Fwd: Re: [Insight-users] 3D deformable registration
Luis Ibanez
luis.ibanez at kitware.com
Fri May 4 10:07:17 EDT 2007
Hi Vijay,
I would suggest you to explore the use of the BSplineDeformable
registration method.
This method fits better with the standard registration framework of ITK,
and *it will* manage without problems images of different number of
pixels as well as different pixel spacing.
You will find instructions on how to use this method in the ITK
Software Guide:
http://www.itk.org/ItkSoftwareGuide.pdf
towards the end of the "Image Registration" chapter.
Regards,
Luis
--------------------------
vijay kumar wrote:
> Hi Luis,
> I know you are very busy, but could you respond to this query of mine? I
> am waiting for your response to proceed further. Which deformable
> registration method would you suggest for me to register two 3D images
> of dissimilar sizes. Image1: [X1,Y1,Z1]; Image2: [X2,Y2,Z2], where X1,
> Y1 and Z1 are not equal to X2, Y2 and Z2 respectively. If ITK doesn't
> have a suitable method, I shall then start exploring other
> options/programs. Otherwise, ITK is what I would like to use.
>
> Thank you very much.
>
> Regards,
> Vijay
>
> */vijay kumar <desivij at yahoo.com>/* wrote:
>
> Date: Thu, 3 May 2007 13:08:27 -0700 (PDT)
> From: vijay kumar <desivij at yahoo.com>
> Subject: Re: [Insight-users] 3D deformable registration
> To: Luis Ibanez <luis.ibanez at kitware.com>
>
> Hi Luis,
> Thank you for your detailed response and suggestions. I looked into
> DeformableRegistration11.cxx and also into the parameter file -
> FiniteElementRegistration3.txt. From what I see, the parameter file
> expects both input 3D images to be of the same size. In my case, the
> images are of size (160x256x256) and (256x256x200), with voxel sizes
> of (1.0x1.0x1.0 mm) and (1.21x1.21x1.23 mm). As you mentioned, the
> voxel sizes are obtained from the Analyze header. How about the
> image sizes? In the section called 'Information about the image
> inputs' there is option for only one set of Nx, Ny and Nz. Does this
> mean that I have to scale the images to the same size before I use
> deformable registration? If so, that may be messy. I was under the
> assumption that deformable registration would take care of reslicing.
>
> Thank you.
>
> Regards,
> Vijay
>
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
>
>
> Hi Vijay,
>
> If you are interested in a 3D version of the FEM deformable
> registration example, you may want to look at the example:
>
> Insight/Examples/Registration/
> DeformableRegistration11.cxx
>
> and the associated input file:
>
>
> Insight/Examples/Data/
> FiniteElementRegistration3.txt
>
>
> The example: DeformableRegistration11.cxx is the 3D version
> DeformableRegistration1.cxx
>
>
>
> The pixel dimensions (pixel spacing) are taken from the
> meta information of the image. There is no need for you
> to put it in the parameters file.
>
>
>
> The values of Elasticity and RhoC must be found through
> experimentation.
>
> As a rule of Thumb, high elasticity implies that a very
> strong force applied to the material will produce very
> small deformations. Therefore, you could start running
> experiments with large values of elasticity. If you find
> that the deformation field has vectors with very small
> magnitudes, then you know that the Elasticity can be
> reduced. If you find that the deformation vectors are too
> large (e.g. the anatomical tissue gets displaced too far)
> then you will know that the Elasticity is too low.
>
> Note that you may have to play with the orders of magnitude
> of the Elasticity.
>
>
> The RhoC factor is used for computing the Mass matrix,
> and its final effect is to multiply the forces applied
> to the model. Therefore, large values of RhoC will result
> on larger deformations, while small values of Rhoc will
> result in smaller deformations.
>
>
>
>
> Regards,
>
>
>
> Luis
>
>
>
> ------------------
> vijay kumar wrote:
> > Hi,
> > I would like to register two 3D images that are of different
> sizes ([nx1
> > ny1 nz1] & [nx1 ny2 nz2] voxels) and different voxel
> dimensions. I
> > modified DeformableRegistration1.cxx to accept 3D images, but
> I have
> > questions about the parameters file
> > (FiniteElementRegistrationParameters1.txt):
> >
> > 1. How do I specify the sizes of both images? The section -
> Information
> > about image inputs has the option to specify only one set of
> sizes. How
> > do I specify the second set?
> >
> > 2. How do I include voxel dimensions? Or, will the program
> get this
> > info from the image header?
> >
> > 3. How do we determine appropriate E, RhoC and Alpha values?
> Are there
> > some guidelines for their choice?
> >
> > Thanks,
> > Vijay
> >
> >
> >
> >
> ------------------------------------------------------------------------
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> >
> >
> >
> >
> >
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