Overview

FreeSurfer is a software package to analyze MRI scans of human brains. The Open Science Grid (OSG) has developed a command line utility, Fsurf, that simplifies running a FreeSurfer 5.3 workflow on the OSG.

Prerequisites

To install and use Fsurf utility, you'll need a few things:

  • A local copy of FreeSurfer installed (for anonymizing scans)
  • A computer using a version of Linux/Unix/macOS released within the last 3 years

Privacy and Confidentiality of Subjects

In order to protect the privacy of your participants’ scans, we request that you submit only defaced and fully deidentified scans for processing by Fsurf. Images can be anonymized and deidentified before they are uploaded to OSG servers as described in the article on anonymizing images.

Introduction to Fsurf

Fsurf is designed to be easily used from any computer running macOS or Linux/Unix. The Fsurf script just requires Python and a network connection in order to run and process MRI scans. When run, the script will upload your scan to the Fsurf server. The Fsurf server then uses compute nodes available through OSG in order to process scans using FreeSurfer and stores the resulting output. When you are notified that a scan has completed, you can use the Fsurf script to download the output to your computer.

What's Next?

Setup up Fsurf on your computer.

Getting Help

For assistance or questions, please email the OSG User Support team at user-support@opensciencegrid.org or visit the help desk and community forums.

Validation Information

A list of Linux kernels on the OSG on which the FreeSurfer workflows have been validated can be found here.

Acknowledging the Open Science Grid

We gratefully request your acknowledgement of the OSG in publications benefiting from this service as described here.

 

This page was updated on Dec 19, 2018 at 07:45 from FsurfRemote/Introduction.md.