FreeSurfer Linux Installation

Installing contents

Installing freesurfer involves simply extracting the contents of the .tar.gz file (will extract to a directory called 'freesurfer'). Installing into the directory /usr/local is recommended. For example:

$> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz

Again, replacing <platform>-<release> with your Linux variant.

Setup and Configuration

Type the following command into a terminal window to setup and source the FreeSurfer environment. Note that you must choose the directory where you extracted freesurfer to become your FREESURFER_HOME (/usr/local/freesurfer in our example):

bash
$> export FREESURFER_HOME=/usr/local/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh

(t)csh
$> setenv FREESURFER_HOME /usr/local/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.csh

Reminder to NMR Center users! You already have FreeSurfer installed on your system!

Freesurfer license file

A license file is required to enable the tools. One can be obtained for free by registering at:

https://surfer.nmr.mgh.harvard.edu/registration.html

Upon receiving the license information by email, copy the three lines of the license information to a file named license.txt and copy that file to your $FREESURFER_HOME.

If you came from the Quick Install page, return to that here.