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| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[TestingFreeSurfer|next]] |
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| == 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. |
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| The tar.gz file will extract to a directory called 'freesurfer'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type: |
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: |
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| tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz | $> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz |
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| == MINC toolkit perl path fix-up == | |
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| Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, as root user, type: | == 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): |
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| mkdir -p /usr/pubsw/bin cd /usr/pubsw/bin ln -s `which perl` |
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 |
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| Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should return version information (v1.10). |
Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
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| A license file is required to enable the tools. One can be | A license file is required to enable the tools. One can be |
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| http://surfer.nmr.mgh.harvard.edu/registration.html | https://surfer.nmr.mgh.harvard.edu/registration.html |
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| lines of the license information to a file named .license (thats DOT license) and copy that file to your $FREESURFER_HOME. |
lines of the license information to a file named license.txt and copy that file to your $FREESURFER_HOME. |
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| == Configuration == | |
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| The defaults should work for most users. However, [wiki:Self:SetupConfiguration this page shows some of the possible configuration changes]. Or, you can proceed to [wiki:Self:TestingFreeSurfer the page on how to test FreeSurfer]. | ------ If you came from the Quick Install page, return to that [[QuickInstall|here]].<<BR>> |
FreeSurfer Linux Installation
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.