FreeSurfer

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

FreeSurfer 5.3 as a global module

In the Compute Canada software stack, you may load the freesurfer/5.3.0 module. For newer versions, please install FreeSurfer in your home directory or in your project space.

FreeSurfer 6.0 and newer versions

Due to a change in the license for the software, Compute Canada can not install it centrally as a module. Instead, users are invited to install the software in their home directory with EasyBuild.

Download the software

Select a version (6.0.0 or newer) in the download repository, and download the corresponding freesurfer-Linux*vX.Y.Z.tar.gz archive on your favourite cluster.

Installation in your Home with Easybuild

The following procedure will install FreeSurfer 6.0.0 in your home directory in .local/easybuild/software/2017/Core/freesurfer/6.0.0/.

1. Go to the folder that contains the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz archive
2. Unload all modules: module purge
3. Install with Easybuild: eb FreeSurfer-6.0.0-centos6_x86_64.eb
4. Your user license will have to go in: $HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license

To load the private module: module load freesurfer/6.0.0

When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for newer versions here.

Installation in a shared folder

It is possible to move installed files (with Easybuild) to the project space, but permissions have to be fixed.

• Recursively set the proper group ID of the freesurfer directory
• Move the data to the desired location in the project space
• Copy the module file to a shared location, and edit all paths in the module file.