BIDS

Brain Imaging Data Structure (BIDS)

Flywheel projects can be downloaded or uploaded in BIDS or Flywheel format. This page describes how download a BIDS compliant directory tree.

Older method ... to be replaced by an API endpoint

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 thisBIDS.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 class methods

bids (constructor)
listSubjectFolders
listDataFiles 
listMetaDataFiles
validate
countSessions

## Examples

### 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() 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 = st.bidsDownload(projectLabel,'destination',<destination directory>);


### NOTE

At present, we have slowed down the upload/download process considerably to account for the indexing time of elastic search. We use elastic search methods for now.  However, soon the Flywheel team will enable us to replace all elastic search calls with direct addressing to the MongoDB.  At that time, the pauses will be removed and the process will become much much faster.