|
Size: 3899
Comment:
|
Size: 1968
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| == Unpacking FreeSurfer == | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[TestingFreeSurfer|next]] |
| Line 3: | Line 3: |
| The distribution consists of the following files which can either be downloaded from http://surfer.nmr.mgh.harvard.edu or obtained from a CDROM. |
= FreeSurfer Linux Installation = |
| Line 7: | Line 5: |
| If you downloaded the distribution, unpack the tarball with this command: |
== Viewing contents == |
| Line 10: | Line 7: |
| `tar zxvf <the-file-you-downloaded>` | 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 12: | Line 13: |
| This will create a directory called freesurfer, which will henceforth be referred to as DISTDIR. |
== Installing contents == |
| Line 15: | Line 15: |
| If you are getting the files from a CDROM, the top level of the CDROM should have the following files in it. Use this directory as DISTDIR. |
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 18: | Line 22: |
| In DISTDIR are the following files: | |
| Line 20: | 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]] `minc.tar.gz` -- MNI MINC tools/binaries[[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 30: | Line 30: |
| == To install FreeSurfer from tar files == | (t)csh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} |
| Line 32: | Line 35: |
| 1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/download.html or from a previous installation. If you are using a previous installation, the license file should be freesurfer/.license. | Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
| Line 34: | Line 37: |
| 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. | == Freesurfer license file == |
| Line 36: | Line 39: |
| 3. Enter the command: | A license file is required to enable the tools. One can be obtained for free by registering at: |
| Line 38: | Line 42: |
| `tar xvfz DISTDIR/freesurfer.tar.gz` | https://surfer.nmr.mgh.harvard.edu/registration.html |
| Line 40: | Line 44: |
| This will create a directory called 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. |
| Line 42: | Line 47: |
| 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 below for details. Regardless, cd into your subjects directory and enter the commands: | |
| Line 44: | Line 48: |
| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz` This will populate your subjects directory with 'average7', and the FS tutorial's sample data set 'bert'. == 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 tools can be downloaded and installed directly from the MNI. As a service to our users, we also offer binaries for the MNI tools. Unfortunately, once the MNI binaries have been created, they will not work unless they are located in the same directory where they were compiled. Accordingly, if you want to install the binaries we supply, you will have to put them in the same place we put them. Also, perl must be in the same place as on our system. === To install our binaries === 1. Create a symbolic link to your perl in the location that matches ours. Execute the following commands. Note that you may need to execute some of them with root permission; su to root, use sudo, or talk to your system administrator. `cd /usr`[[BR]] `mkdir -p pubsw/bin`[[BR]] `cd pubsw/bin`[[BR]] `ln -s `which perl` perl`[[BR]] 2. Untar the MNI binaries and place them into the proper location. Execute the following commands: `cd /usr/pubsw`[[BR]] `mkdir -p packages`[[BR]] `cd packages`[[BR]] `tar xvfz DISTDIR/minc.tar.gz` === Install MNI talairach subject === Those not using the functional stream can skip this step. 1. cd to your subjects directory and enter the following command: `tar xvfz DISTDIR/talairach.tar.gz` This will create a directory called talairach. |
------ 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.