This an example app that can serve as a template.
['bids', 'bids-apps']
This an example app that can serve as a template.
 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-<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.