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."
to-dos for future updates:
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 )
Addresses several issues noted at 1/12/22 readme code review meeting.
Done:
to-dos for future updates: