[Insight-users] registration of gray matters

[Luis Ibanez]

Hi Marc,


1) When you started registering binary images,
    Did you changed the Image Metric  ?

    You probably should use a metric such as the

http://www.itk.org/Insight/Doxygen/html/classitk_1_1KappaStatisticImageToImageMetric.html

    or the

http://www.itk.org/Insight/Doxygen/html/classitk_1_1MatchCardinalityImageToImageMetric.html

    that are intended for binary (or labeled) images.



2) Did you changed the interpolator ?

    Once you use binary images you should only use
    a Nearest Neighbor interpolator.




In any case,
I would suggest you that instead of registering the masks,
you could use the Masks in order to restrict the registration
method to use only the pixels in the Gray matter.


Please read the ITK Software Guide

          http://www.itk.org/ItkSoftwareGuide.pdf

In particular Section 8.11.3:

"Registration using masks constructed with Spatial objects"

in pdf-page 464.



The associated source code example can be found in

          Insight/Examples/Registration/
                      ImageRegistration12.cxx



Note that, depending on the ImageMetric that you are using,
you may want to extend (dilate) the Masks a bit in order to
make sure that a band of pixels *outside* of the gray matter
is also participating in the registration.  The reason why
you need those pixels is that they will help to make your
metric degrade when the two images are not well aligned.



   Regards,



      Luis



---------------
Marc Ruiz wrote:
> Hi!
> 
>  
> 
> I have registered two MRIs. The registration pipeline is first rigid and 
> then affine, and the results are ok.
> 
>  
> 
> But now I would try to register only the gray matter of these two 
> images, because I am only interested in the registration of the cortex. 
> So, I have segmented the 2 images and now I am trying to do the same 
> registration (rigid and affine) with two binary MRIs and with the same 
> program and parameters.
> 
>  
> 
> The problem is that now I get the output image all white.
> 
>  
> 
> First I thought it was only problem of the writer of the output image 
> (the interpolation of the resample filter or something like that, due to 
> the output is a binary image too), but I have applied the same 
> transformation (the one obtained from the registration of two gray 
> matters) to a MRI and the transformation is bad done. So, I think it is 
> problem of the registration…
> 
>  
> 
> So, some idea about the problem??
>  
> 1) I have to change some parameters or the interpolation or…?
> 2)  Which differences I have to think about to readapt the program?
> 3)  Or some idea to register ok the gray matter?
>  
> Thank you!!
> 
> 
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