[Elastix] problems with affine

Floris Berendsen floris at isi.uu.nl
Tue Feb 3 17:02:12 CET 2015

Hi Esmeralda,

The large object will indeed affect the affine registration, since affine
is a global transform (i.e. its scaling, shearing, etc. applies in the same
amount everywhere in the image).
I do expect a better registration too when you removed the large object
(you made the intensities similar to the background?). Can you provide more
information about your registration settings? I.e. what metric do you use,
what is the pyramid schedule, etc. The easiest is to send your parameter
file. And what are the sizes of you images (voxels and/or millimeters). Or
can it be that the small circle is only a cross section of a bigger
structure in 3d, which are registered to each other?


On Tue, Feb 3, 2015 at 1:34 PM, Esmeralda Ruiz Pujadas <
esmeralda.ruizpujadas at gmail.com> wrote:

> Dear all,
> I have a doubt as shown in the image. I am using an affine registration and
> I have a 3d volume as shown in the image with fixed, moving and result,
> respectively.
> I would expect that the result of the small circle (third) to grow and be
> scaled
> as the small circle in the first image as it is larger. And the
> registration does not
> do any transformation instead. Why is it not scaling?. Is it affected by
> the big circle?.
> I also try to obtain the small circle and delete the big one but even like
> this, I
> did not find any result of the affine registration.
> Thanks
> Sincerely
> Esmeralda
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> Elastix at bigr.nl
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