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Hi Carolyn, It's hard to know what's going on here, but I guess that the brain extraction applied to the functional, which is normally a little liberal, to be conservative wrt errors in motion correction. So if the patches of non-brain are only small and the registration to the structural and standard space is good, then I would not worry about it, as you can just mask the results later on in structural/standard space. However, if they are big areas then that isn't normal and we'd need to know a little bit more in order to help. All the best, Mark > On 2 Nov 2016, at 21:13, Carolyn McNabb <[log in to unmask]> wrote: > > Dear FSL, > > I am using the preprocessing function in FEAT but have run into trouble where the filtered_func image includes several patches of non-brain. Looking back at prior analyses, I have not experienced this issue in the past. Our fat suppression was turned on, slice thickness is 2.4 mm, brain extraction of the structural image was good, we used a fieldmap, we used multibanding (which we haven't used before but I don't see how that would affect the extraction), and spatial smoothing was set to 5 mm. > Any help would be much appreciated. I imagine that this will cause problems down the track if it isn't dealt with now. > > Many thanks in advance, > > Carolyn McNabb > University of Auckland