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| [wiki:Self:DownloadAndInstall top] | [wiki:Self:Installation previous] | [wiki:Self: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'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type: {{{ 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: | == MINC toolkit perl path fix-up == |
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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]] |
Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, type: {{{ fixup_mni_perl_path }}} |
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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: | 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). |
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| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz` `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 == | http://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 (thats DOT license) and copy that file to your $FREESURFER_HOME. |
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| 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 == Next: [wiki:Self:SetupConfiguration setup and configure FreeSurfer]. |
[wiki:DownloadAndInstall top] | [wiki:Installation previous] | [wiki:SetupConfiguration next]
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'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type:
tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
Again, replacing <platform>-<release> with your Linux variant.
MINC toolkit perl path fix-up
Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, type:
fixup_mni_perl_path
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).
Freesurfer license file
A license file is required to enable the tools. One can be obtained for free by registering at:
http://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 (thats DOT license) and copy that file to your $FREESURFER_HOME.
Setup and Configuration
Next: [wiki:SetupConfiguration setup and configure FreeSurfer].