An example that illustrates how to wrap a BIDS project with DataLad and then process the images. Since the scripts use DataLad, you can easily reproduce the results. Thus, your data analysis project will be YODA-compliant.
This script takes two arguments, a source directory, and a destination directory. The source directory should be the root of a BIDS repo. The source directory is copied over to the destination directory. Then the destination directory is converted into a DataLad project at both the root level, with nested DataLad projects at the subject and session levels.
Here is the syntax:
create_datalad_data_repo_project.sh source_directory destination_directory
This will take create a directory source_directory and create an equivalent DataLad-wrapped data in destination_directory
Note that destination_directory must either not exist or be empty before running create_datalad_data_repo_project.sh.
This script takes two argument. The first is the root directory of a BIDS repository which is wrapped by a DataLad project (such a directory could be created with the preceding script, create_datalad_data_repo_project.sh. The second argument is the path to a shell script that takes a single argument, the path to a NIfTI file. The script can do anything with this NIfTI file. It can transform the image, analyze it and write the analysis out to a text file, whatever. datalad_run_bids_example.sh walks the directories of the BIDS directory. Everytime it encounters a NIfTI file it runs the user-specified shell script on it. On its way up the BIDS tree the script calls datalad save including at the top level.
Please contact Paul Reiners if you have questions about or run into problems when using these scripts.