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work in progress!!!

= FreeSurfer Linux Installation =
= FreeSurfer Linux Installation !!! work in progress!!! =

[wiki:FreeSurferWiki top] | [wiki:Installation previous] | [wiki:SetupConfiguration next]

FreeSurfer Linux Installation !!! work in progress!!!

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 fileBR license.freesurfer -- license agreementBR freesurfer.tar.gz -- FreeSurfer treeBR talairach.tar.gz -- MNI 305 talairach brainBR bert.raw.tar.gz -- FreeSurfer tutorial dataBR bert.func.tar.gz -- FreeSurfer functional tutorial dataBR bert.recon.tar.gz -- reconstructed FreeSurfer tutorial dataBR average7.tar.gz -- contains average labels for checking spherical morphBR

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: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.gzBR 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.

LinuxInstall (last edited 2015-12-21 17:04:28 by ZekeKaufman)