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FreeSurfer: Difference between revisions
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In the Compute Canada software stack, you may load the <code>freesurfer/5.3.0</code> module. | In the Compute Canada software stack, you may load the <code>freesurfer/5.3.0</code> module. | ||
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: | 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: | ||
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=FreeSurfer 6.0 and newer versions= | =FreeSurfer 6.0 and newer versions= | ||
Due to a change in the license | 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. | ||
==Download the software== | ==Download the software== | ||
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 | |||
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. | |||
==Installation in your Home with Easybuild== | ==Installation in your Home with Easybuild== | ||
The following procedure will install FreeSurfer 6.0.0 in your home directory in <code>.local/easybuild/software/2017/Core/freesurfer/6.0.0/</code>. | The following procedure will install FreeSurfer 6.0.0 in your home directory in <code>.local/easybuild/software/2017/Core/freesurfer/6.0.0/</code>. | ||
# Go to the folder that contains the <code>freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz </code> archive | # Go to the folder that contains the <code>freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz</code> archive | ||
# Unload all modules: <code>module purge</code> | # Unload all modules: <code>module purge</code> | ||
# Install with Easybuild: <code>eb FreeSurfer-6.0.0-centos6_x86_64.eb</code> | # Install with Easybuild: <code>eb FreeSurfer-6.0.0-centos6_x86_64.eb</code> | ||
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# Your user license will have to go in: <code>$HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license</code> | # Your user license will have to go in: <code>$HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license</code> | ||
<code> | <code> | ||
module load freesurfer/6.0.0 | module load freesurfer/6.0.0 | ||
cd $FREESURFER_HOME | cd $FREESURFER_HOME | ||
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==Hippocampus and brainstem processing== | ==Hippocampus and brainstem processing== | ||
To perform processing of the hippocampus and brainstem, download and install matlab runtime 2012b from the freesurfer website: | To perform processing of the hippocampus and brainstem, download and install matlab runtime 2012b from the freesurfer website: | ||