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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
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StudyTemplate fails at PostFreeSurfer #97

Closed jarodroland closed 8 months ago

jarodroland commented 1 year ago

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?

docker with --study_template parameter and a custom age relevant template.

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 https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/13d93a3ccd39d699844622ce6be1a65119221cd4/app/pipelines.py#L743 ... 743: ' --useStudyTemplate={usestudytemplate}' \ +++: ' --studytemplate={studytemplate}' \ +++: ' --studytemplatebrain={studytemplatebrain}' \ 744: ' --printcom={printcom}' ...

LuciMoore commented 10 months ago

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!

madisoth commented 8 months ago

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!