cbinyu/bids_pydeface repository overview

	usage: run.py [-h]
	              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
		      [--session_label SESSION_LABEL [SESSION_LABEL ...]]
	              bids_dir output_dir {participant}

	Pydeface BIDS App.

	positional arguments:
	  bids_dir              The directory with the input dataset formatted
	                        according to the BIDS standard.
	  output_dir            This argument is here for BIDS-Apps
	                        compatibility. All images will be written to the bids_dir
				overwriting the input.
	  {participant}         Level of the analysis that will be performed. Multiple
	                        participant level analyses can be run independently
	                        (in parallel).

	optional arguments:
              -h, --help            show this help message and exit
              --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                                    The label(s) of the participant(s) that should be
                                    analyzed. The label corresponds to
                                    sub-<participant_label> from the BIDS spec (so it does
                                    not include "sub-"). If this parameter is not provided
                                    all subjects will be analyzed. Multiple participants
                                    can be specified with a space separated list.
              --session_label SESSION_LABEL [SESSION_LABEL ...]
                                    The label of the session that should be analyzed. The
                                    label corresponds to ses-<session_label> from the BIDS
                                    spec (so it does not include "ses-"). If this
                                    parameter is not provided all sessions should be
                                    analyzed.
              --modality MODALITY1 [MODALITY2 ...]
                                    The modalities of images that will be defaced. They can be
                                    either suffixes (e.g.: T1w, T2w, bold) or datatype (e.g.:
                                    anat, func, fmap).  Default: anat
              --skip_bids_validator
                                    If set, it will not run the BIDS validator before defacing.

docker run -i --rm \
	-v /Users/filo/data/ds005:/bids_dataset \
	cbinyu/pydeface \
	/bids_dataset /bids_dataset participant --participant_label 01

docker run -i --rm \
            -v /Users/filo/data/ds005:/bids_dataset \
	cbinyu/pydeface \
	/bids_dataset /bids_dataset participant --participant_label 01 --modalities T1w