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Dear FSL experts, as part of a dissertation I am doing some analysis of DTI data and am about to finish the preprocessing soon. For that I use BET (brain extraction using bet2) to create a mask by varying the -f and -g options which works well in most cases. But there are some data where I could not avoid that a part of the eyes or an artifact is included in the mask. Now I am wondering how far this could affect further analysis (e.g. if it provides more inaccuracy for tractography by including "false activation"). I attached two screenshots to give you examples: "Eye" - left eye is affected a bit (this is the most common problem) and right eye is affected a lot (only a very few cases like that but maybe the much bigger problem); I think the main reason for this problem is that the eyes themselves are obviously distorted due to head motion "Artifact" - there is an occipital artifact which is included by the mask Would you see problems with an brain extraction like that and if so, are there any opportunities to create a better fitting mask? Many thanks in advance! Best regards Lukas A. Jung Goethe-University Frankfurt, Germany Department of Psychiatry, Psychosomatic Medicine and Psychotherapy Laboratory of Neurophysiology and Neuroimaging