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← Revision 31 as of 2015-12-21 17:04:28 ⇥
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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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| == FreeSurfer Linux Installation == | = FreeSurfer Linux Installation = |
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| 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'. | == Installing contents == |
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| 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. | 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: |
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| 3. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename downloaded): | {{{ $> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz }}} Again, replacing <platform>-<release> with your Linux variant. |
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| `tar xvfz freesurfer.tar.gz` | |
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| This will create a directory called freesurfer, in which will be the following files: | == 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 |
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| `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]] |
(t)csh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} |
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| 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: | Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
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| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz`[[BR]] `tar xvfz DISTDIR/talairach.tar.gz` |
== Freesurfer license file == |
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| This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'. | A license file is required to enable the tools. One can be obtained for free by registering at: |
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| == MINC installation == | https://surfer.nmr.mgh.harvard.edu/registration.html |
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| !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. | 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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| 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. | |
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| 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.