An BIDS App for running BRAINSAutoWorkup

\author Hans J. Johnson

Every BIDS App needs to follow a minimal set of command arguments common across all of the Apps. This allows users and developers to easily use and integrate BIDS Apps with their environment.

This is an minimalistic example BIDS App consisting of a Dockerfile and simple entrypoint script (written in this case in Python) accepting the standard BIDS Apps command line arguments.

This App has the following comman line arguments:

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

    Example BIDS App entrypoint script.

    positional arguments:
      bids_dir              The directory with the input dataset formatted
                            according to the BIDS standard.
      output_dir            The directory where the output files should be stored.
                            If you are running group level analysis this folder
                            should be prepopulated with the results of
                            theparticipant level analysis.
      {participant,group}   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 should be analyzed. Multiple participants
                            can be specified with a space separated list.

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

docker run -i --rm \
    -v /Users/filo/data/ds005:/bids_dataset \
    -v /Users/filo/outputs:/outputs \
    bids/example \
    /bids_dataset /outputs participant --participant_label 01

After doing this for all subjects (potentially in parallel) the group level analysis can be run:

docker run -i --rm \
    -v /Users/filo/data/ds005:/bids_dataset \
    -v /Users/filo/outputs:/outputs \
    bids/example \
    /bids_dataset /outputs group

For more information about the specification of BIDS Apps see here.