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| All computers on the NMR network should have the directory {{{/usr/local/freesurfer}}}. Inside there, you will see the files nmr-std-env and nmr-dev-env. 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: | [[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-stable53-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-stable53-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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| $ source /usr/local/freesurfer/nmr-std-env}}} You should see the prompt change to {{{(nmr-std-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 tkmedit /space/birn/50/freesurfer/rh7.3/beta/bin/tkmedit}}} |
$ which freeview /space/freesurfer/centos6_x86_64/stable6_0_0/bin/freeview }}} |
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| Your {{{FREESURFER_HOME}}} will actually be {{{/usr/local/freesurfer/beta}}} or {{{/usr/local/freesurfer/dev}}}, so if you'd like to set F{{{REESURFER_HOME}}} manually, you can still do so. You can suppress output from sourcing these scripts with the {{{FS_FREESURFERENV_NO_OUTPUT}}} environment variable: |
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: |
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| setenv FS_FREESURFERENV_NO_OUTPUT}}} | ## csh $> setenv FREESURFER_HOME /usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.csh |
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| You can keep the prompt from changing to {{{(nmr-std-env)}}} or {{{(nmr-dev-env)}}} by setting {{{FSENV_KEEP_PROMPT}}}: {{{ setenv FSENV_KEEP_PROMPT}}} These are the older versions that are still available for compatibility, but will soon be removed. For instructions on how to make a local copy of one of these versions for your private use, see MakingPrivateCopiesOfObseoleteDistributions. There are three older 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 Free``Surfer``Env.csh file in that distribution. For example: {{{ setenv FREESURFRER_HOME ~inverse/freesurfer_alpha source $FREESURFER_HOME/FreeSurferEnv.csh |
## bash $> export FREESURFER_HOME=/usr/local/freesurfer/stable6_0_0 $> source $FREESURFER_HOME/SetUpFreesurfer.sh |
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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. | == Frozen Version == |
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| See * FreeSurferAlpha * FreeSurferBeta * FreeSurferDev |
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-stable53-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-stable53-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.