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Hi, @jarodroland. I've updated the code under the branch postFSstudytemplate. We'll try to test this branch to be thorough within the next month, but if you get to it before us and it works please let us know!
v0.1.4 is now out, which has the fixes from the postFSstudytemplate branch -- we believe it should resolve this issue, but if you still run into problems let us know. Thanks!
What happened?
StudyTemplate and StudyTemplateBrain are not passed to PostFreeSurferPipeline.sh: https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/13d93a3ccd39d699844622ce6be1a65119221cd4/app/pipelines.py#L743C26-L743C26
Fails without error message when AtlasRegistrationToMNI152_ANTsIntermediateTemplate.sh tries to parse the StudyTemplate parameters: https://github.com/DCAN-Labs/DCAN-HCP/blob/92913242419d492aee733a45d454ea319fbaac35/PostFreeSurfer/scripts/AtlasRegistrationToMNI152_ANTsIntermediateTemplate.sh#L114C36-L114C36
What command did you use?
What version of the abcd-hcp pipeline are you using?
v0.1.3
Directory Structure
No response
Relevant log output
No response
Add any additional information or context about the problem here.
Resolved by editing app/pipelines.py below at
abcd-hcp-pipeline/app/pipelines.py
Line 743 in 13d93a3
...
743: ' --useStudyTemplate={usestudytemplate}' \
+++: ' --studytemplate={studytemplate}' \
+++: ' --studytemplatebrain={studytemplatebrain}' \
744: ' --printcom={printcom}'
...
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