[Insight-users] registration of gray matters

[Marc Ruiz]

Hi!

Finally I am able to see the output image, but the registration result is
not good enough! But I think that it will be better with your advices, so
today I will try it.

First I will try changing the metric (the interpolation that I used was
Nearest Neighbor). And later, using Registration using masks constructed
with Spatial objects,

Thanks for your help!!


On 12/7/05, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>
> 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!!
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
>
>
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