[Insight-users] Gradient vector flow calculation : Insight Journal != MIDAS Journal

[Luis Ibanez]

Hi Kana


The paper that you are looking at,
http://www.midasjournal.org/browse/publication/577


is NOT from the


                        Insight Journal


 it is from the

                        MIDAS Journal


          These are two very different Journals.


If this paper were from the Insight Journal you wouldn't
have to be dealing with the pain of reimplementing code.


The paper would have included all the source code, data
and parameters needed for you to replicate the results in
just a matter of hours.


The whole point of the INSIGHT JOURNASL is to overcome
 the inefficiency of a publishing system that only provides
PDF Documents.


The MIDAS Journal (which is differnt from the Insight Journal)
hosts papers for conferences and events that do not have
Open Source requirements.


In this particular case, this paper belongs to one of
the "Beauty Contest"-style events that MICCAI have
recently been overtaken by, in which participants are
only interested in getting symbolic ribbons for the "best"
method, and not interested at all in dissemination of
technology nor in verification of reproducibility.


It is unfortunate that MICCAI has fallen so low in the
standard of scientific practices.


--


If you are interested in centerline extraction methods,
that *actually work*, and that you can *actually use*,

                                 then

you will find more useful the following papers from
the INSIGHT JOURNAL that do indeed include
source code, data and parameters.


A) "Flux driven medial curve extraction"
     http://www.insight-journal.org/browse/publication/165
     Mellado X., Larrabide I., Hernandez M., Frangi A.
     Pompeu Fabra University, University of Zaragoza


B)  "Fast Marching Minimal Path Extraction in ITK"
      http://www.insight-journal.org/browse/publication/213
      Mueller D.
      Queensland University of Technology


C)   "Generalizing vesselness with respect to dimensionality and shape"
       http://www.insight-journal.org/browse/publication/175
       Antiga L.
       Mario Negri Institute, Italy




I would strongly discourage you from reading and
citing paper from Journals and Conferences that do
not support the open dissemination of information.


This is the year 2010, we shouldn't have to restrained
by the publishing practices of the Middle Ages.



      Regards,


             Luis


--------------------------------------------------------------------
On Wed, Feb 10, 2010 at 8:35 AM, Arunachalam Kana
<Kana.Arunachalam at fh-wels.at> wrote:
> Hi User,
>
>
>
> My goal is to implement insight journal paper:
>
> "Edge based tube detection for coronary artery centerline extraction"
>
>
>
> From the paper i understood that i have to calculate the following:
>
> 1. Gradient vector field
>
> 2. Anisotropic diffusion of gradient vector
>
> 3. Gradient vector flow
>
> 4. Hessian matrix
>
>
>
> I calculate the gradientimage using itkGradientImageFilter. I use
> itkGradientVectorFlowImageFilter
>
> to directly calculate the gradient vector flow as it is given the diffusion
> is already inbuilt in
>
> itkGradientVectorFlowImageFilter.
>
>
>
> I use QVTK for visualisation. The image is loaded as vtk image. To apply
>
> itk algorithm, i convert the vtk image to itk image using vtkKWEITKImage.cxx
>
> from vtkedge. The same file is used for itk image to vtk image for display.
>
>
>
> typedef itk::Image< T, 3 >   InputImageType; //input image type
>
> typedef itk::Image< float, 3 >   OutputImageType; //outputimage type
>
>
>
> /// cast filter which converts any inputimage type to outputimage type
>
> typedef itk::CastImageFilter <InputImageType, OutputImageType> castType;
>
> castType::Pointer castfilter = castType::New();
>
>
>
> // image is vtkKWEITKImage object
>
> castfilter->SetInput( dynamic_cast< InputImageType * >( image->GetITKImage()
> ) );
>
>
>
> //itk vector image declaration
>
> typedef itk::CovariantVector<float, 3> VectorPixelType;
>
> typedef itk::Image<VectorPixelType, 3> VectorImageType;
>
>
>
> //calculate the gradient vector of image
>
> typedef itk::GradientImageFilter <OutputImageType, float, float>
> GradientType;
>
> GradientType::Pointer gradient = GradientType::New();
>
> gradient->SetInput(castfilter->GetOutput());
>
> gradient->Update();
>
>
>
> //calculation of gradient vector flow from diffused gradient vector
>
> typedef itk::GradientVectorFlowImageFilter<VectorImageType, VectorImageType,
> double> VectorFlowType;
>
> VectorFlowType::Pointer flowfilter = VectorFlowType::New();
>
> flowfilter->SetInput(gradient->GetOutput());
>
>
>
> //observer of algorithm execution for time
>
> p->Observe( flowfilter );
>
>
>
> //the image object is updated with output image from flowfilter
>
> image->SetImage( flowfilter->GetOutput( ) );
>
> image->Modified();
>
>
>
> flowfilter->ReleaseDataFlagOn();
>
> return EXIT_SUCCESS;
>
>
>
> Questions:
>
>
>
> 1. I would like to know whether itkGradientVectorFlowImageFilter computes
> anisotropic diffusion or gaussian diffusion ?
>
>
>
> 2. I want to visualise the gradient vector flow as arrows. How can i achieve
> this visualisation?
>
>
>
> 3. If there is any example, which would help me fully or partially I would
> like to know.
>
>
>
> Thank you in advance.
>
>
>
> Regards,
>
> Kana
>
>
>
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