[Insight-developers] Mattes mutual information metric additions

[Lydia Ng]

Hi Karthik,

If you go for this approach one more thing you have to do is to also
threshold your image. Currently, the code does not take the mask into
account when it is computing the image max and min. So you would end up with
the same dynamic range issue as below - perhaps this should be logged as a
bug?

- Lydia
On 5/31/06, Blezek, Daniel J (GE, Research) <blezek at crd.ge.com> wrote:
>
> Karthik,
>
> I have to vote with Jim on this one.  There should not be any reason to
> put "modality specific" code in the Mattes.  A very simple fix is to use a
> registration mask for the pixels that map outside of your valid range.  This
> fixes your problem immediately and requires very little work unless you
> decide to do the robust KDE.
>
> -dan
>
> -----Original Message-----
> From: insight-developers-bounces+blezek=crd.ge.com at itk.org
> [mailto:insight-developers-bounces+blezek=crd.ge.com at itk.org]On Behalf
> Of Karthik Krishnan
> Sent: Wednesday, May 31, 2006 12:30 AM
> To: Miller, James V (GE, Research)
> Cc: Lydia Ng; Insight-developers (E-mail)
> Subject: RE: [Insight-developers] Mattes mutual information metric
> additions
>
>
> Hi Jim,
>
> Thanks very much for the detailed answer.
>
> > What could be having an affect is how the pdfs are constructed. When
> > you have a few pixels of high intensity, the sampling of the pdf (bin
> widths)
> > gets out of whack and you loose resolution in the pdf for the features
> > (intensities) you are really interested in.
>
> Yes. Exactly what was happening. The histogram of the PET image had the
> bulk of its intensities in the range 0-2 and hardly any from 2-8.
>
> > Since the pdf representation becomes
> > inaccurate, I could see the registration failing if this happens.
> >
> > This is classic problem in kernel density estimation.  There are several
> > strategies to address it: non-uniform bins, hierarchical pdfs,
> band-width
> > selection techniques, etc.  Perhaps one of these solutions should be
> > investigated.
> >
> > The approach that you are proposing essentially censors the data.  I am
> not
> > sure that I am in favor of this at the Mattes metric layer.  Perhaps
> > data censorship could be handled at a higher level whereby all image
> > metrics could benefit.  Data censorship usually leads to a set a
> > robust statistical techniques (M-estimators to replace least squares,
> etc.).
> > These would have general applicability and solve a number of problems
> > in image registration (registering data pre- and post-implant, etc.).
> >
>
> I agree. Its a lot of work though :)
>
> > Alternatively, you could transform the PET data to SUV (standard uptake
> value)
> > instead of using the raw counts.  This would bring the dynamic range
> > of the data down to [0, 6] or so.
>
> Yes. It was SUV data.
>
> > There are many formulas for calculating
> > SUV based on data in the DICOM header.
> >
> > Jim
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: insight-developers-bounces+millerjv=crd.ge.com at itk.org
> > [mailto:insight-developers-bounces+millerjv=crd.ge.com at itk.org]On Behalf
> > Of Karthik Krishnan
> > Sent: Tuesday, May 30, 2006 2:04 PM
> > To: Lydia Ng
> > Cc: Insight-developers (E-mail)
> > Subject: [Insight-developers] Mattes mutual information metric additions
> >
> >
> > Hi,
> >
> > We've had PET-CT datasets, (the PET ones in particular) with intensity
> > distributions where certain regions have very high pixel intensities
> > that tend to throw the registration off course. I added some code to the
> > mattes that optionally allows the joint PDF computation of the metric to
> > be restricted to a fixed range of intensities and it seems to work well.
> >
> > The API is simple. There are 4 optional methods :
> > SetFixedImageLowerBound( ), SetMovingImageLowerBound( ),
> > SetFixedImageUpperBound( ), SetMovingImageUpperBound( ).
> >
> > I've attached the patch and I would like to commit it, but I want to
> > confirm with the author or others in case you think its just code
> > clutter and I should tailor a derived class for my needs.
> >
> > Thanks
> > -karthik
> >
> > PS: Just to clarify, setting the bounds is different from using a
> > rescale intensity
> > filter on the fixed and moving images prior to computing the metric.
> > Rescale intensity filters clamp the intensities at the bounds.
> Therefore,
> > you will have an intensity peak at the bounds that also contributes to
> > estimation of the joint intensity PDF's and distorts the histogram.
> >
> >
>
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