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| [[DownloadAndInstall|top]] | [[Installation|previous]] | [[SetupConfiguration|next]] | |
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| == To install FreeSurfer from tar files == | = 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 should be freesurfer/.license. | == Viewing 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. | 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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| 3. Enter the command: | == Installing contents == |
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| `tar xvfz DISTDIR/freesurfer.tar.gz` | 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: {{{ cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz }}} Again, replacing <platform>-<release> with your Linux variant. |
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| This will create a directory called freesurfer, in which will be the following files: | Note that for this installation example, your FREESURFER_HOME becomes: {{{ setenv FREESURFER_HOME /usr/local/freesurfer }}} |
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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]] |
Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
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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: | == Freesurfer license file == |
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| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz` `tar xvfz DISTDIR/talairach.tar.gz` |
A license file is required to enable the tools. One can be obtained for free by registering at: |
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| This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'. | https://surfer.nmr.mgh.harvard.edu/registration.html |
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| == MINC installation == | Upon receiving the license information by email, copy the three lines of the license information to a file named .license (that's DOT license) and copy that file to your $FREESURFER_HOME. |
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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. Refer to the file ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README.txt for more information on building the MINC toolkit from the source code. |
== Setup and Configuration == If you came from the Quick Install page, return to that [[QuickInstall|here]].<<BR>> Otherwise, go to this page to [[SetupConfiguration|setup and configure FreeSurfer]]. |
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:
cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
Again, replacing <platform>-<release> with your Linux variant.
Note that for this installation example, your FREESURFER_HOME becomes:
setenv FREESURFER_HOME /usr/local/freesurfer
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 (that's DOT license) and copy that file to your $FREESURFER_HOME.
Setup and Configuration
If you came from the Quick Install page, return to that here.
Otherwise, go to this page to setup and configure FreeSurfer.