oesteban/bidsapp-behavioral-example

This is an example of how to build a BIDS app for behavioral data analysis using pybids

An example BIDS App using pybids

This is a fork of the original BIDS Apps example, which was built prior to the existence of pybids. At the participant level, the entry point script (run.py) will:

• validates and loads a BIDS dataset using pybids
• finds all of the event.tsv files
• computes the mean of the specified response time column (default='RT')
• saves the run means to derivatives/rt/sub-XX/func/sub-XX_task-XX_runMeanRT.tsv

At the group level, it will load all of the participant run mean files, compute the overall mean for each subject, and save them to derivatives/rt/participants.tsv

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

Usage

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.
	  {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
	  --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_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.
		--rt_var_name VARIABLE_NAME
													name for response time variable in events file
                				default='RT'

To build the dockerfile (creating an image called "rt"):

make docker-build

To run it in participant level mode (for all participants):

docker run -i --rm \
	-v <local path to bids dataset>:/bids_dataset \
	rt /bids_dataset participant

To run the group level:

docker run -i --rm \
	-v <local path to bids dataset>:/bids_dataset \
	rt /bids_dataset group

Example

For a working example, download ds001715 from OpenNeuro and then use that directory as the local BIDS dataset path.