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FreeSurfer: Difference between revisions
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=Introduction= <!--T:1--> | =Introduction= <!--T:1--> | ||
[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 the 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= <!--T:2--> | =FreeSurfer 5.3 as a global module= <!--T:2--> | ||
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FreeSurfer | FreeSurfer comes up with a script <code>FreeSurferEnv.sh</code> that should be sourced to set up correctly the environment variables such as PATH and PERL5LIB: | ||
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{{Commands | {{Commands | ||
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=FreeSurfer 6.0 and newer versions= <!--T:4--> | =FreeSurfer 6.0 and newer versions= <!--T:4--> | ||
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 | 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 assistance. | ||
==Download the software== <!--T:5--> | ==Download the software== <!--T:5--> | ||
Select a version (6.0.0 or newer) in the [https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ download repository] | 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== <!--T:6--> | ==Installation in your Home with Easybuild== <!--T:6--> | ||
The following procedure will install FreeSurfer 6.0.0 | The following procedure will install FreeSurfer 6.0.0 in <code>/home/$USER/.local/easybuild/software/2017/Core/freesurfer/6.0.0/</code>. The installation of FreeSurfer requires some memory and due to the restrictions of memory stack size on the login nodes on Compute Canada clusters, the installation may fail because of the memory. To overcome this issue, you may need to use an [[Running_jobs#Interactive_jobs|interactive job]] by asking for enough memory (8 GB or so) to install the code. | ||
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# 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 | # Unload all modules with <code>module purge</code>. | ||
# Install with | # Install with EasyBuild using <code>eb FreeSurfer-6.0.0-centos6_x86_64.eb --disable-enforce-checksums</code>. | ||
# | # Register for the FreeSurfer license key [https://surfer.nmr.mgh.harvard.edu/registration.html]. | ||
# Your user license will have to go in | # Your user license will have to go in | ||
|module load freesurfer/6.0.0 | |module load freesurfer/6.0.0 | ||
|cd $FREESURFER_HOME | |cd $FREESURFER_HOME | ||
}} | }} | ||
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Use nano or any other text editor of your choice and create a file <code>/home/$USER/.license</code> and add the license text (example): | 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): | ||