchitectony. Studying the structure of hippocampal subfields in vivo is crucial to understand volumetric trajectories across the lifespan, from the emergence of episodic memory during early childhood to memory impairments found in older adults. However, segmenting hippocampal subfields on conventional MRI sequences is challenging because of their small size. Furthermore, there is to date no unified segmentation protocol for the hippocampal subfields, which limits comparisons between studies. Therefore, we introduced a novel segmentation tool called HSF short for hippocampal segmentation factory, which leverages an end-to-end deep learning pipeline. First, we validated HSF against currently used tools (ASHS, HIPS, and HippUnfold). Then, we used HSF on 3,750 subjects from the HCP development, young adults, and aging datasets to study the effect of age and sex on hippocampal subfields volumes. Firstly, we showed HSF to be closer to manual segmentation than other currently used tools (p {\textless} 0.001), regarding the Dice Coefficient, Hausdorff Distance, and Volumetric Similarity. Then, we showed differential maturation and aging across subfields, with the dentate gyrus being the most affected by age. We also found faster growth and decay in men than in women for most hippocampal subfields. Thus, while we introduced a new, fast and robust end-to-end segmentation tool, our neuroanatomical results concerning the lifespan trajectories of the hippocampal subfields reconcile previous conflicting results.}, - urldate = {2023-11-25}, - journal = {Frontiers in Neuroinformatics}, - author = {Poiret, Clement and Bouyeure, Antoine and Patil, Sandesh and Grigis, Antoine and Duchesnay, Edouard and Faillot, Matthieu and Bottlaender, Michel and Lemaitre, Frederic and Noulhiane, Marion}, - year = {2023}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/9MA6ZDZR/Poiret et al. - 2023 - A fast and robust hippocampal subfields segmentati.pdf:application/pdf}, -} - -@article{poiret_attention-gated_2024, - title = {Attention-gated {3D} {CapsNet} for robust hippocampal segmentation}, - volume = {11}, - copyright = {All rights reserved}, - issn = {2329-4302}, - doi = {10.1117/1.JMI.11.1.014003}, - abstract = {PURPOSE: The hippocampus is organized in subfields (HSF) involved in learning and memory processes and widely implicated in pathologies at different ages of life, from neonatal hypoxia to temporal lobe epilepsy or Alzheimer's disease. Getting a highly accurate and robust delineation of sub-millimetric regions such as HSF to investigate anatomo-functional hypotheses is a challenge. One of the main difficulties encountered by those methodologies is related to the small size and anatomical variability of HSF, resulting in the scarcity of manual data labeling. Recently introduced, capsule networks solve analogous problems in medical imaging, providing deep learning architectures with rotational equivariance. Nonetheless, capsule networks are still two-dimensional and unassessed for the segmentation of HSF. -APPROACH: We released a public 3D Capsule Network (3D-AGSCaps, https://github.com/clementpoiret/3D-AGSCaps) and compared it to equivalent architectures using classical convolutions on the automatic segmentation of HSF on small and atypical datasets (incomplete hippocampal inversion, IHI). We tested 3D-AGSCaps on three datasets with manually labeled hippocampi. -RESULTS: Our main results were: (1) 3D-AGSCaps produced segmentations with a better Dice Coefficient compared to CNNs on rotated hippocampi (p=0.004, cohen's d=0.179); (2) on typical subjects, 3D-AGSCaps produced segmentations with a Dice coefficient similar to CNNs while having 15 times fewer parameters (2.285M versus 35.069M). This may greatly facilitate the study of atypical subjects, including healthy and pathological cases like those presenting an IHI. -CONCLUSION: We expect our newly introduced 3D-AGSCaps to allow a more accurate and fully automated segmentation on atypical populations, small datasets, as well as on and large cohorts where manual segmentations are nearly intractable.}, - language = {eng}, - number = {1}, - journal = {Journal of Medical Imaging (Bellingham, Wash.)}, - author = {Poiret, Clement and Bouyeure, Antoine and Patil, Sandesh and Boniteau, Cécile and Duchesnay, Edouard and Grigis, Antoine and Lemaitre, Frederic and Noulhiane, Marion}, - month = jan, - year = {2024}, - pmid = {38173654}, - pmcid = {PMC10760147}, - keywords = {MRI, convolutional neural networks, deep learning, equivariance, hippocampal subfields}, - pages = {014003}, -} - -@article{stout_accumulation_2020, - title = {Accumulation of {Lithium} in the {Hippocampus} of {Patients} {With} {Bipolar} {Disorder}: {A} {Lithium}-7 {Magnetic} {Resonance} {Imaging} {Study} at 7 {Tesla}}, - volume = {88}, - copyright = {All rights reserved}, - issn = {1873-2402}, - shorttitle = {Accumulation of {Lithium} in the {Hippocampus} of {Patients} {With} {Bipolar} {Disorder}}, - doi = {10.1016/j.biopsych.2020.02.1181}, - abstract = {BACKGROUND: Lithium (Li) is a first-line treatment for bipolar disorder (BD). To study its cerebral distribution and association with plasma concentrations, we used 7Li magnetic resonance imaging at 7T in euthymic patients with BD treated with Li carbonate for at least 2 years. -METHODS: Three-dimensional 7Li magnetic resonance imaging scans (N = 21) were acquired with an ultra-short echo-time sequence using a non-Cartesian k-space sampling scheme. Lithium concentrations ([Li]) were estimated using a phantom replacement approach accounting for differential T1 and T2 relaxation effects. In addition to the determination of mean regional [Li] from 7 broad anatomical areas, voxel- and parcellation-based group analyses were conducted for the first time for 7Li magnetic resonance imaging. -RESULTS: Using unprecedented spatial sensitivity and specificity, we were able to confirm the heterogeneity of the brain Li distribution and its interindividual variability, as well as the strong correlation between plasma and average brain [Li] ([Li]B ≈ 0.40 × [Li]P, R = .74). Remarkably, our statistical analysis led to the identification of a well-defined and significant cluster corresponding closely to the left hippocampus for which high Li content was displayed consistently across our cohort. -CONCLUSIONS: This observation could be of interest considering 1) the major role of the hippocampus in emotion processing and regulation, 2) the consistent atrophy of the hippocampus in untreated patients with BD, and 3) the normalization effect of Li on gray matter volumes. This study paves the way for the elucidation of the relationship between Li cerebral distribution and its therapeutic response, notably in newly diagnosed patients with BD.}, - language = {eng}, - number = {5}, - journal = {Biological Psychiatry}, - author = {Stout, Jacques and Hozer, Franz and Coste, Arthur and Mauconduit, Franck and Djebrani-Oussedik, Nouzha and Sarrazin, Samuel and Poupon, Joel and Meyrel, Manon and Romanzetti, Sandro and Etain, Bruno and Rabrait-Lerman, Cécile and Houenou, Josselin and Bellivier, Frank and Duchesnay, Edouard and Boumezbeur, Fawzi}, - month = sep, - year = {2020}, - pmid = {32340717}, - keywords = {Brain, Hippocampus, Bipolar disorder (BD), High magnetic field, Lithium-7 ((7)Li), Magnetic resonance imaging (MRI)}, - pages = {426--433}, - file = {Full Text:/home/ed203246/snap/zotero-snap/common/Zotero/storage/T5KTTVNV/Stout et al. - 2020 - Accumulation of Lithium in the Hippocampus of Pati.pdf:application/pdf}, -} - -@patent{duchesnay_method_nodate, - title = {Method for {Developing} an {Information} {Prediction} {Device}, {Use} {Thereof}, and {Corresponding} {Storage} {Medium} and {Apparatus}}, - copyright = {All rights reserved}, - author = {Duchesnay, E}, -} - -@misc{dufumier_rethinking_2023, - title = {Rethinking {Positive} {Sampling} for {Contrastive} {Learning} with {Kernel}}, - copyright = {All rights reserved}, - url = {http://arxiv.org/abs/2206.01646}, - doi = {10.48550/arXiv.2206.01646}, - abstract = {Data augmentation is a crucial component in unsupervised contrastive learning (CL). It determines how positive samples are defined and, ultimately, the quality of the representation. While efficient augmentations have been found for standard vision datasets, such as ImageNet, it is still an open problem in other applications, such as medical imaging, or in datasets with easy-to-learn but irrelevant imaging features. In this work, we propose a new way to define positive samples using kernel theory along with a novel loss called decoupled uniformity. We propose to integrate prior information, learnt from generative models or given as auxiliary attributes, into contrastive learning, to make it less dependent on data augmentation. We draw a connection between contrastive learning and the conditional mean embedding theory to derive tight bounds on the downstream classification loss. In an unsupervised setting, we empirically demonstrate that CL benefits from generative models, such as VAE and GAN, to less rely on data augmentations. We validate our framework on vision datasets including CIFAR10, CIFAR100, STL10 and ImageNet100 and a brain MRI dataset. In the weakly supervised setting, we demonstrate that our formulation provides state-of-the-art results.}, - urldate = {2022-06-07}, - author = {Dufumier, Benoit and Barbano, Carlo Alberto and Louiset, Robin and Duchesnay, Edouard and Gori, Pietro}, - year = {2023}, - keywords = {Computer Science - Computer Vision and Pattern Recognition}, - file = {arXiv Fulltext PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/3IVNUSLV/Dufumier et al. - 2022 - Rethinking Positive Sampling for Contrastive Learn.pdf:application/pdf;arXiv.org Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/U5IGNH4D/2206.html:text/html}, -} - -@phdthesis{duchesnay_neuroimaging_2020, - type = {thesis}, - title = {Neuroimaging {Signatures} of {Brain} {Disorders}: {Fighting} {Overfitting} in {Predictive} {Models}}, - copyright = {All rights reserved}, - shorttitle = {Neuroimaging {Signatures} of {Brain} {Disorders}}, - url = {https://hal-cea.archives-ouvertes.fr/tel-03408786}, - language = {en}, - urldate = {2021-10-29}, - school = {Université Paris-Saclay, FRA.}, - author = {Duchesnay, Edouard}, - month = jul, - year = {2020}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/4Q6MBEW2/Duchesnay - 2020 - Neuroimaging Signatures of Brain Disorders Fighti.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/64CYECSK/tel-03408786.html:text/html}, -} - -@article{le_guen_genetic_2018, - title = {Genetic {Influence} on the {Sulcal} {Pits}: {On} the {Origin} of the {First} {Cortical} {Folds}}, - volume = {28}, - issn = {1047-3211}, - shorttitle = {Genetic {Influence} on the {Sulcal} {Pits}}, - url = {https://doi.org/10.1093/cercor/bhx098}, - doi = {10.1093/cercor/bhx098}, - abstract = {The influence of genes on cortical structures has been assessed through various phenotypes. The sulcal pits, which are the putative first cortical folds, have for long been assumed to be under tight genetic control, but this was never quantified. We estimated the pit depth heritability in various brain regions using the high quality and large sample size of the Human Connectome Project pedigree cohort. Analysis of additive genetic variance indicated that their heritability ranges between 0.2 and 0.5 and displays a regional genetic control with an overall symmetric pattern between hemispheres. However, a noticeable asymmetry of heritability estimates is observed in the superior temporal sulcus and could thus be related to language lateralization. The heritability range estimated in this study reinforces the idea that cortical shape is determined primarily by nongenetic factors, which is consistent with the important increase of cortical folding from birth to adult life and thus predominantly constrained by environmental factors. Nevertheless, the genetic cues, implicated with various local levels of heritability in the formation of sulcal pits, play a fundamental role in the normal gyral pattern development. Quantifying their influence and identifying the underlying genetic variants would provide insight into neurodevelopmental disorders.}, - number = {6}, - urldate = {2024-03-12}, - journal = {Cerebral Cortex}, - author = {Le Guen, Yann and Auzias, Guillaume and Leroy, François and Noulhiane, Marion and Dehaene-Lambertz, Ghislaine and Duchesnay, Edouard and Mangin, Jean-François and Coulon, Olivier and Frouin, Vincent}, - month = jun, - year = {2018}, - keywords = {imaging-genetic, sulcal pits, STS, brain asymmetry}, - pages = {1922--1933}, - annote = {MEDLINE:28444225}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {The following values have no corresponding Zotero field:label: ACL}, - annote = {Unati}, - annote = {UnicogPMID: 28444225}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/54XH832D/Le Guen et al. - 2018 - Genetic Influence on the Sulcal Pits On the Origi.pdf:application/pdf;Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/IW6UP4ZS/Genetic-Influence-on-the-Sulcal-Pits-On-the-Origin.html:text/html}, -} - -@article{lebenberg_framework_2018, - title = {A framework based on sulcal constraints to align preterm, infant and adult human brain images acquired in vivo and post mortem}, - volume = {223}, - issn = {1863-2661}, - url = {https://doi.org/10.1007/s00429-018-1735-9}, - doi = {10.1007/s00429-018-1735-9}, - abstract = {Robust spatial alignment of post mortem data and in vivo MRI acquisitions from different ages, especially from the early developmental stages, into standard spaces is still a bottleneck hampering easy comparison with the mainstream neuroimaging results. In this paper, we test a landmark-based spatial normalization strategy as a framework for the seamless integration of any macroscopic dataset in the context of the Human Brain Project (HBP). This strategy stems from an approach called DISCO embedding sulcal constraints in a registration framework used to initialize DARTEL, the widely used spatial normalization approach proposed in the SPM software. We show that this strategy is efficient with a heterogeneous dataset including challenging data as preterm newborns, infants, post mortem histological data and a synthetic atlas computed from averaging the ICBM database, as well as more commonly studied data acquired in vivo in adults. We then describe some perspectives for a research program aiming at improving folding pattern matching for atlas inference in the context of the future HBP’s portal.}, - language = {en}, - number = {9}, - urldate = {2024-03-12}, - journal = {Brain Structure and Function}, - author = {Lebenberg, J. and Labit, M. and Auzias, G. and Mohlberg, H. and Fischer, C. and Rivière, D. and Duchesnay, E. and Kabdebon, C. and Leroy, F. and Labra, N. and Poupon, F. and Dickscheid, T. and Hertz-Pannier, L. and Poupon, C. and Dehaene-Lambertz, G. and Hüppi, P. and Amunts, K. and Dubois, J. and Mangin, J.-F.}, - month = dec, - year = {2018}, - keywords = {Algorithms, Brain, Humans, Magnetic Resonance Imaging, Software, MRI, Image Processing, Computer-Assisted, Adult, Middle Aged, Databases, Factual, Aged, Aged, 80 and over, Atlases as Topic, Cytoarchitecture, Diffeomorphism, Folding pattern, HBP, Infant, Newborn, Infant, Premature, Spatial normalization}, - pages = {4153--4168}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/UTZ99AGC/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8F53LJM9/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf;Submitted Version:/home/ed203246/snap/zotero-snap/common/Zotero/storage/QM4UDBZI/Lebenberg et al. - 2018 - A framework based on sulcal constraints to align p.pdf:application/pdf}, -} - -@article{mangin_neocortical_2020, - title = {Neocortical morphometry in {Huntington}'s disease: {Indication} of the coexistence of abnormal neurodevelopmental and neurodegenerative processes}, - volume = {26}, - issn = {2213-1582}, - shorttitle = {Neocortical morphometry in {Huntington}'s disease}, - url = {https://www.sciencedirect.com/science/article/pii/S2213158220300486}, - doi = {10.1016/j.nicl.2020.102211}, - abstract = {Huntington's disease (HD) is an inherited, autosomal dominant disorder that is characteristically thought of as a degenerative disorder. Despite cellular and molecular grounds suggesting HD could also impact normal development, there has been scarce systems-level data obtained from in vivo human studies supporting this hypothesis. Sulcus-specific morphometry analysis may help disentangle the contribution of coexisting neurodegenerative and neurodevelopmental processes, but such an approach has never been used in HD. Here, we investigated cortical sulcal depth, related to degenerative process, as well as cortical sulcal length, related to developmental process, in early-stage HD and age-matched healthy controls. This morphometric analysis revealed significant differences in the HD participants compared with the healthy controls bilaterally in the central and intra-parietal sulcus, but also in the left intermediate frontal sulcus and calcarine fissure. As the primary visual cortex is not connected to the striatum, the latter result adds to the increasing in vivo evidence for primary cortical degeneration in HD. Those sulcal measures that differed between HD and healthy populations were mainly atrophy-related, showing shallower sulci in HD. Conversely, the sulcal morphometry also revealed a crucial difference in the imprint of the Sylvian fissure that could not be related to loss of grey matter volume: an absence of asymmetry in the length of this fissure in HD. Strong asymmetry in that cortical region is typically observed in healthy development. As the formation of the Sylvian fissure appears early in utero, and marked asymmetry is specifically found in this area of the neocortex in newborns, this novel finding likely indicates the foetal timing of a disease-specific, genetic interplay with neurodevelopment.}, - urldate = {2024-03-12}, - journal = {NeuroImage: Clinical}, - author = {Mangin, Jean-Francois and Rivière, Denis and Duchesnay, Edouard and Cointepas, Yann and Gaura, Véronique and Verny, Christophe and Damier, Philippe and Krystkowiak, Pierre and Bachoud-Lévi, Anne-Catherine and Hantraye, Philippe and Remy, Philippe and Douaud, Gwenaëlle}, - month = jan, - year = {2020}, - keywords = {MRI, Asymmetry, Cortical morphometry, Huntington's disease, Neurodevelopment, Sylvian fissure}, - pages = {102211}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B9Z93VA9/S2213158220300486.html:text/html;Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/B5Y6HREA/Mangin et al. - 2020 - Neocortical morphometry in Huntington's disease I.pdf:application/pdf}, -} - -@article{hozer_lithium_2021, - title = {Lithium prevents grey matter atrophy in patients with bipolar disorder: an international multicenter study}, - volume = {51}, - issn = {0033-2917, 1469-8978}, - shorttitle = {Lithium prevents grey matter atrophy in patients with bipolar disorder}, - url = {https://www.cambridge.org/core/journals/psychological-medicine/article/abs/lithium-prevents-grey-matter-atrophy-in-patients-with-bipolar-disorder-an-international-multicenter-study/6267A7E11F17EFDF5857F06E4C233D4F}, - doi = {10.1017/S0033291719004112}, - abstract = {BackgroundLithium (Li) is the gold standard treatment for bipolar disorder (BD). However, its mechanisms of action remain unknown but include neurotrophic effects. We here investigated the influence of Li on cortical and local grey matter (GM) volumes in a large international sample of patients with BD and healthy controls (HC).MethodsWe analyzed high-resolution T1-weighted structural magnetic resonance imaging scans of 271 patients with BD type I (120 undergoing Li) and 316 HC. Cortical and local GM volumes were compared using voxel-wise approaches with voxel-based morphometry and SIENAX using FSL. We used multiple linear regression models to test the influence of Li on cortical and local GM volumes, taking into account potential confounding factors such as a history of alcohol misuse.ResultsPatients taking Li had greater cortical GM volume than patients without. Patients undergoing Li had greater regional GM volumes in the right middle frontal gyrus, the right anterior cingulate gyrus, and the left fusiform gyrus in comparison with patients not taking Li.ConclusionsOur results in a large multicentric sample support the hypothesis that Li could exert neurotrophic and neuroprotective effects limiting pathological GM atrophy in key brain regions associated with BD.}, - language = {en}, - number = {7}, - urldate = {2024-03-12}, - journal = {Psychological Medicine}, - author = {Hozer, Franz and Sarrazin, Samuel and Laidi, Charles and Favre, Pauline and Pauling, Melissa and Cannon, Dara and McDonald, Colm and Emsell, Louise and Mangin, Jean-François and Duchesnay, Edouard and Bellani, Marcella and Brambilla, Paolo and Wessa, Michele and Linke, Julia and Polosan, Mircea and Versace, Amelia and Phillips, Mary L. and Delavest, Marine and Bellivier, Frank and Hamdani, Nora and d'Albis, Marc-Antoine and Leboyer, Marion and Houenou, Josselin}, - month = may, - year = {2021}, - keywords = {MRI, lithium, Bipolar disorder, grey matter volume}, - pages = {1201--1210}, -} - -@article{laidi_cerebellar_2019, - title = {Cerebellar parcellation in schizophrenia and bipolar disorder}, - volume = {140}, - copyright = {© 2019 John Wiley \& Sons A/S. Published by John Wiley \& Sons Ltd}, - issn = {1600-0447}, - url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acps.13087}, - doi = {10.1111/acps.13087}, - abstract = {Objective The cerebellum is involved in cognitive processing and emotion control. Cerebellar alterations could explain symptoms of schizophrenia spectrum disorder (SZ) and bipolar disorder (BD). In addition, literature suggests that lithium might influence cerebellar anatomy. Our aim was to study cerebellar anatomy in SZ and BD, and investigate the effect of lithium. Methods Participants from 7 centers worldwide underwent a 3T MRI. We included 182 patients with SZ, 144 patients with BD, and 322 controls. We automatically segmented the cerebellum using the CERES pipeline. All outputs were visually inspected. Results Patients with SZ showed a smaller global cerebellar gray matter volume compared to controls, with most of the changes located to the cognitive part of the cerebellum (Crus II and lobule VIIb). This decrease was present in the subgroup of patients with recent-onset SZ. We did not find any alterations in the cerebellum in patients with BD. However, patients medicated with lithium had a larger size of the anterior cerebellum, compared to patients not treated with lithium. Conclusion Our multicenter study supports a distinct pattern of cerebellar alterations in SZ and BD.}, - language = {en}, - number = {5}, - urldate = {2024-03-12}, - journal = {Acta Psychiatrica Scandinavica}, - author = {Laidi, C. and Hajek, T. and Spaniel, F. and Kolenic, M. and d'Albis, M.-A. and Sarrazin, S. and Mangin, J.-F. and Duchesnay, E. and Brambilla, P. and Wessa, M. and Linke, J. and Polosan, M. and Favre, P. and Versace, A. L. and Phillips, M. L. and Manjon, J. V. and Romero, J. E. and Hozer, F. and Leboyer, M. and Coupe, P. and Houenou, J.}, - year = {2019}, - note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acps.13087}, - keywords = {cerebellum, lithium, parcellation, segmentation}, - pages = {468--476}, - file = {Texte intégral:/home/ed203246/snap/zotero-snap/common/Zotero/storage/8ZYKANPT/Laidi et al. - 2019 - Cerebellar parcellation in schizophrenia and bipol.pdf:application/pdf}, -} - -@inproceedings{auriau_supervised_2024, - title = {Supervised {Diagnosis} {Prediction} from {Cortical} {Sulci}: {Toward} the {Discovery} of {Eurodevelopmental} {Biomarkers} in {Mental} {Disorders}}, - shorttitle = {Supervised {Diagnosis} {Prediction} from {Cortical} {Sulci}}, - url = {https://hal.science/hal-04494994}, - abstract = {Recent advances in machine learning applied to structural magnetic resonance imaging (sMRI) may highlight abnormalities in brain anatomy associated with mental disorders. These disorders are multifactorial, resulting from a complex combination of neurodevelopmental and environmental factors. In particular, such factors are present in cortical sulci, whose shapes are determined very early in brain development and are a valuable proxy for capturing specifically the neurodevelopmental contribution of brain anatomy. This paper explores whether the shapes of cortical sulci can be used for diagnosis prediction using deep learning models. These models are applied to three mental disorders (autism spectrum disorder, bipolar disorder, and schizophrenia) in large multicentric datasets. We demonstrate that the neurodevelopmental underpinnings of these disorders can be captured withsMRI. Finally, we show the potential of visual explanations of models’ decisions in discovering biomarkers for mental disorders.}, - language = {en}, - urldate = {2024-03-13}, - booktitle = {21st {IEEE} {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2024)}, - author = {Auriau, Pierre and Grigis, Antoine and Dufumier, Benoit and Louiset, Robin and Gori, Pietro and Mangin, Jean-François and Duchesnay, Edouard}, - month = may, - year = {2024}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/USG8TCSY/Auriau et al. - 2024 - SUPERVISED DIAGNOSIS PREDICTION FROM CORTICAL SULC.pdf:application/pdf}, -} - -@inproceedings{louiset_sepvae_2024, - title = {{SepVAE}: a contrastive {VAE} to separate pathological patterns from healthy ones}, - shorttitle = {{SepVAE}}, - url = {https://openreview.net/forum?id=yLySzM5yxs}, - abstract = {Contrastive Analysis VAE (CA-VAEs) is a family of Variational auto-encoders (VAEs) that aims at separating the common factors of variation between a {\textbackslash}textit\{background\} dataset (BG) ({\textbackslash}textit\{i.e.,\} healthy subjects) and a {\textbackslash}textit\{target\} dataset (TG) ({\textbackslash}textit\{i.e.,\} patients) from the ones that only exist in the target dataset. To do so, these methods separate the latent space into a set of {\textbackslash}textbf\{salient\} features ({\textbackslash}textit\{i.e.,\} proper to the target dataset) and a set of {\textbackslash}textbf\{common\} features ({\textbackslash}textit\{i.e.,\} exist in both datasets). Currently, all CA-VAEs models fail to prevent sharing of information between the latent spaces and to capture all salient factors of variation. To this end, we introduce two crucial regularization losses: a disentangling term between common and salient representations and a classification term between background and target samples in the salient space. We show a better performance than previous CA-VAEs methods on three medical applications and a natural images dataset (CelebA).}, - language = {en}, - urldate = {2024-04-08}, - booktitle = {Medical {Imaging} with {Deep} {Learning} ({MIDL}) 2024}, - author = {Louiset, Robin and Duchesnay, Edouard and Antoine, Grigis and Dufumier, Benoit and Gori, Pietro}, - month = feb, - year = {2024}, - file = {Full Text PDF:/home/ed203246/snap/zotero-snap/common/Zotero/storage/YMY468M3/Louiset et al. - 2024 - SepVAE a contrastive VAE to separate pathological.pdf:application/pdf}, -} - -@inproceedings{petiton_sara_how_2024, - title = {How and why does deep ensemble coupled with transfer learning increase performance in bipolar disorder and schizophrenia classification}, - booktitle = {21st {IEEE} {International} {Symposium} on {Biomedical} {Imaging} ({ISBI} 2024)}, - author = {Petiton, Sara and Grigis, Antoine and Dufumier, Benoit and Duchesnay, Edouard}, - year = {2024}, -} - -@article{dufumier_exploring_2024, - title = {Exploring the potential of representation and transfer learning for anatomical neuroimaging: {Application} to psychiatry}, - volume = {296}, - issn = {1053-8119}, - shorttitle = {Exploring the potential of representation and transfer learning for anatomical neuroimaging}, - url = {https://www.sciencedirect.com/science/article/pii/S1053811924001605}, - doi = {10.1016/j.neuroimage.2024.120665}, - abstract = {The perspective of personalized medicine for brain disorders requires efficient learning models for anatomical neuroimaging-based prediction of clinical conditions. There is now a consensus on the benefit of deep learning (DL) in addressing many medical imaging tasks, such as image segmentation. However, for single-subject prediction problems, recent studies yielded contradictory results when comparing DL with Standard Machine Learning (SML) on top of classical feature extraction. Most existing comparative studies were limited in predicting phenotypes of little clinical interest, such as sex and age, and using a single dataset. Moreover, they conducted a limited analysis of the employed image pre-processing and feature selection strategies. This paper extensively compares DL and SML prediction capacity on five multi-site problems, including three increasingly complex clinical applications in psychiatry namely schizophrenia, bipolar disorder, and Autism Spectrum Disorder (ASD) diagnosis. To compensate for the relative scarcity of neuroimaging data on these clinical datasets, we also evaluate three pre-training strategies for transfer learning from brain imaging of the general healthy population: self-supervised learning, generative modeling and supervised learning with age. Overall, we find similar performance between randomly initialized DL and SML for the three clinical tasks and a similar scaling trend for sex prediction. This was replicated on an external dataset. We also show highly correlated discriminative brain regions between DL and linear ML models in all problems. Nonetheless, we demonstrate that self-supervised pre-training on large-scale healthy population imaging datasets (N≈10k), along with Deep Ensemble, allows DL to learn robust and transferable representations to smaller-scale clinical datasets (N≤1k). It largely outperforms SML on 2 out of 3 clinical tasks both in internal and external test sets. These findings suggest that the improvement of DL over SML in anatomical neuroimaging mainly comes from its capacity to learn meaningful and useful abstract representations of the brain anatomy, and it sheds light on the potential of transfer learning for personalized medicine in psychiatry}, - urldate = {2024-06-12}, - journal = {NeuroImage}, - author = {Dufumier, Benoit and Gori, Pietro and Petiton, Sara and Louiset, Robin and Mangin, Jean-François and Grigis, Antoine and Duchesnay, Edouard}, - month = aug, - year = {2024}, - keywords = {Anatomical neuroimaging, Deep learning, Individual subject prediction, Machine learning, Psychiatric disorders}, - pages = {120665}, - file = {ScienceDirect Snapshot:/home/ed203246/snap/zotero-snap/common/Zotero/storage/W82F8YSM/S1053811924001605.html:text/html}, -} diff --git a/collaborators.md b/collaborators.md deleted file mode 100644 index 56c50a5..0000000 --- a/collaborators.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -layout: page -title: -permalink: /collaborators/ ---- - -The {{site.title}} team has developped numerous collaborations with colleagues -in different institutions & companies. - - -{% assign collaborators_sorted = site.collaborators | sort: 'subcat' %} -{% assign collaborators_array = '' | split: ',' %} -{% for collab in collaborators_sorted %} - - {% unless collab.subcat == previous %} - {% assign collaborators_array = collaborators_array | push: collab.subcat %} - {% endunless %} - {% assign previous = collab.subcat %} -{% endfor %} -{% assign collaborators_sorted = site.collaborators | sort: 'joined' | reverse %} - -{% for item in collaborators_array %} - -
    -{% if item == 'academic' %} -

    Academic Institutions

    -{% elsif item == 'hospital' %} -

    Hospitals

    -{% elsif item == 'company' %} -

    Companies

    -{% endif %} -
    - -
    - {% for collab in collaborators_sorted %} - {% if collab.subcat contains item %} -
    -

    - {% if collab.avatar %} - - {% else %} - - {% endif %} - {{collab.name}} -

    -
    - {% endif %} - {% endfor %} -
    -
    - -{% endfor %} diff --git a/images/banner.png b/images/banner.png index 3007514..25da5e4 100644 Binary files a/images/banner.png and b/images/banner.png differ diff --git a/images/labs/architecture.png b/images/labs/architecture.png deleted file mode 100755 index e7c5042..0000000 Binary files a/images/labs/architecture.png and /dev/null differ diff --git a/images/labs/brainomics.png b/images/labs/brainomics.png deleted file mode 100755 index 497b0ba..0000000 Binary files a/images/labs/brainomics.png and /dev/null differ diff --git a/images/labs/cati.jpg b/images/labs/cati.jpg deleted file mode 100644 index b656b37..0000000 Binary files a/images/labs/cati.jpg and /dev/null differ diff --git a/images/labs/ginkgo.png b/images/labs/ginkgo.png deleted file mode 100644 index 212638e..0000000 Binary files a/images/labs/ginkgo.png and /dev/null differ diff --git a/images/labs/platform.jpg b/images/labs/platform.jpg deleted file mode 100755 index 1b3930b..0000000 Binary files a/images/labs/platform.jpg and /dev/null differ diff --git a/images/labs/signature.png b/images/labs/signature.png deleted file mode 100644 index aa884f4..0000000 Binary files a/images/labs/signature.png and /dev/null differ diff --git a/images/logo.png b/images/logo.png index 99896cc..309c9c6 100644 Binary files a/images/logo.png and b/images/logo.png differ diff --git a/images/people/a-grigis.jpg b/images/people/a-grigis.jpg deleted file mode 100644 index 3671937..0000000 Binary files a/images/people/a-grigis.jpg and /dev/null differ diff --git a/images/people/default.png b/images/people/default.png deleted file mode 100644 index cbdbc00..0000000 Binary files a/images/people/default.png and /dev/null differ diff --git a/images/people/e-duchesnay.png b/images/people/e-duchesnay.png deleted file mode 100644 index cc548d7..0000000 Binary files a/images/people/e-duchesnay.png and /dev/null differ diff --git a/images/people/legal/educhesnay_Formulaire-Droit-Image_photo_DCOM.pdf b/images/people/legal/educhesnay_Formulaire-Droit-Image_photo_DCOM.pdf deleted file mode 100644 index c01a11b..0000000 Binary files a/images/people/legal/educhesnay_Formulaire-Droit-Image_photo_DCOM.pdf and /dev/null differ diff --git a/images/research/architecture_isomap.png b/images/research/architecture_isomap.png deleted file mode 100644 index 45b1e6c..0000000 Binary files a/images/research/architecture_isomap.png and /dev/null differ diff --git a/images/research/brainomics_languageh2gwas.png b/images/research/brainomics_languageh2gwas.png deleted file mode 100644 index 40f8b39..0000000 Binary files a/images/research/brainomics_languageh2gwas.png and /dev/null differ diff --git a/images/research/ginkgo_micro.jpg b/images/research/ginkgo_micro.jpg deleted file mode 100644 index df60592..0000000 Binary files a/images/research/ginkgo_micro.jpg and /dev/null differ diff --git a/images/research/image.png b/images/research/image.png deleted file mode 100755 index 497b0ba..0000000 Binary files a/images/research/image.png and /dev/null differ diff --git a/images/research/platform_bhb.jpg b/images/research/platform_bhb.jpg deleted file mode 100644 index 12ea835..0000000 Binary files a/images/research/platform_bhb.jpg and /dev/null differ diff --git a/images/research/platform_surfify.png b/images/research/platform_surfify.png deleted file mode 100755 index 850880d..0000000 Binary files a/images/research/platform_surfify.png and /dev/null differ diff --git a/images/research/signature_big2small.png b/images/research/signature_big2small.png deleted file mode 100644 index dfc28c7..0000000 Binary files a/images/research/signature_big2small.png and /dev/null differ diff --git a/index.md b/index.md index 7d95569..4ca2738 100644 --- a/index.md +++ b/index.md @@ -2,43 +2,17 @@ layout: page_lab --- -{% assign lab = "gaia" %} -{% assign teams_sorted = site.labs | where: "cat", lab | where: "subcat", "team" | sort: "title" %} -{% assign cells_sorted = site.labs | where: "cat", lab | where: "subcat", "cell" | sort: "title" %} +{% assign labs_sorted = site.labs | sort: "title" %} +