|
Size: 1662
Comment:
|
Size: 1646
Comment: recommend installing to /usr/local
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 11: | Line 11: |
| 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. | 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 15: | Line 15: |
| 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: |
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: |
| Line 18: | Line 18: |
| cd /usr/local | |
| Line 22: | Line 23: |
| == MINC toolkit perl path fix-up == Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, as root user, type: |
Note that for this installation example, your FREESURFER_HOME becomes: |
| Line 26: | Line 25: |
| mkdir -p /usr/pubsw/bin cd /usr/pubsw/bin ln -s `which perl` |
setenv FREESURFER_HOME /usr/local/freesurfer |
| Line 31: | Line 28: |
| 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). |
Reminder to NMR Center users! [wiki:Self:InternalFreeSurferDistributions You already have Freesurfer installed on your system!] |
| Line 36: | Line 32: |
| A license file is required to enable the tools. One can be | A license file is required to enable the tools. One can be |
[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'. 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:
cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
Again, replacing <platform>-<release> with your Linux variant.
Note that for this installation example, your FREESURFER_HOME becomes:
setenv FREESURFER_HOME /usr/local/freesurfer
Reminder to NMR Center users! [wiki:InternalFreeSurferDistributions 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:
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].