Changes suggested to app/pipelines.py during 2022-02-02 code review:
Stage class lines 486-501
When running from an intermediate stage, remove_expected_outputs can crash the pipeline because it won't remove files whose names have changed in the latest DCANBoldProc update(s)
This GitHub repo's issues have 3-4 variations of the same problem where people report that the pipeline crashes, and then Thomas has to tell them which files to delete
PreFreeSurfer class lines 649-674
T1w's fmap IntendedFor is always imposed onto the T2w, which might be a problem because sometimes T1w and T2w are from different recording sessions
Either fix or clearly document the _get_intended_sefmaps problem where filenames cannot contain "T1w" string
At least document it more clearly in the README, or throw a more descriptive error describing how that's the problem
Reuse the FMRIVolume class's functionality on lines 796-799 to fix this problem
Put this shared functionality into a utility function and call it in both places
FMRIVolume class lines 800-805
Remove this block for the same reason described in the section above
Changes suggested to
app/pipelines.pyduring 2022-02-02 code review:Stage class lines 486-501
remove_expected_outputscan crash the pipeline because it won't remove files whose names have changed in the latestDCANBoldProcupdate(s)PreFreeSurfer class lines 649-674
_get_intended_sefmapsproblem where filenames cannot contain"T1w"stringREADME, or throw a more descriptive error describing how that's the problemFMRIVolumeclass's functionality on lines 796-799 to fix this problemFMRIVolume class lines 800-805