Instructions for using fMRIPrep and other bids apps on the CBS server

With the server upgrade to Ubuntu 20 and the creation of /localscratch, we are now able to support the use of bids apps.

General Comments:

  1. To see which bids apps (and other singularity containers) currently available on the server, check the contents of /srv/containers. Please contact to inquire about having additional containers installed.
  2. Direct both working and output directories to /localscratch. This will avoid any issues with the main file system locking up and decrease processing time by increasing I/O speed.
  3. Users are recommended to upgrade to Power User and use CBS-Heavy to avoid hitting the RAM limits of CBS-Basic.

Bids apps are run using a singularity call:

singularity run -e <bids-app> <bids-dir> /localscratch/<output-dir> participant -w /localscratch/<working-dir>

Specifically for fMRIPrep (basic run including freesurfer):

singularity run -e /srv/containers/fmriprep_20.2.6.sif /localscratch/bids /localscratch/fmriprep_20.2.6-output participant -w /localscratch/working --fs-license-file $FREESURFER_HOME/license.txt

In the above example, the bids directory has been copied into /localscratch to avoid having to read in from a PI datashare. However, it works equally well to leave the input bids directory in a PI datashare space. Technically, only the output and working directories need to be located in /localscratch.

Please remember that /localscratch is temporary storage. You are responsible for copying your output directory to your PI datashare space as soon as possible after processing is complete. Anything stored in /localscratch will be deleted and unrecoverable when your VM is shutdown or reset.

1 Like

Thanks @switt4!

A list of many of the openly-available BIDS apps is here, let us know if you want any additional apps installed and tested!

You can also pull the container yourself to run with singularity pull docker://... (run this on /localscratch too).