Dear Giovanni,
> 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?
Any combination of rotations and translations will always have a unity
Jacobian, and hence will not affect the total Jacobian. So you need
not worry about that component.
Good luck Jesper
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