Matlab Runtime

The brainstem and hippocampal subfield modules in FreeSurfer 6.0 require the Matlab R2012 runtime. This runtime is free, and therefore NO MATLAB LICENSES ARE REQUIRED TO USE THESE PACKAGES. The runtime is installed as follows (note that some commands might require root permissions, if FreeSurfer 6.0 is installed in a system directory such as /usr/local/):

First, we will define the environment variable FREESURFER_HOME, which points at the FreeSurfer 6.0 directory. For example, in tcsh or csh:

setenv FREESURFER_HOME /usr/local/freesurfer

Or, in bash:

export FREESURFER_HOME=/usr/local/freesurfer

Second, change directory to your FreeSurfer 6.0 directory:

cd $FREESURFER_HOME

Next, download the runtime as follows:

In linux:

curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "runtime2012b.tar.gz"

In MAC:

curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bMAC.tar.gz" -o "runtime2012b.tar.gz"

Finally, unpack it with:

tar xvf runtime2012b.tar.gz

You are now done! The brainstem and/or hippocampal subfield modules should now work fine. If that is the case, you can delete the packed runtime file with:

rm $FREESURFER_HOME/runtime2012b.tar.gz