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 can be downloaded from:
Linux:
http://www.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_glnxa64_installer.zip
MAC:
http://www.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_maci64_installer.zip
Once you have installed the runtime, define your environment variable FREESURFER_HOME pointing at your FreeSurfer 6 directory. For example, in tcsh or csh:
setenv FREESURFER_HOME /usr/local/freesurfer
Or, in bash:
export FREESURFER_HOME=/usr/local/freesurfer
Finally, create a symbolic link named MCRv80 in your FreeSurfer directory pointing to the installation directory of the runtime, i.e.:
sudo ln -s <MATLAB_RUNTIME_INSTALLATION_DIRECTORY> $FREESURFER_HOME/MCRv80
The installation directory of the runtime should contain the following subdirectories (independently of whether it is a linux or mac installation):
appdata , bin , etc , extern , java , resources , rtw , runtime , simulink , sys , toolbox , X11