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| There are three main internal distributions of FreeSurfer available at the NMR Center. To use a distribution, set your FREESURFER_HOME environment variable to the directory of the distribution and then source the FreeSurferEnv.csh file in that distribution. For example: | [[FreeSurferWiki|top]] = FreeSurfer Distributions for Internal Users = == Distributions == == Access == Here are instructions on how to set-up your environment to use the Internal !FreeSurfer Distributions. The Internal !FreeSurfer Distributions are 'stable' and 'dev'. All computers on the Martinos Center NMR network should have the directory '''/usr/local/freesurfer'''. Inside there, you will see the files '''nmr-stable60-env''' and '''nmr-dev-env''' (and others). Sourcing these will set up your environment to use the stable or dev version, respectively. For example, to use the stable version, which is what most users should do, use the following setup command: '''stable 6:''' {{{ $> source /usr/local/freesurfer/nmr-stable60-env }}} '''dev:''' {{{ $> source /usr/local/freesurfer/nmr-dev-env }}} '''NOTE:''' Do not put this command in your .cshrc file! If /usr/local/freesurfer is down for whatever reason, then your login will not work. You should see the prompt change to {{{(nmr-stable6--env)}}} and your environment should then be set up to run !FreeSurfer. Note that the programs may appear to be in a different location: |
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| setenv FREESURFRER_HOME ~inverse/freesurfer_alpha source $FREESURFER_HOME/FreeSurferEnv.csh |
$ which freeview /space/freesurfer/centos6_x86_64/stable6_0_0/bin/freeview |
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| Note that you may still have to set up your path. Be sure you are using the right binaries with the {{{which}}} command. | That's OK, because {{{/usr/local/freesurfer}}} is actually a link to a platform specific version that resides in a different directory, much like how {{{/usr/pubsw}}} works. If you don't know what this means, don't worry. |
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| See * FreeSurferAlpha * FreeSurferBeta * FreeSurferDev |
Your {{{FREESURFER_HOME}}} will actually be {{{/usr/local/freesurfer/stable6_0_0}}} or {{{/usr/local/freesurfer/dev}}}, so if you'd like to set {{{FREESURFER_HOME}}} manually, you can still do so: {{{ ## csh $> setenv FREESURFER_HOME /usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.csh ## bash $> export FREESURFER_HOME=/usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.sh }}} == Frozen Version == Users are strongly encouraged to "Freeze" their copy of !FreeSurfer in a project-specific directory like their SUBJECTS_DIR. To make a copy, just download the public distribution from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer == Obsolete Versions == There are the older versions that are still available for compatibility, see the Archives section of the public download page. |
FreeSurfer Distributions for Internal Users
Distributions
Access
Here are instructions on how to set-up your environment to use the Internal FreeSurfer Distributions.
The Internal FreeSurfer Distributions are 'stable' and 'dev'. All computers on the Martinos Center NMR network should have the directory /usr/local/freesurfer. Inside there, you will see the files nmr-stable60-env and nmr-dev-env (and others). Sourcing these will set up your environment to use the stable or dev version, respectively. For example, to use the stable version, which is what most users should do, use the following setup command:
stable 6:
$> source /usr/local/freesurfer/nmr-stable60-env
dev:
$> source /usr/local/freesurfer/nmr-dev-env
NOTE: Do not put this command in your .cshrc file! If /usr/local/freesurfer is down for whatever reason, then your login will not work.
You should see the prompt change to (nmr-stable6--env) and your environment should then be set up to run FreeSurfer. Note that the programs may appear to be in a different location:
$ which freeview /space/freesurfer/centos6_x86_64/stable6_0_0/bin/freeview
That's OK, because /usr/local/freesurfer is actually a link to a platform specific version that resides in a different directory, much like how /usr/pubsw works. If you don't know what this means, don't worry.
Your FREESURFER_HOME will actually be /usr/local/freesurfer/stable6_0_0 or /usr/local/freesurfer/dev, so if you'd like to set FREESURFER_HOME manually, you can still do so:
## csh $> setenv FREESURFER_HOME /usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.csh ## bash $> export FREESURFER_HOME=/usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.sh
Frozen Version
Users are strongly encouraged to "Freeze" their copy of FreeSurfer in a project-specific directory like their SUBJECTS_DIR. To make a copy, just download the public distribution from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer
Obsolete Versions
There are the older versions that are still available for compatibility, see the Archives section of the public download page.