Differences between revisions 4 and 10 (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, cd into 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

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

rm $FREESURFER_HOME/runtime2012b.tar.gz

-  ⇤ ← Revision 4 as of 2015-04-29 06:50:06 → 
  Size: 1357
  Editor: JuanIglesias
  Comment:
+   ← Revision 10 as of 2015-04-29 09:21:37 → ⇥
  Size: 1500
  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 can be downloaded from:
+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 (note that some commands might require root permissions, if FreeSurfer 6.0 is installed in a system directory such as /usr/local/):
 Line 5:
-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:
+ * First, we will define the environment variable FREESURFER_HOME, which points at the FreeSurfer 6.0 directory. For example, in tcsh or csh:
-Line 22:
+Line 14:
-Finally, create a symbolic link named MCRv80 in your FreeSurfer directory pointing to the installation directory of the runtime, i.e.:
+ * Second, cd into your FreeSurfer 6.0 directory:
-Line 24:
+Line 16:
-sudo ln -s <MATLAB_RUNTIME_INSTALLATION_DIRECTORY> $FREESURFER_HOME/MCRv80
+cd $FREESURFER_HOME
-Line 26:
+Line 18:
-The installation directory of the runtime should contain the following subdirectories (independently of whether it is a linux or mac installation):
-Line 28:
+Line 19:
-appdata , bin , etc , extern , java , resources , rtw , runtime , simulink , sys , toolbox , X11
+ * 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
}}}

 * If the brainstem and/or hippocampal subfield modules are working fine, you can delete the packed runtime file with:
{{{
rm $FREESURFER_HOME/runtime2012b.tar.gz
}}}