The FSL software is fMRI, MRI and DTI analysis software from Oxford University. See 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-stable51-env