FreeSurfer

FreeSurfer is a software package used to anaylze nueroimaging data.

Availability & Restrictions

Versions

The following versions of FreeSurfer are available on OSC clusters:

VERSION OAKLEY RUBY OWENS
6.0.0    

X*

* Curent default version

Access

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

Usage

Usage on Owens

Set-up

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

source $FREESURFER_HOME/SetUpFreeSurfer.sh

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 

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