https://github.com/bids-apps/example

This an example app that can serve as a template.
https://github.com/bids-apps/example

bids bids-apps

Last synced: 15 days ago
JSON representation

This an example app that can serve as a template.

• Host: GitHub
• URL: https://github.com/bids-apps/example
• Owner: bids-apps
• License: apache-2.0
• Created: 2016-07-28T17:58:07.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2026-03-16T10:01:39.000Z (3 months ago)
• Last Synced: 2026-04-03T17:32:48.651Z (2 months ago)
• Topics: bids, bids-apps
• Language: Python
• Homepage: https://doi.org/10.1371/journal.pcbi.1005209
• Size: 128 KB
• Stars: 17
• Watchers: 1
• Forks: 33
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
## 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](https://docs.google.com/document/d/1E1Wi5ONvOVVnGhj21S1bmJJ4kyHFT7tkxnV3C23sjIE/).

### 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- 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.