|
Size: 2323
Comment:
|
Size: 1968
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| [[DownloadAndInstall|top]] | [[Installation|previous]] | [[TestingFreeSurfer|next]] | |
| Line 2: | Line 3: |
| == To install FreeSurfer from tar files == | = FreeSurfer Linux Installation = |
| Line 4: | Line 5: |
| 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 == |
| Line 6: | Line 7: |
| 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. |
| Line 8: | Line 13: |
| 3. Enter the command: | == Installing contents == |
| Line 10: | Line 15: |
| `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: {{{ $> tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz }}} Again, replacing <platform>-<release> with your Linux variant. |
| Line 12: | Line 22: |
| This will create a directory called freesurfer, in which will be the following files: | |
| Line 14: | Line 23: |
| `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]] |
== 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 |
| Line 23: | Line 30: |
| 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: | (t)csh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} |
| Line 25: | Line 35: |
| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz` `tar xvfz DISTDIR/talairach.tar.gz` |
Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
| Line 29: | Line 37: |
| This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'. | == Freesurfer license file == |
| Line 31: | Line 39: |
| == MINC installation == | A license file is required to enable the tools. One can be obtained for free by registering at: |
| Line 33: | Line 42: |
| 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. | https://surfer.nmr.mgh.harvard.edu/registration.html |
| Line 35: | Line 44: |
| 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. | 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 [[QuickInstall|here]].<<BR>> |
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:
$> 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.