FreeSurfer¶

Overview¶

FreeSurfer is a software package to analyze MRI scans of human brains.

OSG used to have a hosted service, called Fsurf. This is no longer available. Instead, OSG provides a container image, and one of our collaborators provides an optional workflow using that container.

Container image: /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-freesurfer:latest and defined at https://github.com/opensciencegrid/osgvo-freesurfer
FreeSurfer Workflow

The container can be used with simple jobs as described below.

Prerequisites¶

To use the FreeSurfer on the Open Science Pool (OSPool), you need:

Your own FreeSurfer license file (see: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#License)
An account on an OSPool access point.

Privacy and Confidentiality of Subjects¶

In order to protect the privacy of your participants’ scans, we require that you submit only defaced and fully deidentified scans for processing.

Single Job¶

The following example job has three files: job.submit, freesurfer-wrapper.sh and license.txt

job.submit contents:

container_image = /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-freesurfer:latest

executable = freesurfer-wrapper.sh
transfer_input_files = license.txt, sub-THP0001_ses-THP0001UCI1_run-01_T1w.nii.gz

error = job.$(Cluster).$(Process).error
output = job.$(Cluster).$(Process).output
log = job.$(Cluster).$(Process).log

request_cpus = 1
request_memory = 1 GB
request_disk = 4 GB

queue 1

freesurfer-wrapper.sh contents:

#!/bin/bash

set -e

# freesurfer environment
. /opt/setup.sh

# license file comes with the job
export FS_LICENSE=`pwd`/license.txt

export SUBJECTS_DIR=$PWD

recon-all -subject THP0001 -i sub-THP0001_ses-THP0001UCI1_run-01_T1w.nii.gz -autorecon1 -cw256

# tar up the subjects directory so it gets transferred back
tar czf THP0001.tar.gz THP0001
rm -rf THP0001

license.txt should have the license data obtained from the Freesurfer project.