Pydeface BIDS App

This a BIDS App wrapper for Pydeface. Like every BIDS App it consists of a container that includes all of the dependencies and run script that parses a BIDS dataset. BIDS Apps run on Windows, Linux, Mac as well as HCPs/clusters.

Description

Pydeface BIDS App will grab the images corresponding to the subject and image modality requested and run Pydeface on them, overwritting the original images.

Documentation

Please read the official Pydeface docs.

Error Reporting

Experiencing problems? Please open an issue and explain what's happening so we can help.

Usage

This App has the following command line arguments:

	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.

To run it in participant level mode (for one participant):

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

To run it for a specific modality of images:

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