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Updates (or "patches") are available from the FSL and FreeSurfer websites, and can be installed with a few manual steps.
Go to the FSL patch download location (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL).
Select the correct file; this is tricky because you can't see the filename unless the cursor is over it.
From the FSL wiki (Google FSL), go to patches.
Go to the downloads page