BIDS

Brain Imaging Data Structure (BIDS)

The scitran Matlab client (@scitran) includes a class definition (@bids) for BIDS (Brain Imaging Data Structure). The @bids class constructor is invoked by

thisBIDS = bids(dataDir)

where dataDir is the local directory containing a BIDS formatted directory tree. The constructor scans the directory and returns a bids object that contains a listing of all the BIDS directories, meta data files and imaging data files. There is a @bids.validate method, and a few other utilities to help you check that the directory is compliant.

Directory names in the bids object are stored relative to the home of the data directory.

@bids methods include - bids (constructor), listSubjectFolders, listDataFiles, listMetaDataFiles, validate, countSessions

BIDS uploading to Flywheel

The @scitran class has a method (bidsUpload) for uploading the @bids data to Flywheel. The following code creates a Flywheel project that contains the data and meta data from the BIDS compliant directory in bidsDir.

st = scitran(<your flywheel instance>)
thisBids = bids(bidsDir);
thisBids.projectLabel = 'The project label you choose';
st.bidsUpload(thisBids,'group label');

BIDS downloading from Flywheel

To download a BIDS project that is stored on Flywheel use

 projectLabel = 'The FW project label'
 bidsDir = @scitran.bidsDownload(projectLabel,'destination',<destination directory>);

General downloading from Flywheel

More generally, you can download any project to a tar file simply using

project = st.search('projects','project label','VWFA');
st.download('project',project{1}.id,'destination','tarfile name');