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FreeSurfer Linux Installation

Viewing contents

To view the contents of a distribution, once downloaded, type:

tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz

replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file.

Installing contents

The tar.gz file will extract to a directory called 'freesurfer'. Installing into the directory /usr/local is recommended. To install, mv the tar.gz file to whereever you wish to install freesurfer (in this example /usr/local) and type:

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):

 export FREESURFER_HOME=/usr/local/freesurfer

If you are using tcsh, run this command instead:

setenv FREESURFER_HOME /usr/local/freesurfer

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:

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.