.. _scil_bids_validate:

scil_bids_validate
==================

::

	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