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FreeSurfer: Difference between revisions
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Select a version (6.0.0 or newer) in the [https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ download repository], and download the corresponding <code>freesurfer-Linux*vX.Y.Z.tar.gz</code> archive on your favorite cluster. | Select a version (6.0.0 or newer) in the [https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ download repository], and download the corresponding <code>freesurfer-Linux*vX.Y.Z.tar.gz</code> archive on your favorite cluster. | ||
==Checking the easybuild recipes== | |||
You can check the easybuild recipes for freesurfer [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer online] on GitHub or via a command line from any Compute Canada clusters: | |||
{{Commands | |||
eb -S FreeSurfer | |||
CFGS1=/cvmfs/soft.computecanada.ca/easybuild/easyconfigs/f/FreeSurfer | |||
CFGS2=/cvmfs/soft.computecanada.ca/easybuild/ebfiles_repo/2017/FreeSurfer | |||
* $CFGS1/FreeSurfer-5.3.0-centos4_x86_64.eb | |||
* $CFGS1/FreeSurfer-5.3.0-centos6_x86_64.eb | |||
* $CFGS1/FreeSurfer-5.3.0-matlab-2013.patch | |||
* $CFGS1/FreeSurfer-6.0.0-centos6_x86_64.eb | |||
* $CFGS1/FreeSurfer-6.0.1-centos6_x86_64.eb | |||
* $CFGS1/FreeSurfer-7.1.0-centos6_x86_64.eb | |||
* $CFGS1/FreeSurfer-7.1.0-centos7_x86_64.eb | |||
* $CFGS2/FreeSurfer-5.3.0-centos4_x86_64.eb | |||
* $CFGS2/FreeSurfer-5.3.0-centos6_x86_64.eb | |||
* $CFGS2/FreeSurfer-5.3.0-matlab-2013.patch | |||
* $CFGS2/FreeSurfer-6.0.0-centos6_x86_64.eb | |||
}} | |||
==Installation in your Home with Easybuild== | ==Installation in your Home with Easybuild== | ||
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When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer newer versions here]. | When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer newer versions here]. | ||
==Installation in a shared folder== | ==Installation in a shared folder== | ||
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</pre> | </pre> | ||
If it complains about checksums, add the option <code>--disable-enforce-checksums</code> | If it complains about '''checksums''', add the option <code>--disable-enforce-checksums</code> to the <code>eb</code> command. | ||
To make the program accessible for all members of the group, two more steps are required: | To make the program accessible for all members of the group, two more steps are required: | ||
* You need to give all members of your group read and exec access to the installation directory </home/$USER/projects/def-someuser/$USER>. To see how to give them access to this directory, please visit the [[Sharing data/en|data sharing]] page. | * You need to give all members of your group read and exec access to the installation directory <code>/home/$USER/projects/def-someuser/$USER,</code>. To see how to give them access to this directory, please visit the [[Sharing data/en|data sharing]] page. | ||
* Each member of the group will need to put the module file in their own home directories. The module file is within the directory: | * Each member of the group will need to put the module file in their own home directories. The module file is within the directory: | ||
<pre> | <pre> | ||
/home/$USER/.local/easybuild/software/2017/Core/freesurfer/6.0.1 | /home/$USER/.local/easybuild/software/2017/Core/freesurfer/6.0.1.lua</code> | ||
</pre> | </pre> | ||
/home/ | Each member of the group will need to create the directory <code>/home/$USER/.local/easybuild/software/2017/Core/freesurfer</code> and put the file <code>6.0.1.lua</code>: | ||
{{Commands | |||
|mkdir -p /home/$USER/.local/easybuild/software/2017/Core/freesurfer | |||
mkdir -p /home/$USER/.local/easybuild | |cp 6.0.1.lua /home/$USER/.local/easybuild/software/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. | The above will set the module (only the module file that points to the installation directory under project) in their own directory. | ||
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The module can be loaded from their own accounts using: | The module can be loaded from their own accounts using: | ||
module load | {{Commands | ||
|module load freesurfer/6.0.1 | |||
|cd $FREESURFER_HOME | |||
}} | |||
==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 | |||
cd $FREESURFER_HOME | |||
curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "matlab_runtime2012bLinux.tar.gz" | |||
tar xvf matlab_runtime2012bLinux.tar.gz | |||
</pre> | |||
==Example of working batch script for freesurfer version >= 6.0.0== | ==Example of working batch script for freesurfer version >= 6.0.0== | ||