[Insight-users] kernel transform registration (without fixed image)

[Mauro Maiorca]

Hello all,

I have an image which contains an object I'm interested to. The object
has a slightly deformed rectangular cuboid shape and it is slightly
inclined. I would like to slightly rotate+deform the object in order
to completely stretch, flatten and fit it in a new image.
More in detail, it's an electron tomography image of a biological
sample. Prior to imaging the sample had the nice rectangular cuboid
shape, but the reconstructed tomogram is slightly deformed due to the
exposition to the electron beam and slightly inclined. I assume the
electron beam is so consistent to give a "global" impact to the target
rather then just locally deform it.

My idea is to use a rotation (i.e. Euler3DTransform) plus kernel
transform to give to the imaged target the original rectangular cuboid
shape (and finally crop the region and paste in a new image). I know
how to register two images using ITK, however in this case I don't
have the "fixed image" but I know how the overall image should look
like (a nice rectangular cuboid).
Do you know an easy way to overcome this problem?

cheers,
Mauro