Converting Data to BIDS

Once you've finished collecting your data, email Yarik (director of the Center for Open Neuroscience) for help converting your data to BIDS format. Give him the path to your raw data—should be something like: /Meyer/Eleanor/1033-emporient

Conveniently, Yarik's pipeline also converts the data from PAR/REC files to nifti files, which is the format you'll need for analyses.

Transferring Data

After each scan, MRI data gets exported to a computer called Rolando. We can’t actually run any analyses on here. Instead, we need to transfer it from Rolando to somewhere we can run our analyses: i.e. our lab share on the Discovery cluster.

  1. Make sure you have a personal folder set up on the lab share on Discovery. See The Cluster for more info on logging into Discovery

  2. Copy the path to the folder you want to store your data in on Discovery—should be something like: /dartfs-hpc/rc/lab/M/MeyerM/YourName/NameOfStudy

  3. Log on to Rolando by opening a terminal window (on the server) and typing:

    • ssh

    • You'll be prompted to enter your password (Change!t by default)

  4. Next, locate your data by typing:

    • cd /inbox/BIDS/Meyer/YourFirstName/your-study

    • If you type ‘ls’ you should see all of the scans you’ve collected. (If you’re missing subjects, you may need to send SIDs and accession numbers to Yarik and request that he convert them to BIDS format.)

  5. Transfer your files on Rolando to your desired folder on Discovery using the following command:

    • scp -r FolderOnRolando

    • You'll be prompted to enter your password for Discovery, which is just your Dartmouth password

Note: if you need to connect to Rolando or Discovery from off-campus, see The Cluster for instructions.