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:

Linux

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, cd into your FreeSurfer 6.0 directory:

cd $FREESURFER_HOME

Next, download the runtime as follows:

wget 

Finally, unpack it with:

If the brainstem and/or hippocampal subfield modules are working fine, you can delete the packed runtime file with:

rm $FREESURFER_HOME/runtime2012bLinux.tar.gz

setenv MCR_INSTALL_DIR /usr/local/MCR_runtime

Or, in bash:

export FREESURFER_HOME=/usr/local/freesurfer

export MCR_INSTALL_DIR=/usr/local/MCR_runtime

Then, from an empty directory with enough space, download the runtime installation files with wget and then unzip them:

wget http://www.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_glnxa64_installer.zip

unzip MCR_R2012b_glnxa64_installer.zip

Next, execute the installer:

./install

and MCR_INSTALL_DIR, which points at the directory where we want to install the Matlab runtime. This can be any directory of your choice, but you will need root permissions if you want to install the runtime under a system directory (e.g., /usr/local).

This will open a graphical interaface that will guide you through the installation process. When you are prompted to specify the installation folder, simply type: $MCR_INSTALL_DIR a window that ask you in which directory you want to install the runtime. This can be any directory of your choice, but you will need root permissions if you want to install the runtime under a system directory (e.g., /usr/local). Let's call this directory <RUNTIME_INSTALL_DIR>.

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 as follows:

sudo ln -s <RUNTIME_INSTALL_DIR>/v80 $FREESURFER_HOME/MCRv80

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 as follows:

sudo ln -s <RUNTIME_INSTALL_DIR>/ $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