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Freesufer cluster installation

Freesurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.

Check system requirements and download. Note that registration and a license key is required for functionality, but not installation.

Create a source directory, change to it, download, extract, discover that everything is bundled, create the application directory and move everything across.


mkdir /usr/local/src/FREESURFER
cd /usr/local/src/FREESURFER
wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Li...
tar xvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
mkdir -p /usr/local/freesurfer/5.3.0
cd /usr/local/freesurfer/5.3.0
mv /usr/local/src/FREESURFER/freesurfer/* .

Change to the appropriate modules directory, check for .desc and .version and .base, create a symlink to .base


cd /usr/local/Modules/modulefiles/freesurfer
ln -s .base 5.3.0

When installing new versions check through the .base file for any alterations that may be required (e.g., new perl path or vtk library).

The .base install file looks like the following:


#%Module1.0#####################################################################
##
## $name modulefile
##
set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set loading [module-info mode load]
set desc [join [read [ open "/usr/local/Modules/modulefiles/$name/.desc" ] ] ]
set home /usr/local/$name/$ver/
proc ModulesHelp { } {
puts stderr "\tThis module sets the envinronment for $name v$ver"
}
module-whatis "$desc (v$ver)"
prepend-path PATH $home/bin:$home/mni/bin:$home/fsfast/bin
prepend-path FREESURFER_HOME $home
prepend-path LD_LIBRARY_PATH $home/lib/vtk/lib/vtk-5.6
setenv FS_OVERRIDE 0
setenv PERL5LIB $home/mni/lib/perl5/5.8.5
setenv OS Linux
setenv LOCAL_DIR $home/local
setenv FSFAST_HOME $home/fsfast
setenv MNI_PERL5LIB $home/mni/lib/perl5/5.8.5
setenv FMRI_ANALYSIS_DIR $home/fsfast
setenv FSF_OUTPUT_FORMAT nii
setenv MINC_BIN_DIR $home/mni/bin
setenv SUBJECTS_DIR $home/subjects
setenv FUNCTIONALS_DIR $home/sessions
setenv MINC_LIB_DIR $home/mni/lib
setenv MNI_DIR $home/mni
setenv FIX_VERTEX_AREA ""
setenv MNI_DATAPATH $home/mni/data

Add user licenses (license.txt) in the root directory of the application.