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Dear FSL experts - I am working with a new dataset and have noticed that BET is failing to completely extract the functional data during preprocessing. As you can see in the attached pictures, parts of the skull are not fully removed. I have had similar issues with the structural data when using BET without the default options (but I'm able to successfully extract the structurals using the center of gravity option). However, the feat GUI does not offer any alternate options for extracting the functional data. I've never seen BET fail to work on the functional data so I'm at a loss for what to do! I have a few questions: 1. What could be causing this? Is it the angle in which the scans were acquired? 2. How best to successfully brain-extract the functional data? -- I assume it will not be possible to do my preprocessing in the GUI, since I'll need to use some special options for BET. If so, at what point in the preprocessing pipeline should I perform the brain extraction (i.e. before and after what steps) in order to preserve the order used in FSL's pre-stats GUI? 3. Should this issue concern me for any other reason? In other words, once the functional data is skull-stripped, do we need to worry about any other related issues? Pictures (I can also upload data if that would be helpful): http://tinypic.com/r/aaxdth/9 http://tinypic.com/r/5drwvm/9 http://tinypic.com/r/2z66u8o/9 http://tinypic.com/r/2q1i5qg/9 Thanks so much for your help! Best, Lauren