BIDS (deprecated)

A BIDS directory can be uploaded to Flywheel using the scitran method bidsUpload. A Flywheel project created by uploading from a BIDS directory can be downloaded using the scitran methods bidsDownload. The scitran methods and bids class are described here.

Constructing a BIDS object

If you have a BIDS data directory (bDir), we you can build a description of the directory using

thisBIDS = bids(bDir)

We expect that bDir is a directory on your computer that contains a BIDS formatted directory tree. The bids() constructor scans the directory and returns a bids object containing all the BIDS directories, metadata files and imaging data files. You can validate the BIDS compliance using

thisBIDS.validate

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

Uploading

You can upload the BIDS data using these Matlab commands. The example points to a directory on my disk (fw_test) that contains a BIDS directory tree. I upload the data to a project assigned to my group (BIDSup).

data = bids(fullfile(stRootPath,'local','BIDS-examples','fw_test'));
data.projectLabel = 'BIDSUpload';
groupLabel = 'Wandell Lab'; 
project = st.bidsUpload(data,groupLabel);

The metadata attachments, but not the data files, have the string 'bids@' prepended to them. I do these for now anticipating that it will be helpful when we do the bidsDownload method. This may change.

TODO - it is possible for us to extract information from the metadata files and place them in the info fields. JR does this in the Python script, and we could do the same here.

Downloading

This method has not yet been converted to the new SDK calls. That will be next weekend's project.

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

Notes

• We are creating API methods to validate that a Flywheel project has the necessary BIDS information and can be downloaded as a BIDS directory.
• Several BIDS applications (fMRIprep and XXX) are implemented as Gears on Flywheel.
• There is a Python method for uploading and downloading.

BIDS class methods

bids (constructor)
listSubjectFolders
listDataFiles 
listMetaDataFiles
validate
countSessions