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known_issues.md

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List of issues, notes, and resolutions.

DICOM

  • We now need a custom script to "claim" dicoms on BIC server before downloading them locally
  • Some participants have multiple dicom dirs for same session (most likely from issues during scanning)
    • Heuristic filter: select dicom_dir with most files
  • Some dicoms are now "tarred" on bic server and need to be extracted before reorganizing
  • Some dicoms do not have visit / session info in the filename (i.e. MRI01)
    • Cross-ref date with recruitment spreadsheet for identifying sessions
  • Some dicoms have derived tag in the header
    • These are excluded from symlinking from raw_dicom to dicom before bids conversion

BIDS

  • dwi error on volume count for all participants. See neurostars issue
  • fmap sidecars for PA direction (e.g. sub-<>_ses-<>_acq-bold_dir-PA_run-1_epi.json) have wrong PhaseEncodingDirection for some participants. This will fail the downastream fmriprep processing at SDC stage.
    • List of participant ids: PD00296,PD00869,PD01090,PD01165,PD01232,PD01306,PD01360,PD01435,PD01551,PD01753
    • This is manually changed from i --> j

proc_pipes

fmriprep

  • fmap sidecars have wrong PhaseEncodingDirection for some participants. This will cause failure of fmriprep processing at SDC stage.