FreeSurfer: Difference between revisions

When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer newer versions here].

==Checking the easybuild recipes for freesurfer== <!--T:11-->

You can check the easybuild recipes for freesurfer [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer online] on GitHub or via a command line ,<code>eb -S FreeSurfer</code>, from any Compute Canada cluster. If the version you are looking for is not listed, you may try to install the program with the option <code>--try-software-version=<the new version></code>. If that did not work, please contact the [[Technical support/en|technical support]] for help.

Using EasyBuild, it is possible to install the program in a shared location (like project) and make the code available for any other member of the group. The following will install freesurfer under the project <code>def-someuser</code> under the directory <code>/home/$USER/projects/def-someuser/$USER/software</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/2017/Core/freesurfer</code>.  

* You need to give all members of your group read and exec access to the installation directory <code>/home/$USER/projects/def-someuser/$USER</code>. To see how to give them access to this directory, please visit the [[Sharing data/en|data sharing]] page.

Each member of the group will need to create the directory <code>/home/$USER/.local/easybuild/modules/2017/Core/freesurfer</code> and put the file <code>6.0.1.lua</code>:

The above will set the module (only the module file that points to the installation directory under project) in their own directory.

To perform processing of the hippocampus and brainstem, download and install matlab runtime 2012b from the freesurfer website: