The FSL software is fMRI, MRI and DTI analysis software from Oxford University.  See [[http://www.fmrib.ox.ac.uk/fsl/|FSL - FMRIB Software Library]].

The software is installed locally at the NMR center in {{{/usr/pubsw/packages/fsl}}}. The most current locally tested version is always symlinked through the 'current' link.  

When FreeSurfer is setup (via {{{source /usr/local/freesurfer/nmr-stable51-env}}} it will also setup the FSL version linked to 'current'.

To override the version setup by FreeSurfer, first find the FSL version number you want in the {{{/usr/pubsw/packages/fsl}}} directory, for example, v5.0.0, then type this (using the 5.0.0 as the example) prior to sourcing the freesurfer setup:

{{{
setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0
source /usr/local/freesurfer/nmr-stable53-env
}}}