Differences between revisions 6 and 12 (spanning 6 versions)

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

Frequently asked questions (FAQ)

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

If you already have Matlab 2012b installed on your system, there is no need to dowload the runtime. Note that it has to be this specific version of Matlab; if it is not 2012b, you need to download the runtime as described above. If it is indeed 2012b, all you need to do is to create a symbolic link named MCVv80 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 6.0 directory:

cd $FREESURFER_HOME

Finally, create the symbolic link:

ln -s <MatlabRootDirectory> ./MCRv80

where the matlab root directory can be easily obtained by executing the command "matlabroot" in Matlab R2012b. It typically looks like "/Applications/MATLAB_R2012b.app/" in MAC, and "/usr/local/matlab/8.0" in Linux.

-  ⇤ ← Revision 6 as of 2015-04-29 08:29:34 → 
  Size: 3617
  Editor: JuanIglesias
  Comment:
+   ← Revision 12 as of 2016-07-28 11:38:00 → ⇥
  Size: 2718
  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 R2012 runtime. 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, if FreeSurfer 6.0 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:
+ * First, we will define the environment variable FREESURFER_HOME, which points at the FreeSurfer 6.0 directory. For example, in tcsh or csh:
 Line 16:
-Second, cd into your FreeSurfer 6.0 directory:
+ * Second, change directory to your FreeSurfer 6.0 directory:
 Line 21:
-Next, download the runtime as follows:
+ * Next, download the runtime as follows:

In linux:
-Line 23:
+Line 25:
-wget
+curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "runtime2012b.tar.gz"
-Line 26:
+Line 28:
-Finally, unpack it with:
+In MAC:
-Line 28:
+Line 30:
+curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bMAC.tar.gz" -o "runtime2012b.tar.gz"
-Line 31:
+Line 33:
-If the brainstem and/or hippocampal subfield modules are working fine, you can delete the packed runtime file with:
+ * Finally, unpack it with:
-Line 33:
+Line 35:
-rm $FREESURFER_HOME/runtime2012bLinux.tar.gz
+tar xvf runtime2012b.tar.gz
-Line 36:
+Line 38:
-setenv MCR_INSTALL_DIR /usr/local/MCR_runtime

Or, in bash:
+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:
 Line 40:
-export FREESURFER_HOME=/usr/local/freesurfer

export MCR_INSTALL_DIR=/usr/local/MCR_runtime
+rm $FREESURFER_HOME/runtime2012b.tar.gz
-Line 46:
+Line 44:
-Then, from an empty directory with enough space, download the runtime installation files with wget and then unzip them:
+=== Frequently asked questions (FAQ) ===
-Line 48:
+Line 46:
-{{{
wget http://www.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_glnxa64_installer.zip
+ * '''I already have Matlab 2012b installed on my system. Do I really need to download and install the runtime?'''
-Line 51:
+Line 48:
-unzip MCR_R2012b_glnxa64_installer.zip
}}}
+If you already have Matlab 2012b installed on your system, there is no need to dowload the runtime. '''Note that it has to be this specific version of Matlab'''; if it is not 2012b, you need to download the runtime as described above. If it is indeed 2012b, all you need to do is to create a symbolic link named MCVv80 in your FreeSurfer directory that points to the main Matlab directory.
-Line 54:
+Line 50:
-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. In tcsh or csh:
-Line 74:
+Line 59:
-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 6.0 directory:
-Line 77:
+Line 61:
-sudo ln -s <RUNTIME_INSTALL_DIR>/v80 $FREESURFER_HOME/MCRv80
+cd $FREESURFER_HOME
-Line 80:
+Line 64:
-== 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:
+Finally, create the symbolic link:
-Line 87:
+Line 66:
-setenv FREESURFER_HOME /usr/local/freesurfer
+ln -s <MatlabRootDirectory> ./MCRv80
-Line 89:
+Line 68:
-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
+where the matlab root directory can be easily obtained by executing the command "matlabroot" in Matlab R2012b. It typically looks like "/Applications/MATLAB_R2012b.app/" in MAC, and "/usr/local/matlab/8.0" in Linux.