An example BIDS App (template repository)

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 a minimalist example of a BIDS App consisting of a Dockerfile and a simple entry point script (written in this case in Python) accepting the standard BIDS Apps command line arguments. This repository can be used as a template for new BIDS Apps.

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

Description

This is a placeholder for a short description explaining to the user what your App will doing.

Documentation

Provide a link to the documentation of your pipeline.

How to report errors

Provide instructions for users on how to get help and report errors.

Acknowledgments

Describe how would you would like users to acknowledge use of your App in their papers (citation, a paragraph that can be copy pasted, etc.)

Usage

This App has the following command line arguments:

usage: run.py [-h] [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--skip_bids_validator] [-v]
            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) using the same output_dir.

options:
-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.
--skip_bids_validator
                        Whether or not to perform BIDS dataset validation
-v, --version         show program's version number and exit

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

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

Special considerations

Describe whether your app has any special requirements. For example:

• Multiple map reduce steps (participant, group, participant2, group2 etc.)
• Unusual memory requirements
• etc.