FreeSurfer: Difference between revisions

=Introduction=

[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki FreeSurfer] is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

FreeSurfer come up with a script <code>FreeSurferEnv.sh</code> that should be sourced to setup correctly the environment variables such as PATH and PERL5LIB:

{{Commands

|module load freesurfer/5.3.0

|source $EBROOTFREESURFER/FreeSurferEnv.sh

}}

=FreeSurfer 6.0 and newer versions=

Due to a change in the [https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense license terms], we '''now longer''' install the code as a central module. If needed, please install it in your home directory or in your project space with EasyBuild. Please follow the instructions below and if needed, contact the [[Technical Support|technical support]] for more assistance.  

# register for the FreeSurfer license key [https://surfer.nmr.mgh.harvard.edu/registration.html]

# Your user license will have to go in: <code>$HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license</code>

{{Commands

|module load freesurfer/6.0.0

|cd $FREESURFER_HOME

}}

Use nano or any other text editor of your choice and create a file <code>/home/$USER/.license</code> and add the license text (example):

<pre>

name.name@university.ca

ABCd0EFgHijKl

</pre>

To load the private module:  

<code>module load freesurfer/6.0.0</code>

The instructions are:

<pre>

newgrp def-someuser

eb FreeSurfer-6.0.1-centos6_x86_64.eb --installpath-modules=${moduledir} --prefix=${installdir} --sourcepath=${pathtosrc}

</pre>

If it complains about '''checksums''', add the option <code>--disable-enforce-checksums</code> to the <code>eb</code> command.

Each member of the group will need to create the directory <code>/home/$USER/.local/easybuild/modules/2017/Core/freesurfer</code> and put the file <code>6.0.1.lua</code>:

{{Commands

|mkdir -p /home/$USER/.local/easybuild/modules/2017/Core/freesurfer

|cp 6.0.1.lua /home/$USER/.local/easybuild/modules/2017/Core/freesurfer/

}}

The above will set the module (only the module file that points to the installation directory under project) in their own directory.

==Hippocampus and brainstem processing==

To perform processing of the hippocampus and brainstem, download and install matlab runtime 2012b from the freesurfer website:

<pre>

module load freesurfer/6.0.0

tar xvf matlab_runtime2012bLinux.tar.gz  

</pre>

==Example of working batch script for freesurfer version >= 6.0.0==

{{File

|name=mysub.sh

echo "Program finished with exit code $? at: `date`"

}}

==Examples of required walltimes==

* recon-all -hippocampal-subfields-T1 : <code>#SBATCH --time=00:40:00</code>

* recon-all -brainstem-structures: <code>#SBATCH --time=00:30:00</code>