|
Size: 2434
Comment:
|
Size: 1603
Comment: note on using fixup_mni_perl_path
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| == To install FreeSurfer from tar.gz files == | [wiki:Self:DownloadAndInstall top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] |
| Line 3: | Line 3: |
| 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'. | = FreeSurfer Linux Installation = |
| Line 5: | Line 5: |
| 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. | == Viewing contents == |
| Line 7: | Line 7: |
| 3. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename 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 9: | Line 13: |
| `tar xvfz freesurfer.tar.gz` | == Installing contents == |
| Line 11: | Line 15: |
| This will create a directory called freesurfer, in which will be the following files: | 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. |
| Line 13: | Line 22: |
| `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]] |
== MINC toolkit perl path fix-up == |
| Line 22: | Line 24: |
| 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: | Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, type: {{{ fixup_mni_perl_path }}} |
| Line 24: | Line 29: |
| `tar xvfz DISTDIR/average7.tar.gz` [[BR]] `tar xvfz DISTDIR/bert.recon.tar.gz`[[BR]] `tar xvfz DISTDIR/talairach.tar.gz` |
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). |
| Line 28: | Line 31: |
| This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'. | == Freesurfer license file == |
| Line 30: | Line 33: |
| == MINC installation == | A license file is required to enable the tools. One can be obtained for free by registering at: |
| Line 32: | Line 36: |
| !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. | http://surfer.nmr.mgh.harvard.edu/registration.html |
| Line 34: | Line 38: |
| 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 (thats DOT license) and copy that file to your $FREESURFER_HOME. == 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].