FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

Running Freesurfer GUI

To use Freesurfer GUI, select TReNDS Interactive desktop from under TReNDS interactive apps on https://hemera.rs.gsu.edu/. Once the session is launched, open a terminal and run the following commands for loading the module and setup.

$ module load freesurfer/7.3.2
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

Then you should be able to use any GUI application.

$ freeview

Running Freesurfer in terminal

# Login to the cluster
$ ssh -XY <campusID>@arclogin.rs.gsu.edu

# Start an interactive bash session
$ srun -p qTRD -A <slurm_account_code> -v -n1 -c1 --mem=10g -t60 --pty /bin/bash

# Load the Freesurfer module and setup environment
$ module load freesurfer/7.3.2
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh