[Insight-users] Re: ITK advice needed
Luis Ibanez
luis.ibanez at kitware.com
Mon Aug 22 13:08:22 EDT 2005
Hi Siddarth,
Welcome to ITK,
You will find useful to follow the examples
in the ITK Software Guide:
http://www.itk.org/ItkSoftwareGuide.pdf
You will find there typical values for the
parameters of most filters.
If an ITK program failed when reading your
data, chances are that you are providing
a file with an image format that is not
supported by ITK. Please refer to the chapter
"Reading and Writing Images" for a full list
of the image file formats supported in ITK.
You will also find useful to read the material
of the ITK Tutorials:
http://www.itk.org/HTML/Tutorials.htm
Please let us know if you have further questions,
Thanks
Luis
-------------------------
Siddharth Vikal wrote:
> Hello Luis,
>
> I'm working on Dr. Gabor's project of Brachytherapy seed segmentation.
>
> I've no previous experience with ITK, but I'm learning to get some. I'm
> trying to use ITK with Visual Studio .Net. I've compiled the library in
> a different directory using CMake as directed in the documentation. To
> get familiar, I was trying to run the example programs. They build fine,
> but for example, Derivative Image Filter example, when I give it an
> input file (one from example data or my own, it doesn't matter), the
> program gives a run time error & terminates.
>
> I tried to trace & debug, the error seems to be coming at
> filter->update() method during some memory allocation I guess...So I"m
> unable to proceed further. This is true even for the
> GradientMagnitudeFilter.
>
> Also, in the documentation for DerivativeImageFilter, it is not clear
> what values & what range of values is accepted in arguments of
> SetOrder(int..) & SetDirection (int.) functions, I can just imagine that
> I have to supply unsigned int values & nothing more.
>
> Can you please clear my doubts.
>
> Thanking you in anticipation and looking forward to hear from you.
>
> regards
> siddharth
>
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
>
>
> Hi Gabor,
>
>
> As a complement of what Stephen already described, here are some
> names of filters and ITK examples that you may find useful to
> look at for approaching your problem.
>
>
> 1) For detection of BBS
>
> You could use filters such as
>
>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1HessianRecursiveGaussianImageFilter.html
> and variations of the Hessian space like
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1Hessian3DToVesselnessMeasureImageFilter.html
>
> You could also use the Hat filters
>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1HMaximaImageFilter.html
>
>
>
> 2) For calibration correction,
> once you gather the images from grids that Stephen suggested,
> you can use the following classes in order to compute
> correction fields:
>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1KernelTransform.html
>
> and any of its derived classes:
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ElasticBodyReciprocalSplineKernelTransform.html
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ElasticBodySplineKernelTransform.html
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ThinPlateR2LogRSplineKernelTransform.html
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ThinPlateSplineKernelTransform.html
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1VolumeSplineKernelTransform.html
>
>
> You could also use BSplines with the classes
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1BSplineDeformableTransform.html
>
>
>
> 3) One application that you may want to look at is
>
>
> InsightApplications/
> IntensityBased2D3DRegistration
>
>
> This code is available in the InsightApplications module
> that you get with the releases, and that yo! u can get
> through CVS too.
>
>
>
> You probably want to take a look also at
>
>
> InsightApplications/
> Curve2DExtractor
>
>
> and
>
> InsightApplications/
> Curve3DExtractor
>
>
>
> 4) The 3D/2D registration problem for the treatment seeds is probably
> better approached using the combination of the Levenberg-Marquardt
> optimizer
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1LevenbergMarquardtOptimizer.html
>
> and the Rigid3DPerpective transform
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1Rigid3DPerspectiveTransform.html
>
> along with a Metric of your choice, that in the case of BBS, and
> extracted features may be something like the
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1EuclideanDistancePointMetric.html
>
>
>
>
> As Stephen already pointed out, there are many different ways
> of approaching these problems, and there are many classes in ITK
> that could be used for implementing those app! roaches. In a typical
> application you probably will end up using many of the existing ITK
> methods, and then customizing one or two for your particular type
> of clinical problem.
>
>
>
>
>
> Please let us know if you have further questions,
>
>
>
> Regards,
>
>
>
> Luis
>
>
>
> -------------------------
> Gabor Fichtinger wrote:
>
> > Dear Steve and Luis,
> >
> > Few days ago I talked with Bill Lorensen in Betheada about a clinical
> > software problem that my group must solve rather urgently. (We
> must go
> > clinical during the fall, so we work on an accelerated time scale
> here.)
> > Bill suggested that I should seek your expert advice in the matter.
> >
> > The project involves reconstruction of the location of implanted
> prostate
> > brachytherapy seeds from a limited number of C-arm fluoroscopy
> shots. The
> > image processing work at hand entails segmentation of various
> metal objects:
> > fid! ucials (ellipses, straight line segments, BBs) and seeds
> (5x1 mm metal
> > pellets)
> > from C-arm fluoroscopic images. Calibration fixtures and
> dewarping grids are
> > also need be segmented from the C-arm images. I have the following
> > questions:
> >
> > (1) What filters and segmentation tools are available in ITK to
> support
> > these tasks?
> >
> > (2) Are there any fluoro calibration/distortion correction
> modules in or
> > outside ITK that we could use as an example/template?
> >
> > (3) Are there any application-level ITK examples that we could
> use as an
> > example/template?
> >
> > Steve, if I am not mistaken, you have done extensive work on
> fluoro/CT
> > registration of liver images that might have involved some of the
> problems
> > we are facing here. Please copy my associates on your reply. Our lead
> > software engineer is Anton Deguet whom you probably remember from
> various
> > ITK work! shops.
> >
> > Thanks so very much, in advance, and have a great weekend.
> >
> > --gabor
> >
> > --
> > Gabor Fichtinger, Ph.D.
> > Associate Research Professor of
> > Computer Science, Mechanical Engineering and Radiology
> > Director of Engineering
> > Center for Computer-Integrated Surgery
> > Johns Hopkins University
> > 3400 North Charles Street
> > Baltimore MD 21218-2682
> > New Engineering Bldg, Room B26
> > Office: (410) 516-4057
> > Mobile: (410) 562-6955
> > Fax : (410) 516-5553
> > mailto:gabor at cs.jhu.edu
> > Assistant: Luwanna Spells
> > (410) 516-6235, lspells at cs.jhu.edu
> >
> >
> >
>
>
>
> ------------------------------------------------------------------------
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