scil_bids_validate.py

usage: __main__.py [-h] [--bids_ignore BIDS_IGNORE] [--fs FS] [--clean]
                   [--readout READOUT] [-v [{DEBUG,INFO,WARNING}]] [-f]
                   in_bids out_json

Create a json file from a BIDS dataset detailling all info
needed for tractoflow
- DWI/rev_DWI
- T1
- fmap/sbref (based on IntendedFor entity)
- Freesurfer (optional - could be one per participant
              or one per participant/session)

The BIDS dataset MUST be homogeneous.
The metadata need to be uniform across all participants/sessions/runs

Mandatory entity: IntendedFor
Sensitive entities: PhaseEncodingDirection, TotalReadoutTime, direction

Formerly: scil_validate_bids.py

positional arguments:
  in_bids               Input BIDS folder.
  out_json              Output json file.

options:
  -h, --help            show this help message and exit
  --bids_ignore BIDS_IGNORE
                        If you want to ignore some subjects or some files, you can provide an extra bidsignore file.Check: https://github.com/bids-standard/bids-validator#bidsignore
  --fs FS               Output freesurfer path. It will add keys wmparc and aparc+aseg.
  --clean               If set, it will remove all the participants that are missing any information.
  --readout READOUT     Default total readout time value [0.062].
  -v [{DEBUG,INFO,WARNING}]
                        Produces verbose output depending on the provided level.
                        Default level is warning, default when using -v is info.
  -f                    Force overwriting of the output files.

Scilpy version: 2.0.2