FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions


The following versions of FreeSurfer are available on OSC clusters:

5.3.0 X


* Curent default version

You can use module spider freesurfer to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


FreeSurfer is available to all academic OSC users with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 


Usage on Owens


Load the FreeSurfer module with  module load freesurfer. This will load the default version. Then, to continue configuring your environment, you must source the setup script for Freesurfer. Do this with the following command that corresponds to the Linux shell you are using. If using bash, use:


If using tcsh, use:

source $FREESURFER_HOME/SetUpFreeSurfer.csh

To finish configuring FreeSurfer, set the the FreeSurfer environment variable SUBJECTS_DIR to the directory of your subject data. The SUBJECTS_DIR variable defaults to the FREESURFER_HOME/subjects directory, so if this is your intended directory to use the enviornment set-up is complete.

To alter the SUBJECTS_DIR variable, however, again use the following command that corresponds to the Linux shell you are using. For bash:

export SUBJECTS_DIR=<path to subject data>

For tcsh:

setenv SUBJECTS_DIR=<path to subject data>

Note that you can set the SUBJECT_DIR variable before or after sourcing the setup script.

Further Reading 

Fields of Science: