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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'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type:

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

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

MINC toolkit perl path fix-up

Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, as root user, type:

mkdir -p /usr/pubsw/bin
cd /usr/pubsw/bin
ln -s `which perl`

Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should return version information (v1.10).

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 (thats DOT license) and copy that file to your $FREESURFER_HOME.

Setup and Configuration

Next: [wiki:SetupConfiguration setup and configure FreeSurfer].