[Insight-users] Re: the sigmoid image is entirely white for GeodesicActiveContourLevelSet

[Luis Ibanez]

Hi Goo:


A couple of comments:


1) What are you using for visualizing the images ?

    e.g. what is the viewer that leads you to conclude
    that your float images are "full white". ?



2) If you get to a case where the Gradient Magnitude
    looks fine, and the Sigmoid looks "full white", then
    you need to *REDUCE* the value of the Beta parameter
    in the Sigmoid filter.

    In order to find an appropriate value for Beta, you
    should study the values of the Gradient Magnitude image
    on the edges of the structures that you intend to segment.



    Please read the ITK Software Guide:

        http://www.itk.org/ItkSoftwareGuide.pdf

    advice on how to set up the Alpha and Beta parameters
    in the context of the LevelSets framework is given in
    sections:


     9.3.1 "Fast Marching Segmentation" in pdf-page 565.
           Please read attentively pdf-page 569 and the
           discussion about K1 and K2 values.

    and, of course, please read section:

    6.3.2.  "Non linear mappings", in pdf-page 181-183.




Regards,


    Luis



-------------
Goo wrote:
> notice something:
> 
> (1)
> if the ExternalImageType used as float, the image of result will be white
> entirely in every step (smooth,gradient and sigmoid).
> 
> (2)
> And if both ExternalImageType and InternalImageType are signed short,
> 
> the image of smooth and gradient are fine but sigmoid image is whole white.
> 
> (3) Unfortunately , the format for level set must be float.
> How do I solve this problem???
> 
> 
> 2007/3/27, Goo <gtshowtime at gmail.com <mailto:gtshowtime at gmail.com>>:
> 
>     Hi All:
> 
>     This question is so confused to me.
>     The output of sigmoid image is shown white entirely but gradient
>     image fine.
> 
>     The following are my programs:
>     if the ExternalImageType used as float, the image of result will be
>     white entirely in smooth,gradient and sigmoid.
> 
>     Please give me some guidance.
>     Regards.
> 
>     //----------------------------------CODE-------------------------------------------
> 
>         typedef itk::Image< signed short, 3 >  InternalImageType;
>         typedef itk::Image< signed short, 3 >  ExternalImageType;
> 
>         typedef itk::RescaleIntensityImageFilter<ExternalImageType,
>     InternalImageType> InputCastType;
>         typedef itk::RescaleIntensityImageFilter<InternalImageType,
>     ExternalImageType> OutputCastType;
> 
>         OutputCastType::Pointer            m_SmoothObserver;
>         OutputCastType::Pointer            m_GradientObserver;
>         OutputCastType::Pointer            m_SigmoidObserver;
> 
>             typedef itk::ResampleImageFilter<
>                                 InternalImageType , InternalImageType > 
>     FilterType;
>             FilterType::Pointer SubSample = FilterType::New();
> 
>             typedef itk::AffineTransform< double, 3 >  TransformType;
>             TransformType::Pointer transform = TransformType::New();
> 
>             typedef itk::NearestNeighborInterpolateImageFunction<
>                                InternalImageType, double > 
>     InterpolatorType;
>             InterpolatorType::Pointer interpolator =
>     InterpolatorType::New(); 
> 
>             SubSample->SetInterpolator( interpolator );
>             SubSample->SetDefaultPixelValue( 50 );
> 
>             double spacing[ 3 ];
>             spacing[0] = InputCaster->GetOutput()->GetSpacing()[0];
>             spacing[1] = InputCaster->GetOutput()->GetSpacing()[1];
>             spacing[2] = InputCaster->GetOutput()->GetSpacing()[2];
>             SubSample->SetOutputSpacing( spacing );
> 
>             double origin [3];
>             origin[0] = 80*spacing[0];
>             origin[1] = 80*spacing[1];
>             origin[2] = 15*spacing[2];
>             SubSample->SetOutputOrigin(origin);
> 
>             InternalImageType::SizeType   size;
> 
>             size[0] = 100;
>             size[1] = 100;
>             size[2] = 5;
> 
>             SubSample->SetSize( size );
>             SubSample->SetInput( InputCaster->GetOutput() );
>             SubSample->SetTransform( transform );
>             transform->SetIdentity();
> 
>             SubSample->Update();
> 
> 
>             typedef itk::CurvatureAnisotropicDiffusionImageFilter
>                         < InternalImageType,InternalImageType > 
>     SmoothingFilterType;
>            
>             typedef itk::GradientMagnitudeRecursiveGaussianImageFilter
>                         < InternalImageType,InternalImageType > 
>     GradientFilterType;
> 
>             typedef itk::SigmoidImageFilter
>                         < InternalImageType,InternalImageType > 
>     SigmoidFilterType;
> 
>             SmoothingFilterType::Pointer    m_smoothing =
>     SmoothingFilterType::New();  
>             GradientFilterType::Pointer        m_gradientMagnitude =
>     GradientFilterType::New();
>             SigmoidFilterType::Pointer        m_sigmoid =
>     SigmoidFilterType::New();   
> 
>             m_smoothing->SetNumberOfIterations(  m_SmoothIter );
>             m_smoothing->SetConductanceParameter( m_SmoothConductance );
>             m_smoothing->SetTimeStep( m_TimeStep );
> 
>             m_gradientMagnitude->SetSigma(  m_sigma  );
> 
>             m_sigmoid->SetOutputMinimum(  m_SigmoidOutMin  );
>             m_sigmoid->SetOutputMaximum(  m_SigmoidOutMax  );
>             m_sigmoid->SetAlpha( m_alpha );
>             m_sigmoid->SetBeta(  m_beta  );
> 
>             m_smoothing->SetInput(     SubSample->GetOutput() );
>             m_gradientMagnitude->SetInput( m_smoothing->GetOutput() );
>             m_sigmoid->SetInput( m_gradientMagnitude->GetOutput() );
> 
>             m_SmoothObserver->SetInput(m_smoothing->GetOutput());
>             m_GradientObserver->SetInput(m_gradientMagnitude->GetOutput());
>             m_SigmoidObserver->SetInput(m_sigmoid->GetOutput());
> 
>             m_SmoothObserver->Update();
>             m_GradientObserver->Update();
>             m_SigmoidObserver->Update();
> 
> 
> 
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