[Insight-users] Question about resampling and warping

[Luis Ibanez]

Hi Rosario,



Thanks for the detailed description of your problem.


Please find some comments below:



1) For visualizing a 3D deformation field, you may want
    to keep using ParaView but before adding Glyphs to the
    vector field, extract a slice from the field by using
    the "Cut" filter.

    In this way you will be able to move the slice back
    and forth, as well as change its orientation, and then
    see the vectors on that slice.  This will prevent vectors
    from other planes to occlude the ones that you are trying
    to examine.



2) The Demons registration method may still work with your
    images, as long as you use the Histogram Matching filter
    before passing the images to the Demons registration filter.

    The Histogram Matching filter is actually compensating
    for the intensity differences between your images.



3) It is very likely that the reason why you don't see anything
    on the deformation field produced by the Demons filter is that
    the vector are too small.  You can easily verify this assumption
    by using the Scale option that ParaView offers in the Glyph menu

    This option will be in the "Parameters" tab, on the "Orient/Scale"
    frame, and with the title:   "Scale Factor".

    Try setting a larger value in this scale factor, and let us know
    if that makes your vectors visible.




    Thanks



       Luis



------------------
Rosario Sance wrote:
> 
> Hi everybody,
> 
> I´m dealing with a project of motion correction in 3D DCE-MRI series. Up 
> to now, I´ve tried several elastic registration algorithms, using MI and 
> different optimizers, and aplying multirresolution strategies. Since 
> there are intensity changes in my series along the time, I think that 
> the most appropriate approach is to use multimodality methods, in spite 
> of I only work with MRI.
> 
> Every suggestion of my previous work will welcomed.
> 
> Now, my questions:
> 
> 1) When I define a BSpline grid and obtain a transform from the 
> registration process, I achieve the registered image using the 
> itk::ResampleImageFilter 
> <http://www.itk.org/Doxygen/html/itkResampleImageFilter_8h-source.html>. 
> But since I´m working with 3D and respiratory motion, I have some 
> difficulties in visualizing the deformation field and interpreting it. I 
> have tried with the Glyph option of the Paraview tool. Would you 
> recommend me another way?
> 
> 2) I have also tried the code of 
> Examples/Registration/DeformableRegistration2.cxx and 
> Examples/Registration/DeformableRegistration5.cxx, so I have checked the 
> possibilities of  the DemonsRegistrationFilter and the 
> LevelSetMotionRegistrationFilter. In principle it should not work 
> because the dependence with the voxel intensity and the histogram, but I 
> got surprised because these algorithms reached a good registration 
> outcomes, correcting the position of the input images. However:
>         - The resampled image looks absolutely fine about the position, 
> but not about the intensities, which seem to be adapted/very similar to 
> those in the reference image. Actually I am taking the spacing and 
> origin of the fixed image, but since I´m applying the output of the 
> warping filter on the moving image, shouldn´t be kept the intensities 
> and corrected only the position? I can´t understand how does the warping 
> filter works, in spite I have searched in the documentation...
>         - On the other hand, I write the deformation field as an image 
> of vectors from the output of the warping filter, and keep it in a .vtk 
> file. But when I try to visualize it as I did with the deformation 
> fields of the resample filter, I don´t get to see any field. How does 
> this filter store the vectors field and could it been visualized? Which 
> are the differences between the use of both of the filters?
> 
> Thanks a lot in advance.
> Rosario
> 
> 
> 
> Rosario Sance Garzón
> Dpto. Ingeniería Electrónica
> E.T.S.I. Telecomunicación
> Avda. Ciudad Universitaria s/n
> E-28040 - Madrid (SPAIN)
> ___________________________________________________
> 
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