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FreeSurfer Distributions for Internal Users

Distributions

The InternalFreeSurferDistributions are FreeSurferStable and FreeSurferDev. Please see ReleasePolicy for information on the release policy for these distributions.

Access

Here are instructions on how to set-up your environment to use the InternalFreeSurferDistributions.

All computers on the Martinos Center 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:

$ 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/freesurfer/centos4.0/stable/bin/tkmedit}}}

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/stable or /usr/local/freesurfer/dev, so if you'd like to set FREESURFER_HOME manually, you can still do so.

You can suppress output from sourcing these scripts with the FS_FREESURFERENV_NO_OUTPUT environment variable:

setenv FS_FREESURFERENV_NO_OUTPUT

You can keep the prompt from changing to (nmr-std-env) or (nmr-dev-env) by setting FSENV_KEEP_PROMPT:

setenv FSENV_KEEP_PROMPT

Frozen Version

For instructions on how to freeze one of these releases, see MakingPrivateCopiesOfDistributions.

Obsolete Versions

There 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 MakingPrivateCopiesOfObsoleteDistributions.

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 FreeSurferEnv.csh file in that distribution. For example:

setenv FREESURFRER_HOME ~inverse/freesurfer_alpha
source $FREESURFER_HOME/FreeSurferEnv.csh

Note that you may still have to set up your path. Be sure you are using the right binaries with the which command.

InternalFreeSurferDistributions (last edited 2022-03-28 13:47:57 by AndrewHoopes)