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.
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.
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.