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Dear Ilka, to my knowledge there's no default option to obtain a skull-stripped version at the moment, but you could easily generate one within a batch using some Imcalc function based on the original T1 and the c1 (GM), c2 (WM), c3 (CSF), something like i1. * ((i2 + i3 + i4)>.5). Just try a few parameters like .5 , .75, ... to get an impression of your data. Coregistration of the skull-stripped version might help to get a better outcome, but not necessarily. In that case you might still have to adjust the data manually (at least along z, the other coordinates look okay). Hope this helps, Helmut