✨ Introduce mri_robust_template as option for longitudinal template generation
#2165
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…nal (new default) [skip ci]
…longitudinal template space
I think yes and yes for "C-PAC legacy". Here I added some functionality to grab the outputs from the previousl-run graph C-PAC/CPAC/longitudinal/wf/utils.py Lines 157 to 197 in 1e2079f
This section was what I was unsure about, but I think it makes sense. In this refactor, we go from looping over the sessions 3× (once before template generation and twice after) to 2× (once before and once after).
I think the idea was for it to work seamlessly with C-PAC-generated or previously-generated longitudinal templates so long as they're named in the BIDS-ish way C-PAC expects, but that there's been slippage between what C-PAC expects generally and what this specific section of the codebase expects & generates. |
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At this point the outputs of a test run are looking like this: treethumbnailsanat
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There's definitely some weirdness in the outputs. There are outputs with even though they have differentiating |
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Looks like the empty BOLD files are from the bandpass not passing anything through, could be data-specific. I'm going to try rerunning without bandpass. |
pre-preprocone per subject-session C-PAC/CPAC/longitudinal/wf/anat.py Lines 355 to 373 in 6339798 
template nodeone per subject C-PAC/CPAC/longitudinal/wf/anat.py Lines 398 to 499 in 6339798 
post-template preprocone per subject-session C-PAC/CPAC/longitudinal/wf/anat.py Lines 508 to 657 in 6339798 
main workflowone per subject-session C-PAC/CPAC/pipeline/cpac_pipeline.py Lines 471 to 602 in 6339798 
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Fixes
Related to #2164 by @shnizzedy & @Shinwon Park
Description
usingoption tolongitudinal_template_generationwith a choice ofmri_robust_template(default) orC-PAC legacyC-PAC/CPAC/resources/configs/pipeline_config_default.yml
Line 243 in e6d33f5
C-PAC/CPAC/resources/configs/pipeline_config_default.yml
Lines 253 to 255 in e6d33f5
flowchart LR anat_longitudinal_pre-preproc("<code>anat_longitudinal_pre-preproc</code><br>(one per subject session)") --> template_node_brain("<code>template_node_brain</code><br>(one per subject)") template_node_brain --> ses_wf("<code>ses_wf</code><br>(one per subject session)")anatdirectory that's a sibling to all the session directories, and that thatanatdirectory has all the subject-but-not-session-specific outputs in it.from-T1w_to-longitudinalandfrom-longitudinal_to-{template}andfrom-T1w_to-{template}or do we want to leave any out to be recalculated as needed?Technical details
Still to do
Tests
Screenshots
tree sub-70009Checklist
Update index.md).prep_for/mri_robust_templatebranch of the repository.Developer Certificate of Origin
Developer Certificate of Origin