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FreeSurfer: Difference between revisions
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=Introduction= | =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. | [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 5.3 as a global module= | =FreeSurfer 5.3 as a global module= | ||
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: | ||
<code>source $EBROOTFREESURFER/FreeSurferEnv.sh</code> | <code>source $EBROOTFREESURFER/FreeSurferEnv.sh</code> | ||
=FreeSurfer 6.0 and newer versions= | =FreeSurfer 6.0 and newer versions= | ||
Due to a change in the [https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense license terms], we '''now longer''' install the code as a central module. If needed, please install it in your home directory or in your project space with EasyBuild. | Due to a change in the [https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense license terms], we '''now longer''' install the code as a central module. If needed, please install it in your home directory or in your project space with EasyBuild. | ||
==Download the software== | ==Download the software== | ||
Select a version (6.0.0 or newer) in the [https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ download repository], and download the corresponding <code>freesurfer-Linux*vX.Y.Z.tar.gz</code> archive on your favorite cluster. | Select a version (6.0.0 or newer) in the [https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ download repository], and download the corresponding <code>freesurfer-Linux*vX.Y.Z.tar.gz</code> archive on your favorite cluster. | ||
==Checking the easybuild recipes== | ==Checking the easybuild recipes== | ||
You can check the easybuild recipes for freesurfer [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer online] on GitHub or via a command line ,<code>eb -S FreeSurfer</code>, from any Compute Canada cluster. | You can check the easybuild recipes for freesurfer [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer online] on GitHub or via a command line ,<code>eb -S FreeSurfer</code>, from any Compute Canada cluster. | ||
==Installation in your Home with Easybuild== | ==Installation in your Home with Easybuild== | ||
The following procedure will install FreeSurfer 6.0.0 in your home directory in <code>/home/$USER/.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>/home/$USER/.local/easybuild/software/2017/Core/freesurfer/6.0.0/</code>. | ||
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To load the private module: | To load the private module: | ||
<code>module load freesurfer/6.0.0</code> | <code>module load freesurfer/6.0.0</code> | ||
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==Installation in a shared folder== | ==Installation in a shared folder== | ||
Using EasyBuild, it is possible to install the program in a shared location (like project) and make the code available for any other member of the group. The following will install freesurfer under the project <code>def-someuser</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/2017</code>. | Using EasyBuild, it is possible to install the program in a shared location (like project) and make the code available for any other member of the group. The following will install freesurfer under the project <code>def-someuser</code> and the module under the user's directory <code>/home/$USER/.local/easybuild/modules/2017</code>. | ||
The instructions are: | The instructions are: | ||
<pre> | <pre> | ||
newgrp def-someuser | newgrp def-someuser | ||
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{{Commands | {{Commands | ||
|module load freesurfer/6.0.1 | |module load freesurfer/6.0.1 | ||
}} | }} | ||
==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: | ||