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Hi Jasper. If I use fnirt the way you suggest, that is: fnirt --ref=JHU-ICBM-FA-2mm --in=FA --affine=affine.mat -- config=conf.cnf --cout=LinearAndnonLinear inside "LinearAndnonLinear" there is also the roto-translational (rigid body) component of the affine transformation, that (I think, but I'm not sure) could prevent the comparison among jacobians of different subjects (because the rigid-body component of the affine transformation is not a true "deformation" of the original image, and could be different from subject to subject, so I'm trying to exclude it). Is that true? Thank you Giovanni