4. Brain Extraction - Removing the Skull from a 3D image

The brain extraction tool  is used to remove the skull from an image, leaving only the region occupied by actual brain tissue. It segments these by using the dark space between the skull and brain, occupied by the CSF.  This tool comes from the external program FSL's toolkit (see the FSL webpage). Thus, it will only appear if FSL is installed. (Such integration is only possible on Unix systems at this point, extending this to MS-Windows is work in progress).