Differences between revisions 1 and 10 (spanning 9 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 1 as of 2015-03-05 10:45:59 → 
  Size: 20
  Editor: NickSchmansky
  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.
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+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/):

 * 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
}}}