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FreeSurfer Distributions for Internal Users

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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.

InternalFreeSurferDistributions (last edited 2017-06-06 12:39:39 by ZekeKaufman)