[Insight-developers] Re: MR Segmentation

[Stephen R. Aylward]

Hi Nils,

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.

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 :)

As you go along, if you have suggestions for how we can better group the
methods, summarize their utility, etc, we would really appreciate it.  
One thing, this year is going to focus on documenting the application of
itk to a variety of different medical image analysis tasks (as part of
method validation), and so the examples section is going to greatly
expand and perhaps that will help others in your position in the future.
Until then....

Thanks for your patience,
Stephen

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