Freesurfer

Environment Variables

In order for Freesurfer to work, the followings environment variables need to be set:

In bash:

$ export FREESURFER_HOME=/apps/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

In tcsh:

$ setenv FREESURFER_HOME /apps/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.csh

Optional Configuration Settings

The defaults declared in the SetUpFreeSurfer.csh script should work for most installations. However, users should feel free to edit this file to customize certain environment variables:

1. Your declaration of the FREESURFER_HOME variable could be moved within the SetUpFreeSurfer.csh script.

2. The default SUBJECTS_DIR, which is $FREESURFER_HOME/subjects, is most likely the first variable that you will want to customize, as you may keep different groups of subjects in different directories. You may include the following either directly in the SetUpFreeSurfer.csh script, or prior to calling it:

     setenv SUBJECTS_DIR <full path to subject dir> 

3. If you do NOT intend to use the functional tools, then add the following line to the additional configuration section:

     setenv NO_FSFAST 

If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:

     fsfasthome = getenv('FSFAST_HOME');
     fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
     path(path,fsfasttoolbox);

4. You may also wish to declare a path to an FSL installation you might have:

     setenv FSL_DIR /usr/local/fsl 

5. Save the file. You will need to source this file (SetUpFreeSurfer.csh) every time you want to use Freesurfer.