C-PAC Version 1.3.0.post2 Beta

C-PAC v1.3.0 with the following updates:

• #844 resolved (666040a, d8ce36d)
• bids-validator installation repaired (bcabb15)

C-PAC Version 1.8.7 Beta

New Features

• Newly-Integrated Packages - these functionalities are now accessible via the cpac command-line wrapper:
  • cpac tsconcat: Timeseries Concatenation via the DAIR group’s tsconcat
  • cpac gradients: Gradients via the DAIR group’s ba-timeseries-gradients
• The FSL-BET brain mask generation option in C-PAC now has an optional RobustFOV sub-workflow to crop images ensuring removal of neck regions that may appear in the skull-stripped images for some harder-to-skullstrip data.
• C-PAC can now throttle memory usage of workflow steps to mitigate excessive memory usage, an issue which can cause C-PAC runs to be canceled when users pass a memory usage limit on a shared cluster.
  • For these throttled steps, C-PAC will allocate all available resources to each such step, so a multithreaded pipeline will run linearly at each of these steps.

Improvements

• Ingress of FreeSurfer outputs into C-PAC is now much more convenient, with the new ability to provide the FreeSurfer output directory path to C-PAC directly from the command line. This also facilitates easier automation of large-scale runs with many different FreeSurfer paths.
• Writing out the DVARS motion measure output is now optional.

Contributor Improvements

• Autoversioning and the documentation auto-updating of pipeline configuration files have been moved from the CI infrastructure to pre-commit.
  • In addition to simplifying the auto-updating process, this also keeps the versioning, config documentation, and Dockerfile setup updates within the same commit as the original contribution.

Bug Fixes

• Fixed a bug where ingressing fmriprep outputs into C-PAC with a blank nuisance confounds field in the C-PAC pipeline configuration file would cause a crash.
• Fixed a bug where spatial smoothing and z-scoring of final outputs would sometimes fail to run when running a C-PAC pipeline that would ingress fmriprep outputs.
• Fixed a bug where ingress of distortion correction-related field map metadata would sometimes fail to recognize both echo times, when there were two present, leading to an error message claiming an echo time is missing.
• Changed an extraneous default pipeline configuration setting - surface_connectivity is now disabled in the default configuration as intended.
• Updated the FSL-BET configuration options to automatically default -mask-boolean flag as on, and removed all mask-boolean keys from configs. This error caused the possibility of masking the brain too early in the pipeline which could have led to crashes when a downstream node expected a binary mask.

C-PAC Version 1.8.6 Beta

New Features

• C-PAC can now ingress fMRIPrep output data.
  • Users can now perform further processing on fMRIPrep-processed data through C-PAC, using any template-space processing they wish to employ. This includes using the nuisance confounds generated by fMRIPrep to perform nuisance denoising on the preprocessed BOLD data.
  • A fMRIPrep-ingress pre-configured pipeline configuration (pre-config) has been created to make it easy to get started. This pre-config can be modified to suit a user's specific processing needs.
  • This is part of a wider project leading to the ability to easily ingress any BIDS-format output directory.

Improvements

• The motion parameter and motion derivative outputs have been converted to BIDS-compliant formats.
• A tip box has been added to appear when C-PAC returns with a "missing outputs" error.
• The data configuration builder tool can now easily add FreeSurfer output directories for the purpose of ingressing FreeSurfer data into your C-PAC pipeline.
• A large number of C-PAC's dependencies has been upgraded to more recent versions, including
  • Ubuntu (18.04 'Bionic Beaver' → 22.04 'Jammy Jellyfish')
  • Python (3.7.13 → 3.10.6)
  • AFNI (21.1.00 'Domitian' → 23.3.09 'Septimius Severus')
  • ANTs (2.3.3 'Leptomyrmex' → 2.4.3 'Emplastus')
  • FSL (5.0.9 → 6.0.6.5)
  • Nipype (1.5.1 → 1.8.6)
• Please refer to the "Upgraded dependencies" section of the changelog for 1.8.6 or the release notes in the user guide for a full list of these upgrades.
• torch, a large dependency that is used by U-Net and nothing else in C-PAC, has been removed from the pre-installed dependencies in the C-PAC image and is now installed in the container at runtime if U-Net is selected in the configuration being run.

Bug Fixes

• When motion parameters are filtered, C-PAC now uses the filtered version of the motion parameters downstream - for example, in nuisance regression/denoising.
• Fixed a bug where some connectivity matrices wouldn't generate if anatomical and functional outputs were in different resolutions.
• Repaired the handling of 3dECM (network centrality) outputs for AFNI ≥ 21.1.1.
• Fixed a bug (introduced in v1.8.0) where sparsity thresholds were not being scaled for network centrality.
• Fixed a bug where calculate_motion_first would not calculate motion at all.
• Fixed an error message that was reporting missing resources in pipeline nodeblocks, but was referring to the incorrect nodeblock in question.

C-PAC Version 1.8.5 Beta

New Features

• Extension of Template-Space Processing.
  • In an effort to support compatibility with other tools being used in the field, C-PAC now has the option of performing several operations in template space, where they have historically only been supported within C-PAC in native space. These features now include:
    • Time series despiking via AFNI 3dDespike.
    • Nuisance correction and denoising.
    • Calculation of the ALFF, f/ALFF and ReHo derivatives.
    • Connectome computation (already supported; included for completeness)
• Improved Robustness of Default Pipeline Configuration.
  • A modified version of the legacy C-PAC default pipeline has been released that improves stability across datasets. This pipeline largely maintains the original preprocessing choices, with the modification of employing robust FSL BET for T1w brain mask generation rather than AFNI. This change was motivated by a difference in design of these two components, where AFNI would exclude ventricles from brain mask generation, occasionally leading to downstream errors in nuisance signal correction.
  • The pre-1.8.5 default pipeline is still available for users as a preconfigured pipeline under the name default-deprecated.
• Downsampling of surface data.
  • While surface analysis is typically performed on high resolution surfaces and then downsampled to the resolution of the structural images being acquired, further downsampling may be required when working with functional data. To minimize the influence of signal interpolation on downstream markers, such as Regional Homogeneity, we now support downsampling of surface data to a resolution that matches the input functional data resolution.
• Motion estimate filter forking capability expanded.
  • Previous versions of C-PAC allowed for the application of 0‒1 motion estimate filters. C-PAC now supports configuring any number of motion estimate filters; each filter is applied independently.
• Support for Fail-Fast workflow execution.
  • To minimize waste of computational resources and reduce the possibility of misunderstanding of partial derived datasets, the new fail-fast option in C-PAC tells the workflow engine to stop running in the event of any failed or incomplete processing step.

Improvements

• Freesurfer outputs ingress overhaul.
  • The process of ingressing Freesurfer recon-all outputs into the C-PAC pipeline has been streamlined. Freesurfer output directories are now linked in the C-PAC data configuration YAML files, rather than pipeline configurations, for each participant and session of data.
  • Preconfigured pipelines which employ Freesurfer-based surface processing, such as the abcd-options pipeline, now use the surface-derived T1w brain mask as the default, rather than redundantly computing separate masks.
• Output directory BIDS-Derivatives compliance and naming improvement.
  • The output files in template space now feature the specific space-* tag, mapping to standardized names for the template entities, instead of the more generic space-template tag.
  • Data that has been nuisance corrected now feature BIDS labels which name the user-provided regressor strategy name, instead of providing this information in the information-dense sidecar JSONs.
• Corrected erroneous forking in ABCD-options pipeline.
  • While no errors were produced in the terminal outputs, redundant computation was previously taking place which led to a slowdown for this configuration, or others which may have used the post-freesurfer processing blocks. The source of this issue has been identified and corrected.
• For Nilearn-generated correlation matrices, diagonals are now set to all 1s (were all 0s).
• Distortion correction improvements.
  • Fixed an issue where the distortion correction un-warps were not being applied to the final template-space BOLD time series data, depending on pipeline configuration decisions.
  • Replaces DwellTime with EffectiveEchoSpacing in the application of FSL FUGUE, consistent with the intention of the documentation and correcting inconsistent nomenclature.
  • Added the ability to ingress TotalReadoutTime from epi field map meta-data from JSON sidecars.
  • Added the ability to use TotalReadoutTime of epi field maps in the calculation of FSL topup distortion correction.
  • Identified future directions for refining distortion correction further, including the modernization of some libraries to support the adoption of the sdcflows library.
• Run directory and logging improvements.
  • Added a level of depth to working directories to match log and output directory structure.
  • Renamed participant-pipeline-level output directory prefix to pipeline_ to match log and working paths.
  • Added crash messages from during and before graph building to logs.
  • Added data-config-specific hash string to C-PAC-generated config files.

Error Fixes

• Single-step resampling has been fixed such that motion-corrected BOLD time series data is blocked from being used as the input, as the motion correction transforms are factored into the transform application.
• Fixed a bug in which generated pipeline configs were not representative of the input configurations being specified. The only affected configurable option discovered in testing was when seed-based correlation analysis was used, the engine was always reverting to the default configuration.
• Fixed bug that was causing cpac run to fail when passing a manual random seed via --random_seed rather than directly in the pipeline config file.
• Fixed an issue that was causing some epi field maps to not be ingressed if the BIDS tags were not in a specific (BIDS-compliant) order.
• Fixed an issue where phase-difference GRE field map files were not properly being ingressed if the filenames were not expected, such as including an index for cases with multiple maps.
• Fixed a bug where ALFF & f/ALFF would not run if frequency filtering was disabled earlier in the pipeline.
• Fixed a bug where Freesurfer directories were not successfully ingressed at runtime.
• Added public read access to some overly restricted packaged templates.
• Fixed a bug where the notch filter was always assuming the sampling frequency was 2.0.

C-PAC Version 1.8.4 Beta

Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3

• Fixed a bug that was causing single_step_resampling, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.
  • This bug caused any affected fmriprep-options-based pipeline configurations (including fx-options and rbc-options) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.
  • Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with desc-preproc and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.
  • If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.

Summary
Here’s what’s new with C-PAC Version 1.8.4

RBC-options pipeline
RBC-options pipeline was built and integrated in C-PAC based on the Reproducible Brain Charts initiative, which aims to aggregate and harmonize phenotypic and neuroimage data to delineate node mechanisms regarding developmental basis of psychopathology in youth and yield reproducible growth charts of brain development (Scopel Hoffman et. al., 2021)

Scopel Hoffmann, M., Salum, G., Moore, T. M., Milham, M., & Sattherwaite, T. (2021, December 13). Reproducible Brain Charts initiative - Reliability and Validity of Bifactor Models of Dimensional Psychopathology in Youth. doi:10.17605/OSF.IO/UWY5N

Surface outputs
Previously in C-PAC, the main output for the surface pipeline was the CIFTI timeseries (.dtseries) file. Now we are also outputting CIFTI parcellations (.dlabel) in Desikan-Killiany and Destrieux spaces in 164K and 32K resolutions.

Relicense
C-PAC was relicensed from BSD-3-Clause to LGPL-3.0-or-later. This license freely allows use, distribution, and modification under the conditions of disclosing the source, license and copyright notice, propagating the license in redistributions and when modified, stating what was changed. Any modifications to LGPL-covered components are required to be made available under the same version or newer of the LGPL or the more restrictive GPL.

Additional v1.8.4 improvements, changes, and fixes can be seen throughout the rest of this release note.

Pipeline Harmonization Updates

• Updated the rbc-options configuration, based on the Reproducible Brain Charts (RBC) initiative.
• Updated XCP-QC files to better adhere to the PennLINC XCPEngine pipeline.
  • https://www.pennlinc.io/
  • https://xcpengine.readthedocs.io/

New Features

• Surface pipeline now outputs 164k and 32k CIFTI parcellations in each of Desikan-Killiany and Destrieux spaces to output directory.
• Added a log of expected outputs, generated at the beginning of each C-PAC run.

Improvements

• Made ndmg correlation matrices a configurable option, as it used to automatically run for all pipelines before.
• Made surface output filenames more BIDS-compliant.
• Added the ability to follow symlinks for BIDS directories.
• Updated templates used for rodent pipeline and added outputs that were missing.
• Added the ability to disable the exception raised if the initial resource check estimates more memory is needed.
• Added --runtime_usage and --runtime_buffer flags and related pipeline config entries and functionality.
• Added additional error checks and a more informative message for node block connecting in the engine.
• Expanded some surface post-processing workflows to be more flexible with other pipeline configurations.
• Added list of preconfigured pipelines to the usage string.
• Relicensed C-PAC from BSD-3-Clause to LGPL-3.0-or-later.

Bug Fixes

• Fixed a bug that was causing single_step_resampling to crash with 3dVolReg.
• Fixed a bug that was causing datasets containing phase-difference field maps to crash.
• Fixed a merge error preventing QC files and surface derivatives copying to output directory and renaming connectome → connectivity matrix files.
• Fixed a bug where subsequent subjects' logs were being appended to prior subjects' logs.
• Fixed a bug in which ITK header imprecision was causing N4 bias correction to crash.
• Fixed a bug where a node with zero nanoseconds in timing information causes report generation to fail.
• Fixed a bug in which --tracking_opt-out was not applied to calls to utils.

Developer Improvements

• Updated CI to only rebuild software dependencies on change.
• Added lint definition file.
• Added smoke tests.

C-PAC Version 1.8.3 Beta

This version of C-PAC is deprecated due to a bug in single_step_resampling. Unless you have a specific reason to use this version of C-PAC, we recommend upgrading to at least version 1.8.4. See https://fcp-indi.github.io/docs/latest/user/release_notes/v1.8.4 for more information about C-PAC v1.8.4. To use this version anyway, you can pull fcpindi/c-pac:release-v1.8.3-DEPRECATED from Docker Hub.

Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3

• Fixed a bug that was causing single_step_resampling, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.

  • This bug caused any affected fmriprep-options-based pipeline configurations (including fx-options and rbc-options) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.

  • Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with desc-preproc and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.

  • If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.

---

New features

• Added XCP-style quality control file
• Added RBC-options pipeline preconfiguration
• Added engine.log (when verbose debugging is on)
• Added ability to fix random seed for
  • antsAI
  • antsRegistration
  • Atropos (fixed but not specified)
  • fslmaths
  • mri_vol2vol
  • recon-all
• Added ability to use lateral ventricles mask in place of cerebrospinal fluid mask when when segmentation is Off, specifically for the rodent pipeline, but works on any dataset when segmentation is off

Improvements

• In a given pipeline configuration, segmentation probability maps and binary tissue masks are warped to template space, and those warped masks are included in the output directory

  • if registration_workflows['functional_registration']['EPI_registration']['run segmentation'] is On and segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation'] includes EPI_Template

    and/or

  • if registration_workflows['anatomical_registration']['run'] is On and segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation'] includes T1_Template

• Renamed connectivity matrices from *_connectome.tsv to *_correlations.tsv
• Moved some ephemeral logging statements into pypeline.log

Bug fixes

• Fixed bug in which working connectivity matrix filepaths were generated incorrectly, preventing generating matrices depending on container bindings
• Fixed broken links in README
• Fixed bug in which anatomical-only configurations required functional data directories
• Fixed bug in which nuisance regressors would crash when segmentation is off and no CSF mask is provided

C-PAC Version 1.8.2 Beta

This version of C-PAC is deprecated due to a bug in single_step_resampling. Unless you have a specific reason to use this version of C-PAC, we recommend upgrading to at least version 1.8.4. See https://fcp-indi.github.io/docs/latest/user/release_notes/v1.8.4 for more information about C-PAC v1.8.4. To use this version anyway, you can pull fcpindi/c-pac:release-v1.8.2-DEPRECATED from Docker Hub.

Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3

• Fixed a bug that was causing single_step_resampling, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.

  • This bug caused any affected fmriprep-options-based pipeline configurations (including fx-options and rbc-options) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.

  • Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with desc-preproc and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.

  • If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.

---

• Usability testing and optimization for the following minimal processing pipelines employed in the Li et al., Milham manuscript (BioRxiv) is complete and they are available:
  • CPAC:CCS
  • CPAC:ABCD-BIDS
  • CPAC:fMRIPrep
  • CPAC:Default
• The ABCD-BIDS surface-based postprocessing pipeline is implemented, though final usability testing and optimization is pending and will be in next release.

Added

• Added FSL-TOPUP as an option for distortion correction.
• Added changelog
• Added CHD8 mouse template (/cpac_templates/chd8_functional_template_noise_mask_ag.nii.gz)
• Added commandline flags --T1w_label and --bold_label
• Added the ability to ingress an entire FreeSurfer output directory to bypass surface analysis if already completed elsewhere
• Added AFNI and Nilearn implementations of Pearson and partial correlation matrices

Changed

• Expanded meta-data ingress for EPI field maps to include more fields when parsing BIDS sidecar JSONs.
• Updated possible inputs for T2w processing and ACPC-alignment blocks to increase the modularity of these pipeline options.
• master branch renamed main
• Packaged templates in https://github.com/FCP-INDI/C-PAC_templates

Deprecated

• master branch name (renamed main)

Fixed

• Fixed bug in which the preprocessed T2w data would not be found in the resource pool when expected.
• Fixed bug in which distortion correction-related field map ingress would raise IndexError: list index out of range when ingressing the field maps.
• Fixed bug in which some nodes would raise KeyError: 'in_file' when estimating memory allocation
• Improved memory management for multi-core node allocation.
• Fixed bug where --participant_label [A B C] would skip first and last labels (A and C).
• Stripped the ABI tag note (which was preventing the library from loading dynamically on some host operating systems) from libQt5Core.so.5 in the ABCD-HCP variant image.
• Fixed an issue blocking non-C-PAC output data from being read in without sidecar meta-data.

C-PAC Version 1.8.1 Beta

This version of C-PAC is deprecated due to a bug in single_step_resampling. Unless you have a specific reason to use this version of C-PAC, we recommend upgrading to at least version 1.8.4. See https://fcp-indi.github.io/docs/latest/user/release_notes/v1.8.4 for more information about C-PAC v1.8.4. To use this version anyway, you can pull fcpindi/c-pac:release-v1.8.1-DEPRECATED from Docker Hub.

Critical Alert for fMRIPrep-Options in C-PAC v1.8.1 - v1.8.3

• Fixed a bug that was causing single_step_resampling, when combined with certain other configurations, to inadvertently cause unexpected forks in the pipeline past transform application.

  • This bug caused any affected fmriprep-options-based pipeline configurations (including fx-options and rbc-options) to produce BOLD time series write-outs to the output directory in template space which were not nuisance regressed or filtered, for C-PAC versions 1.8.1 through 1.8.3.

  • Although these outputs were not expressly labeled as nuisance regressed or filtered, they were labeled as preprocessed with desc-preproc and were the only functional data transformed to template space and used for downstream processing, such as ROI-based timeseries extraction.

  • If you are unsure if you have been affected, you can check the side-car JSON for your template-space BOLD data from these versions for those pipeline configurations, as the JSON will still accurately reflect what operations had been performed on the data.

---

New Features & Pipeline Harmonization

• ABCD-BIDS Pipeline Harmonization.
  • The ABCD-BIDS pipeline of the ABCD study can now be reproduced by running the abcd-options preconfig in C-PAC.
• CCS Pipeline Harmonization.
  • A new BOLD masking option, CCS_Anatomical_Refined, has been added. This has been adapted from the BOLD mask method from the CCS pipeline.
  • New T1 masking options using Freesurfer have been added to facilitate the harmonization with the CCS pipeline.
  • A preconfigured pipeline that reproduces the CCS pipeline is now available.
• fmriprep Pipeline Harmonization Updated.
  • The fmriprep-options preconfigured pipeline, which reproduces the fmriprep pipeline, has been updated to reflect recent changes.

Improvements

• NOTE: The C-PAC default pipeline has been updated to use the whole-head T1w image as the input (moving) image for ANTs T1w-to-template registration. Comparisons with previous versions of C-PAC will show this change.
• Further improvements to memory management for less frequent hanging have been integrated, in an ongoing process.
• Freesurfer's Recon-All functionality in C-PAC has been opened to further configurability.
• More options for selecting a reference for slice-timing correction have been added.
• Description and other meta-data fields have been added to some output JSON sidecar files in an ongoing process to make output data descriptors clearer.
• DVARS calculation is now performed using AFNI 3dTto1d, increasing computation speed.
• Manually inserting input data to a C-PAC output directory for ingress is now easier. A sidecar JSON containing meta-data will be produced for the data automatically if one is not provided.
• For developers: improvements to the codebase have streamlined the process of adding new output data types to C-PAC through a central table, in line with recent v1.8 changes and the move to BIDS-Derivatives compliance.

Bug Fixes

• Choosing On/Off for nuisance regression once again correctly produces the non-cleaned BOLD outputs in addition to any nuisance regression strategies.
• Forking T1 and EPI based registration while simultaneously forking ANTs and FSL registration options no longer crashes the pipeline.
• An error where the DVARS calculation step would cause the pipeline to hang has been resolved.
• All nuisance regression choices are now available for EPI-registration based pipelines.
• The mem_gb input parameter for memory allocation no longer overrides other memory selections, when left unspecified.
• The selected_volume option for motion correction reference is now working again.

C-PAC Version 1.8.0 Beta

New Features

• BIDS-Derivatives Compatibility. C-PAC can now both ingress data and write data out according to the BIDS-Derivatives standard, enhancing interoperability with other BIDS-compatible neuroimaging packages.

  • This allows users to inject already-processed data directly into key intermediate points of the C-PAC pipeline.
  • In addition, clearer information on provenance of pipeline steps for multiple C-PAC strategies are also provided in BIDS-compatible JSON files for all output data.
  • The implementation of BIDS-Derivatives compatibility and its use flow regarding interoperability with other neuroimaging packages will continue to grow and adapt throughout later releases; stay tuned for changes and upgrades.
  • [https://bids-specification.readthedocs.io/en/latest/05-derivatives/01-introduction.html]

• Freesurfer Integration for Surface-Based Processing. The C-PAC pipeline can now run Freesurfer to generate surfaces, and to produce brain masks or tissue segmentation masks for use in the voxel-based pipeline, if the user desires.

  • Note: Due to the size of the Freesurfer installation, a separate, smaller C-PAC container without Freesurfer is also available if users wish to bypass surface-based analysis.
  • [https://surfer.nmr.mgh.harvard.edu/]

New Features - Pipeline Harmonization

• New BOLD Masking Option. A new anatomical brain mask-based BOLD masking option has been adapted from the ABCD pipeline of DCAN Labs.

  • [https://innovation.umn.edu/developmental-cognition-and-neuroimaging-lab/]
  • [https://github.com/DCAN-Labs/abcd-hcp-pipeline]

• New Frequency Filtering Option. AFNI 3dBandpass has been integrated as another option for frequency filtering of BOLD data during nuisance correction.

  • [https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBandpass.html]

Improvements

• Memory Usage Optimization. C-PAC’s memory usage estimates have been improved - this should reduce the occurrence of pipeline crashes caused by exceeding the memory limits of shared computing resources.
• Cleaner Pipeline Configuration. The pipeline configuration YAML format has been upgraded to a cleaner, easier-to-read nested format.
• Pipeline Configuration Importing. If configuring your pipeline directly through a YAML file, C-PAC’s pre-configured pipelines can now be imported into a YAML file. This allows users to specify only small segments of the pipeline they wish to change, when basing off of a default or pre-configured pipeline.

Developer Improvements

• Modularized Pipeline Blocks. C-PAC's workflow segments have been modularized for easier development and methods integration, and for easier testing.

Bug Fixes

• An error sometimes preventing users from supplying custom nuisance regressors to C-PAC has been resolved.

In addition, the C-PAC Docker and Singularity images, as well as the AWS AMI, have all been updated. These provide a quick way to get started.

And as always, you can contact us here for user support and discussion:
https://groups.google.com/forum/#!forum/cpax_forum

C-PAC Version 1.7.2 Beta

New Features

• Anatomical-Based BOLD Masking. Adapted from the DCAN Labs implementation, a new BOLD masking option is now available. Users can select this method to produce a BOLD mask that is produced by transforming the anatomical brain mask to BOLD space.

Improvements

• The motion estimate filter can now be forked, where the user can run a pipeline both with and without this processing step.
• Template-to-native space transformations within the pipeline have been made more robust to possible mis-transformations that would sometimes occur when the template-space images did not have much anatomical contrast.

Error Fixes

• The time series despiking step (performed by AFNI 3dDespike) is now able to be forked again.
• An error preventing EPI field maps for blip-up/down distortion correction from being parsed into the data configuration when labeled with unconventional dir- tags has been fixed.

Coming Soon

• Pipeline Dashboard
• Surface-Based Processing
• BIDS-Derivatives Compatibility

In addition, the C-PAC Docker and Singularity images, as well as the AWS AMI, have all been updated. These provide a quick way to get started.

And as always, you can contact us here for user support and discussion:
https://groups.google.com/forum/#!forum/cpax_forum