Deletions are marked like this. | Additions are marked like this. |
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tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz | $> tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz |
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tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz | $> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz |
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export FREESURFER_HOME=/usr/local/freesurfer }}} |
bash $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh |
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If you are using tcsh, run this command instead: {{{ setenv FREESURFER_HOME /usr/local/freesurfer |
(t)csh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh |
FreeSurfer Linux Installation
Viewing contents
To view the contents of a distribution, once downloaded, type:
$> tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz
replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file.
Installing contents
The tar.gz file will extract to a directory called 'freesurfer'. Installing into the directory /usr/local is recommended. To install, mv the tar.gz file to whereever you wish to install freesurfer (in this example /usr/local) and type:
$> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
Again, replacing <platform>-<release> with your Linux variant.
Setup and Configuration
Type the following command into a terminal window to setup and source the FreeSurfer environment. Note that you must choose the directory where you extracted freesurfer to become your FREESURFER_HOME (/usr/local/freesurfer in our example):
bash $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh (t)csh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh
Reminder to NMR Center users! You already have FreeSurfer installed on your system!
Freesurfer license file
A license file is required to enable the tools. One can be obtained for free by registering at:
https://surfer.nmr.mgh.harvard.edu/registration.html
Upon receiving the license information by email, copy the three lines of the license information to a file named license.txt and copy that file to your $FREESURFER_HOME.
If you came from the Quick Install page, return to that here.