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| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[TestingFreeSurfer|next]] = FreeSurfer Linux Installation = == Installing contents == Installing freesurfer involves simply extracting the contents of the .tar.gz file (will extract to a directory called 'freesurfer'). Installing into the directory {{{/usr/local}}} is recommended. For example: {{{ $> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz }}} Again, replacing <platform>-<release> with your Linux variant. |
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| work in progress!!! | == 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! [[InternalFreeSurferDistributions|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. |
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== FreeSurfer Linux Installation == 1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/registration.html or from a previous installation. If you are using a previous installation, the license file is found in the main freesurfer directory and is called '.license'. 2. cd to the directory just above where you want !FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition. 3. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename downloaded): `tar xvfz freesurfer.tar.gz` This will create a directory called freesurfer, in which will be the following files: `INSTALL` -- this file[[BR]] `license.freesurfer` -- license agreement[[BR]] `freesurfer.tar.gz` -- !FreeSurfer tree[[BR]] `talairach.tar.gz` -- MNI 305 talairach brain[[BR]] `bert.raw.tar.gz` -- !FreeSurfer tutorial data[[BR]] `bert.func.tar.gz` -- !FreeSurfer functional tutorial data[[BR]] `bert.recon.tar.gz` -- reconstructed !FreeSurfer tutorial data[[BR]] `average7.tar.gz` -- contains average labels for checking spherical morph[[BR]] 4. The default subjects directory (the directory in which your subjects' data will be placed) is freesurfer/subjects. You may wish set to up your installation differently, e.g. if you have a large external hard drive you want to use for subject data. See the [wiki:Self:SetupConfiguration 'Setup and Configuration'] section for details. Regardless, cd into your subjects directory (the default is called 'subjects', located within the freesurfer installation directory) and enter the commands: `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz`[[BR]] `tar xvfz DISTDIR/talairach.tar.gz` This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'. == MINC installation == !FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through !FreeSurfer. The [http://www.bic.mni.mcgill.ca/software/distribution MNI-BIC software distribution page] contains binaries for most platforms. Note: the Mac OS X FreeSurfer distribution contains the MINC toolkit in its installation. An alternative is to build the tools required by !FreeSurfer from source. A special [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz source code bundle], with build scripts, has been prepared by MGH for !FreeSurfer users. Refer to the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README.txt README file] for more information on building the MINC toolkit from this source code bundle. |
------ If you came from the Quick Install page, return to that [[QuickInstall|here]].<<BR>> |
FreeSurfer Linux Installation
Installing contents
Installing freesurfer involves simply extracting the contents of the .tar.gz file (will extract to a directory called 'freesurfer'). Installing into the directory /usr/local is recommended. For example:
$> 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.