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Hi Javier, The anisotropy is not necessarily a problem for FLIRT, but it is a bit hard to guess what is going on without seeing the images. Would it be possible to share some screenshots along with the options you used when running it? Cheers, Eelke > On 17 Jun 2015, at 10:48, Javier Sanz Perez <[log in to unmask]> wrote: > > Hi everyone, > > > > I’m having problems trying to register anisotropic anatomic rat images (0.2x0.2x1 mm3) to an isotropic template (1.25x1.25x1.25 mm3) with FLIRT, 6 and 12 DoF. The resulting image is not properly registered to the template. > > > > I was wondering if the problem was due to the high anisotropy of the images (1/0.2=5) compared to the isotropy of the template. How can the registration improve? > > > > Thank you, > > All the best, > > > > Javier >