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Dear, FSL users... I'm quite a newbie at FSL. I wanted to run BET on some of our 3D T1 images. In some images, the segmentation is wonderful, however in some cases, some of non-brain matter below the brain and eye-socket are not removed. I tried to raise the Fractional intensity threshold, but that removes brain matters as well. Also, CSF comes out to be larger than grey or white matter when I perform FAST on those ones that have problem. Is there something that i can do to improve the segmentation? Image sets that are having these problems have following scan parameters: Slice thickness = 1.5 FOV =24 TR = 9 TE = 1.8 FA = 10 Image sets that are great with BET and FAST have following scan paramters: slice thickness = 1.2 FOV = 25 TR = 20 TE = 6 FA = 20 Both are 3D-SPGR images. Can any of you tell me what factors might affect BET and FAST procedures and the solution for those problems? Thank you very much. Aaron****************************EMAIL DISCLAIMER****************************This e-mail and any files transmitted with it may be confidential and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient or the individual responsible for delivering the e-mail to the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. If you have received this e-mail in error, please delete it and notify the sender or contact Health Information Management 312.413.4947.