Fails without fieldmaps when DWI files are present #40
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madisoth
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Jan 13, 2022
Addresses several issues noted at 1/12/22 readme code review meeting.
Done:
- Update Docker link
- add link to DCAN HCP pipeline code base at top of README
- Could also link to Docker page within README
- possibly add instructions for running outside of Docker/Singularity
- add note under Usage about which BIDS formatting our pipeline does and does not accept
- add information about stages for "--stage:" possibly just link to code repo README or published paper
- "--check-outputs-only" should specify that it only checks for a subset of the outputs, not all (could add link to the json)
- "--stage:" add more explanation about the fact that it sets start and finish stage
- Example: start with more basic example. add explanations for bandstop filter and study-templates under the Usage. Possibly move the advanced example down or delete entirely
- Update the directory tree: add DCANBoldProc, update name of executive summary folder, missing T2w folder, etc
- Rerunning: add more explanation here
- Possibly remove section on "Special Pipeline" or add information here up in usage descriptions
- BIDS spec: add that fieldmaps should be PEpolar fmaps and link to description of PEpolar fmaps here
- "Some current limitations" mention/link QSIprep here and remove/modify a lot of language (added issues - dwi, motion filtering not going to be added, etc)
- clarify the statement "Other parameters would have to be processed by creating separate BIDS datasets for sessions with varied fMRI parameters."
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Remaining to-do:
- Misc: need to check if pipeline doesn't run with gradient field maps anymore, if so should update language
- Flags: in general, could add more details to flags. could look at infant-pipeline readme for reference
- Test whether --abcd-task is usable in the current version; if unusable then document that in the readme
- add description of bug in --ignore {func,dwi}: if there is dwi data in raw data, then pipeline will crash if there are no fmaps (see issue #40 )
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I am able to process data that doesn't have fieldmaps if no DWI data is present. If DWI data is present and there are no fieldmaps, it fails looking for fmap metadata.
Note: --ignore dwi did not solve this problem
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