Differences between revisions 5 and 15 (spanning 10 versions)

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.

-  ⇤ ← Revision 5 as of 2015-04-29 08:24:27 → 
  Size: 3191
  Editor: JuanIglesias
  Comment:
+   ← Revision 15 as of 2018-01-17 08:05:25 → ⇥
  Size: 3634
  Editor: JuanIglesias
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-The [[https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures|brainstem]] and [[https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields|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:
+The [[https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures|brainstem]] and [[https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields|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'''.
 Line 5:
-== Linux ==
+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/):
 Line 7:
-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 

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:
+ * First, we will define the environment variable FREESURFER_HOME the same way as above. For example, in tcsh or csh:
-Line 50:
+Line 16:
+ * Second, change directory to your FreeSurfer directory:
{{{
cd $FREESURFER_HOME
}}}
-Line 51:
+Line 21:
-Finally, create a symbolic link named MCRv80 in your FreeSurfer directory pointing to the installation directory of the runtime as follows:
+ * Next, download the runtime as follows:

In linux, for FreeSurfer 6.0 or development versions from 2017:
-Line 53:
+Line 25:
-sudo ln -s <RUNTIME_INSTALL_DIR>/v80 $FREESURFER_HOME/MCRv80
+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
-Line 57:
+Line 52:
-== MAC ==
+=== Frequently asked questions (FAQ) ===
-Line 59:
+Line 54:
-http://www.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_maci64_installer.zip
+ * '''I already have Matlab 2012b/2014b installed on my system. Do I really need to download and install the runtime?'''
-Line 61:
+Line 56:
-Once you have installed the runtime, define your environment variable FREESURFER_HOME pointing at your FreeSurfer 6 directory. For example, in tcsh or csh:
+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:
-Line 70:
+Line 67:
-Finally, create a symbolic link named MCRv80 in your FreeSurfer directory pointing to the installation directory of the runtime as follows:
+Second, change directory to your FreeSurfer directory:
-Line 72:
+Line 69:
-sudo ln -s <RUNTIME_INSTALL_DIR>/ $FREESURFER_HOME/MCRv80
+cd $FREESURFER_HOME
-Line 74:
+Line 71:
-The installation directory of the runtime should contain the following subdirectories (independently of whether it is a linux or mac installation):
-Line 76:
+Line 72:
-appdata , bin , etc , extern , java , resources , rtw , runtime , simulink , sys , toolbox , X11
+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.