Matlab Runtime

The brainstem and hippocampal subfield modules in FreeSurfer 6.0 require the Matlab R2012b (v8.0) runtime (note that development versions from January 2018 onwards require the Matlab R2014b - v8.4 - runtime instead). 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 - i.e., prepend them by sudo - if FreeSurfer is installed in a system directory such as /usr/local/):

First, we will define the environment variable FREESURFER_HOME the same way as above. 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 directory:

cd $FREESURFER_HOME

Next, download the runtime as follows:

In linux, for FreeSurfer 6.0 or development versions from 2017:

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

or for development versions from January 2018 onwards:

curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz" -o "runtime.tar.gz"

In MAC, for FreeSurfer 6.0 or development versions from 2017:

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

or for development versions from January 2018 onwards:

curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bMAC.tar.gz" -o "runtime.tar.gz"

Finally, unpack it with:

tar xvf runtime.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/runtime.tar.gz

Frequently asked questions (FAQ)

I already have Matlab 2012b/2014b installed on my system. Do I really need to download and install the runtime?

If you already have the right version of Matlab installed on your system, there is no need to dowload the runtime. Note that it has to be the specific version of Matlab, depending on your FreeSurfer version: Matlab R2012b for FreeSurfer 6.0 or dev versions from 2017, and Matlab R2014b for dev versions from 2018 on; if it is not 2012b, you need to download the runtime as described above. If it is indeed 2012b/2014b, all you need to do is to create a symbolic link named MCRv80/MCRv84 in your FreeSurfer directory that points to the main Matlab directory.

First, we will define the environment variable FREESURFER_HOME. 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 directory:

cd $FREESURFER_HOME

Finally, create the symbolic link. For FreeSurfer 6.0 and dev versions from 2017:

ln -s <MatlabRootDirectory> ./MCRv80

And, for dev versions from 2018:

ln -s <MatlabRootDirectory> ./MCRv84

The matlab root directory can be easily obtained by executing the command "matlabroot" in Matlab. It typically looks like "/Applications/MATLAB_R201Xb.app/" in MAC, and "/usr/local/matlab/8.X" in Linux.