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.
This is a placeholder for a short description explaining to the user what your App will doing.
Provide a link to the documentation of your pipeline.
Provide instructions for users on how to get help and report errors.
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.)
This App has the following command line arguments:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
bids_dir output_dir {participant,group}
Example BIDS App entry point 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 a group level analysis, this folder
should be prepopulated with the results of
the participant 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 will 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: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
Describe whether your app has any special requirements. For example:
- Multiple map reduce steps (participant, group, participant2, group2 etc.)
- Unusual memory requirements
- etc.