[Insight-developers] RE: MR Segmentation

[Nils Hanssen]

Hi Stephen,

> I think I misunderstood your problem - you don't want just the bones -
> you want everything in the pelvic area. Right?  Sorry for the
> confusion.

We are in fact not limited to the pelvic area. We are interested in this
topic but we are also going to extract bones and soft-tissues for
craniofacial surgery. One of our projects
is the design of autologous grafts from the bone of the pelvis.

> Watershed is a great approach for this.   Fuzzy connectedness should
> also be considered.   It is a hard problem, though.   This is one
> application that really needs a user interface/visualization
> in order to
> evaluate, control, and edit the segmentation process.   Stay tuned for
> itk2 :)

Yes, we try to utilize itk for segmentation in our medical software
framework. It offers interaction and visualization capabilities and we hope
that the segmentation can be done intuitive and fast for various use-cases.

Nils


>
> Nils Hanssen wrote:
> >
> > Hi Stephen,
> >
> > thank you very much for your step-by-step list. In fact i just had a
> > conversation with lydia ycl about segmentation in the
> pelvic area because
> > she deals with this topic.
> >
> > Instead of being limited to the pelvic area, we have a
> general interest in
> > the segmentation capabilities of itk for CT and MR data. So
> far, we used vtk
> > for visualization and used thresholding as well as region
> growing for
> > segmentation and marching cubes for surface generation of
> bony structures.
> > Since vtk's segmentation capabilities are (obviously) very
> limited, we were
> > looking forward to become a first version of itk.
> >
> > I am very impressed by itk from the software-engineering
> point of view! I
> > like the concepts and the realization of some design
> patterns. However, it's
> > not easy to get an overview of the whole system and how
> everything belongs
> > together.
> >
> > Currently i try to get the streamed watershed filter running.
> >
> > Nils
> >
> > > It looks like Nils wants to segment the pelvis from CT and MR.
> > >
> > > This should be do-able with itk now...
> > >
> > > 1) Region grow (itkRegionGrowImageFilter or
> > > itkFuzzyConnectednessImageFilter.h)
> > > 2) morphological erosion (2cm - remove ribs)
> > > 3) morphological dilate (3cm - restore to original size +
> > > fill in marrow
> > > holes)
> > > 4) morphological erosion (1cm - restore to original size)
> > >
> > > The problem with abdominal MR are the intensity inhomogeneities.
> > >
> > > Try the MRBiasFieldCorrection method and then do the above
> > > for MR (bones
> > > being dark).
> > >
> > > Stephen
> > >
> > >
> > >
> > > --
> > > ===============================================
> > > Dr. Stephen R. Aylward
> > > Assistant Professor of Radiology
> > > Adjunct Assistant Professor of Computer Science
> > > http://caddlab.rad.unc.edu
> > > aylward@unc.edu
> > > (919) 966-9695
> > >
>
> --
> ===============================================
> Dr. Stephen R. Aylward
> Assistant Professor of Radiology
> Adjunct Assistant Professor of Computer Science
> http://caddlab.rad.unc.edu
> aylward@unc.edu
> (919) 966-9695
>