usage: __main__.py [-h] [--bids_ignore BIDS_IGNORE] [--fs FS] [--clean]
[--readout READOUT] [--match_t1_run]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-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
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].
--match_t1_run If set, when multiple T1 files are found for a subject/session, select the one matching the DWI run entity. If not set, no T1 is selected in this ambiguous case.
-v [{DEBUG,INFO,WARNING,ERROR}]
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.
2.2.2