[Insight-users] Re: the sigmoid image is entirely white for
GeodesicActiveContourLevelSet
Goo
gtshowtime at gmail.com
Tue Mar 27 10:16:43 EST 2007
I am using EZDicom to visualize my result.
and discovering the value of intensity is full -32768.
it seems like overflow.
>
>
> 2007/3/27, Luis Ibanez < luis.ibanez at kitware.com>:
> >
> >
> > 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();
> > >
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > Insight-users mailing list
> > > Insight-users at itk.org
> > > http://www.itk.org/mailman/listinfo/insight-users
> >
>
>
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