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Hi, That's very strange indeed. Have you checked whether the registration worked? Also, the structures look rather small - is the voxel size set correctly in your images? If neither of these are the problem then please feel free to upload your data to our upload site and I'll have a look at it when I return from the FSL course next week. All the best, Mark On 16 Jun 2009, at 10:47, Niels Focke wrote: > Dear FSL experts, > > using the new FIRST version in FSL 4.1.4 we experienced some strange > output > of the run_first_all command using default settings. In > the ...auto.firstseg file > some regions are misplaced to the downward, right, posterior corner > of the > image (s. attached PNGs). Has anyone else noticed this problem and / > or can > offer a fix? > > Any help would be much appreciated. > > Niels > > <First-problem.jpg>