Updates (or "patches") are available from the FSL and FreeSurfer websites, and can be installed with a few manual steps.
FSL
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 the files look the same unless the cursor is over it, when you can read the name in the status bar.
Look for the Linux version (Centos 6 64-bit ), and the file that starts from the current version; if not sure choose the one that includes all patches (with the "x" in it, e.g., 5.0.x below). The other file only upgrades the latest step (the size will be smaller).
Download this file, and move it to the LinuxShare folder.
