🧐 run minimal preprocessing on all exemplars, comparing three runs

[shnizzedy]

Related problem

Related to https://github.com/FCP-INDI/TheWay/issues/7 and https://github.com/FCP-INDI/TheWay/issues/9

Proposed feature

run minimal preprocessing on all exemplars, comparing three runs: actual fMRIPrep (volume only), CPAC-fMRIPRep, and CPAC-RBC configs. (Note please run w/ distortion correction on when maps are avail)

Acceptance criteria

• [x] all exemplars run through all pipelines
  • [x] CCNP
    • [x] transferred to ACCESS
    • [x] through fMRIPrep
    • [x] through C-PAC:fmriprep-options
    • [x] through C-PAC:rbc-options
  • [x] HBN
    • [x] transferred to ACCESS use from S3
    • [x] through fMRIPrep
    • [x] through C-PAC:fmriprep-options in progress
    • [x] through C-PAC:rbc-options in progress
  • [x] HRC
    • [x] transferred to ACCESS
    • [x] through fMRIPrep
    • [x] through C-PAC:fmriprep-options in progress
    • [x] through C-PAC:rbc-options in progress
  • [x] NKI
    • [x] transferred to ACCESS
    • [x] through fMRIPrep
    • [x] through C-PAC:fmriprep-options in progress
    • [x] through C-PAC:rbc-options in progress
  • [x] PNC
    • [x] transferred to ACCESS
    • [x] through fMRIPrep
    • [x] through C-PAC:fmriprep-options in progress
    • [x] through C-PAC:rbc-options in progress
• [ ] outputs compared
  • [ ] preprocessed BOLD
  • [ ] generated Schaefer-200 matrix in progress

Additional context

• [x] Symlinking from cis210040p to med220004p
• [x] Before re-running rbc-options:
  • [x] Merging locally (in med220004p)
    • [x] https://github.com/FCP-INDI/C-PAC/pull/1761
    • [x] https://github.com/FCP-INDI/C-PAC/pull/1769
    • [x] https://github.com/FCP-INDI/C-PAC/pull/1770
  • [x] Turning off nuisance regression for this round of runs (https://github.com/FCP-INDI/RBC-on-ACCESS/commit/4e4406d7e4eebf596f168c8c9450530110cd3838)

[shnizzedy]

Giving an S3 path to fMRIPrep for the positional bids_dir didn't work (

fmriprep: error: Path does not exist: <s3://fcp-indi/data/Projects/HBN/BIDS_curated/>

), so I split the HBN run script into a C-PAC script and an fMRIPrep script and added

  aws s3 sync --no-sign-request s3://fcp-indi/data/Projects/HBN/BIDS_curated/${SUB} /ocean/projects/med220004p/shared/data_sandbox/derived/RBC-testing/data/UPenn/HBN/${SUB}

before giving the local path in the fMRIPrep script.