Differences between revisions 5 and 11 (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

-  ⇤ ← Revision 5 as of 2015-04-29 08:24:27 → 
  Size: 3191
  Editor: JuanIglesias
  Comment:
+   ← Revision 11 as of 2015-04-29 09:25:07 → ⇥
  Size: 1549
  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:
+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 ==

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, which points at the FreeSurfer 6.0 directory. For example, in tcsh or csh:
-Line 50:
+Line 14:
-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 53:
+Line 16:
-sudo ln -s <RUNTIME_INSTALL_DIR>/v80 $FREESURFER_HOME/MCRv80
+cd $FREESURFER_HOME
-Line 56:
+Line 19:
+ * Next, download the runtime as follows:
-Line 57:
+Line 21:
-== 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:
+In linux:
-Line 63:
+Line 23:
-setenv FREESURFER_HOME /usr/local/freesurfer 
}}}
Or, in bash: 
{{{
export FREESURFER_HOME=/usr/local/freesurfer
+curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "runtime2012b.tar.gz"
-Line 70:
+Line 26:
-Finally, create a symbolic link named MCRv80 in your FreeSurfer directory pointing to the installation directory of the runtime as follows:
+In MAC:
-Line 72:
+Line 28:
-sudo ln -s <RUNTIME_INSTALL_DIR>/ $FREESURFER_HOME/MCRv80
+curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bMAC.tar.gz" -o "runtime2012b.tar.gz"
-Line 74:
+Line 30:
-The installation directory of the runtime should contain the following subdirectories (independently of whether it is a linux or mac installation):
-Line 76:
+Line 31:
-appdata , bin , etc , extern , java , resources , rtw , runtime , simulink , sys , toolbox , X11
+ * 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
}}}