[Insight-users] Active Contour not Propagating
Andrey Sklyar
skyar at wpi.edu
Sat May 2 11:45:11 EDT 2009
Hi Louis,
The boundary actually starts some distance inside the lungs and does
not stop on the boundary of the lungs. The border expands about 1
pixel away from the starting region and grows no further, regardless
of the number of iterations I let it run for (I tried 10, 100, and
1000). I also made sure that it wasn't stopping to the RMS getting too
low either, so the full number of iterations were used.
The speed image around the boundary has values around 1 (aka, full
speed ahead for the propagation) and around 0 at the lung border. The
curvature scaling has an effect on the boundary - it smoothes it out,
but the propagation scaling does not.
The only thing that I can think of is that the anisotropic voxel size
is interfering somehow - each slice has 256 x 256 pixels, with pixel
dimensions 1.367mm x 1.367mm, where as the slices themselves are 4mm
thick with a 2mm gap in between the slices.
- Andrey
On Sat, May 2, 2009 at 11:20 AM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
> Hi Andrey,
>
> From your description, it looks like the level set is stopping at
> the boundary of the Lungs,
>
> Is that correct ?
>
> If so, then the Level set is behaving correctly, since it is
> supposed to stop at the location where the speed image has zero values.
>
>
> A) Is it your goal to segment the lungs ?
>
> or
>
> B) Are you trying to grow a front that starts at the Lungs and
> then propagates further ?
>
>
> Maybe a couple of screenshots with annotations will help to
> present your problem in a clearer manner.
>
>
> Regards,
>
>
> Luis
>
>
> ----------------------
> Andrey Sklyar wrote:
>>
>> I am trying to use GeodesicActiveContourLevelSetImageFilter to extract
>> the boundary of the lungs from a series of sagittal MRI slices through
>> a patient. For testing purposes, I'm only using 6 slices.
>>
>> After extracting an initial rough boundary of the lungs, I generate a
>> signed distance map using SignedDanielssonDistanceMapImageFilter to
>> use as the initial level set to the active contour filter. The
>> feature image is generated using the same pipeline as in Software
>> Guide, pg 537, and is fully defined in the code excerpt below.
>>
>> The problem that I am running into is that the boundary does not
>> expand even though the propagation force is positive, and the
>> speed/feature image has values close to 1 around the boundary. The
>> curvature force has a visible effect though - the boundary is smoothed
>> out.
>>
>> I can think of a couple of possible causes of these problems, but I am
>> not intimately familiar with the implementation of these filters, so I
>> would like to get the advice of others who are more experienced in
>> their use than I am. Here are my hypotheses:
>>
>> - The image is too skinny in the z-dimension - the resolution in each
>> xy slice is high (~128x128), but I'm only using 6 images in the z
>> direction.
>> - The voxels have a different size in the z-dimension (the slice
>> thickness is large compared to the in-slice pixels' size) - does the
>> active contour filter expect the voxels to be the same size in all
>> dimensions?
>> - The contour is touching the image boundary in the z-dimesion and is
>> stopping because of this - I ran some experiments in 2D to check this
>> case, but the boundary still keeps evolving even after it hits the
>> border, so this is unlikely to be the problem
>>
>> I would also not be surprised if it were a completely different
>> problem all together. Any insight into why the propagation scaling
>> would not be having any effect on the boundary evolution would be of
>> great help!
>>
>> - Andrey
>>
>> // ============================== Code Excerpt
>> ================================
>> // ===== You can copy and paste this into a text editor for easier viewing
>> ====
>> //
>> ============================================================================
>> // Seed Region Extraction #include statements
>> // ...
>> #include <itkBinaryThresholdImageFilter.h>
>>
>> // Active Contour Include Statements
>> #include <itkSignedDanielssonDistanceMapImageFilter.h>
>> #include <itkCurvatureAnisotropicDiffusionImageFilter.h>
>> #include <itkGradientMagnitudeRecursiveGaussianImageFilter.h>
>> #include <itkSigmoidImageFilter.h>
>> #include <itkGeodesicActiveContourLevelSetImageFilter.h>
>>
>> class Segmenter
>> {
>> public:
>> typedef signed short PixelType;
>> typedef float FloatPixelType;
>>
>> // Setter Methods for Filter Parameters
>> // ...
>>
>> // Getter Methods for Intermediate Images in the Pipeline
>> // ...
>>
>> private:
>> // Seed Region Extraction Types
>> // ...
>> typedef itk::Image<PixelType, num_dims> ImageType;
>>
>> typedef itk::BinaryThresholdImageFilter<
>> ImageType, ImageType> Extractor;
>>
>> // Active Contour Types
>> typedef itk::Image<
>> FloatPixelType, num_dims> FloatImageType;
>>
>> typedef itk::SignedDanielssonDistanceMapImageFilter<
>> ImageType, FloatImageType> ContourInitializer;
>>
>> typedef itk::CurvatureAnisotropicDiffusionImageFilter<
>> ImageType, FloatImageType> Smoother;
>>
>> typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<
>> FloatImageType, FloatImageType> Gradient;
>>
>> typedef itk::SigmoidImageFilter<
>> FloatImageType, FloatImageType> Sigmoid;
>>
>> typedef itk::GeodesicActiveContourLevelSetImageFilter<
>> FloatImageType, FloatImageType> ActiveContourFilter;
>>
>> typedef itk::BinaryThresholdImageFilter<
>> FloatImageType, ImageType> ContourExtractor;
>>
>> // Seed Extraction Variables
>> // ...
>> Extractor::Pointer extractor;
>>
>> // Active Contour Variables
>> ContourInitializer::Pointer initializer;
>> Smoother::Pointer smoother;
>> Gradient::Pointer gradient;
>> Sigmoid::Pointer sigmoid;
>> ActiveContourFilter::Pointer activeContourFilter;
>> ContourExtractor::Pointer contourExtractor;
>> };
>>
>> Segmenter::Segmenter()
>> {
>> // Initializers
>> initializer = ContourInitializer::New();
>> smoother = Smoother::New();
>> gradient = Gradient::New();
>> sigmoid = Sigmoid::New();
>> activeContourFilter = ActiveContourFilter::New();
>> contourExtractor = ContourExtractor::New();
>>
>> // Parameters
>> smoother->SetTimeStep( 0.0625 );
>> smoother->SetConductanceParameter( 9.0 );
>>
>> gradient->SetSigma(1.0);
>>
>> sigmoid->SetOutputMinimum(0.00001);
>> sigmoid->SetOutputMaximum(1.0);
>>
>> sigmoid->SetAlpha(-5.0);
>> sigmoid->SetBeta(100.0);
>>
>> activeContourFilter->SetPropagationScaling(1.0);
>> activeContourFilter->SetAdvectionScaling(1.0);
>> activeContourFilter->SetCurvatureScaling(0.1);
>> activeContourFilter->SetMaximumRMSError(0.05);
>> activeContourFilter->SetNumberOfIterations(NUM_ITERS);
>>
>> contourExtractor->SetLowerThreshold( -1000.0 );
>> contourExtractor->SetUpperThreshold( 0.0 );
>> contourExtractor->SetOutsideValue(0);
>> contourExtractor->SetInsideValue(thresholdValue);
>>
>> // Pipeline
>> initializer->SetInput(extractor->GetOutput());
>> smoother->SetInput(reader->GetOutput());
>> gradient->SetInput(smoother->GetOutput());
>> sigmoid->SetInput(gradient->GetOutput());
>> activeContourFilter->SetInput(initializer->GetOutput());
>> activeContourFilter->SetFeatureImage(sigmoid->GetOutput());
>> contourExtractor->SetInput(activeContourFilter->GetOutput());
>> }
>>
>> // Segmenter Setter Function Definitions
>> // ...
>>
>> // Segmenter Image Getter Function Definitions
>> // ...
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