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.