[elastix] Anisotropic Rigidity
Kannan U V
kannanuv at cshl.edu
Tue Jun 21 17:42:33 CEST 2011
Thanks for your reply.
1) I use tif files as input image. So I don't have voxel spacing info
in that file. So I use a final grid spacing of 5x5x2 since the spacing
of TIF file is 20 micron x 20 mixron x 50 micron. Correct me if I am
wrong, I assumed this takes care of the image spacing issue.
2a) I used a input image where value of all voxels of slice "n" had
values n just to visualize the contributing z-slices on the final
images and saw that some where pulled from as far as +/-7 slices which
doesn't happen anatomically (I apply the bspline trasnformation only
and not the affine transformation). We would like some elasticity in
z-dimension as well. Is it possible to use something as follows?
(MovingImageDerivativeScales 1 1 0.2)
2b) I currently use 2 transform parameter file, one for affine and one
for bspline, let know if adding MovingImageDerivativeScales to the
bspline param file affects the affine transformation too?
3&4) SInce I use anisoptropic final grid spacing already, I hope my
pyramid schedule will be anisotropic too, it this assumption correct?
Let me know if there are some best practices/recommendations on
elastix manual that I don't follow when I setup the experiment.
On Tue, Jun 21, 2011 at 10:47 AM, Stefan Klein <s.klein at erasmusmc.nl> wrote:
> Hi Kannan,
> What do you exactly mean with "make the Z dimension" more rigid?
> There are some options which might do what you want.
> 1) (perhaps superfluous explanation, but just to be sure:) In principle,
> elastix does already take into account the voxel spacing of your images.
> 2) If you want to avoid any deformations in the Z-dimension, you can add the
> following option to the parameter file:
> (MovingImageDerivativeScales 1 1 0)
> Then you will only have deformation in plane. But note: also no rigid
> deformation out of plane! You could do a registration in 2 stages, first a
> rigid without the movingimagederivative scales option, and then a bspline
> with the option.
> 3) The bspline grid spacing can be given a different value for each
> dimension. Intuitively, you may want to set the spacing higher in the
> z-dimension, to achieve a more rigid behaviour in that direction. But
> probably that's not what you want, since that will also result in a stronger
> coupling of the in-plane deformations between the consecutive planes. But
> maybe this is appropriate for your application.
> 4) You could experiment with using an anistropic ImagePyramidSchedule.
> (ImagePyramidSchedule 8 8 1 4 4 1 2 2 1 1 1 1)
> for example. This causes less blur in the Z-dimension in the initial
> resolutions, and thus may decrease the capture range in that direction (and
> thus hopefully avoiding large displacements in that direction).
> Kind regards,
> On 17/06/2011 16:21, Kannan U V wrote:
>> I am working with anisotrophic images with a ratio of 2:2:5. I want to
>> make the Z dimension to be more rigid when finding the elastic
>> transformation. Is it possible to set such a thing in elastix?
>> elastix mailing list
>> elastix at bigr.nl
> Stefan Klein
> +31 10 7043049
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