FreeSurfer

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This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

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.

source $EBROOTFREESURFER/FreeSurferEnv.sh to correctly set environment variables such as PATH and PERL5LIB.

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.