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CSci 6971: Image Registration Lecture 20: Demons Registration April 16, 2004

CSci 6971: Image Registration Lecture 20: Demons Registration April 16, 2004. Prof. Chuck Stewart, RPI Dr. Luis Ibanez, Kitware. Deformable Registration. Deformable Registration. Deformable Transforms. Deformable Transforms. Deformable Transformation. y. y. Transform. x. x.

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CSci 6971: Image Registration Lecture 20: Demons Registration April 16, 2004

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  1. CSci 6971: Image Registration Lecture 20: Demons RegistrationApril 16, 2004 Prof. Chuck Stewart, RPI Dr. Luis Ibanez, Kitware

  2. Deformable Registration Deformable Registration Lecture 20

  3. Deformable Transforms Deformable Transforms Lecture 20

  4. Deformable Transformation y y Transform x x Fixed Image Moving Image Lecture 20

  5. Deformable Transformation y y Transform x x Fixed Image Moving Image Lecture 20

  6. Deformable Transformation y y Transform x x Fixed Image Moving Image Lecture 20

  7. Image Resampling Interpolator FixedImage Resample Image Filter MovingImage DeformedImage Transform Lecture 20

  8. Image Resampling Interpolator FixedImage Resample Image Filter MovingImage High Order Polynomials Splines Explicit Vector Field Orthogonal Basis DeformedImage Transform Lecture 20

  9. Kernel Splines Transforms Target Landmarks Source Landmarks Interpolated Values Displacement Vectors Lecture 20

  10. Kernel Spline Transforms • Thin Plates • Thin Plates R2 log R • Elastic Body • Elastic Body Reciprocal • Volume Lecture 20

  11. Kernel Spline Transforms InsightApplications / ThinPlateSplines Lecture 20

  12. Resampling: Kernel Spline Transform #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkLinearInterpolateImageFunction.h" #include "itkElasticBodySplineKernelTransform.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointerfixedImage = GetFixedImage(); ImageType::ConstPointermovingImage = GetMovingImage(); typedef itk::LinearInterpolateImageFunction<ImageType, double >InterpolatorType; InterpolatorType::Pointerinterpolator = InterpolatorType::New(); typedef itk::ResampleImageFilter< ImageType, ImageType > FilterType; FilterType::Pointerresampler = FilterType::New(); Lecture 20

  13. Resampling: Kernel Spline Transform typedef itk::ElasticBodySplineKernelTransform<double, 2 > TransformType; TransformType::Pointertransform = TransformType::New(); resampler->SetInterpolator( interpolator ); resampler->SetInput( movingImage ); ImageType::RegionTyperegion = fixedImage->GetBufferedRegion(); resampler->SetSize(region->GetSize() ); resampler->SetOutputStartIndex( region->GetIndex() ); resampler->SetOutputSpacing( fixedImage->GetSpacing() ); resampler->SetOutputOrigin( fixedImage->GetOrigin() ); Lecture 20

  14. Resampling: Kernel Spline Transform resampler->SetTransform(transform ); typedef TransformType::PointSetType PointSetType; PointSetType::PointersourceLandmarks = PointSetType::New(); PointSetType::PointertargetLandmarks = PointSetType::New(); transform->SetSourceLandmarks(sourceLandmarks ); transform->SetTargetLandmarks(targetLandmarks ); typedef PointSetType::PointsContainer PointsContainer; PointsContainer::Pointer sources = sourceLandmarks->GetPoints(); PointsContainer::Pointer targets = targetLandmarks->GetPoints(); Lecture 20

  15. Resampling: Kernel Spline Transform sources->Reserve( numberOfLandmarks ); targets->Reserve( numberOfLandmarks ); typedef PointSetType::PointType PointType; PointTypesource; PointTypetarget; for( int i = 0; i < numberOfLandmarks; i++ ) { inputFile >> source; inputFile >> target; sources->InsertElement(i, source ); targets->InsertElement(i, target ); } transform->ComputeWMatrix(); resampler->Update(); // Finally !! ImageType::ConstPointerdeformedImage = resampler->GetOutput(); Lecture 20

  16. Kernel Spline Transforms VolView : ITK Plugin Lecture 20

  17. Kernel Spline Transforms VolView : ITK Plugin Lecture 20

  18. Deformable Transforms Deformation Fields Lecture 20

  19. Deformation Vector Field ParaView: http://www.paraview.org Lecture 20

  20. Warp Image Filter #include "itkImage.h" #include "itkWarpImageFilter.h" #include "itkLinearInterpolateImageFunction.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointerfixedImage = GetFixedImage(); ImageType::ConstPointermovingImage = GetMovingImage(); typedef itk::LinearInterpolateImageFunction<ImageType, double >InterpolatorType; InterpolatorType::Pointerinterpolator = InterpolatorType::New(); typedef itk::Vector< float, 2 > VectorType; typedef itk::Image< VectorType , 2 > VectorFieldType; VectorFieldType::PointervectorField = GetVectorField(); Lecture 20

  21. Warp Image Filter typedef itk::WarpImageFilter< ImageType, ImageType, VectorFieldType > WarpFilterType; WarpFilterType::PointerwarpFilter = WarpFilterType::New(); warpFilter->SetInterpolator( interpolator ); warpFilter->SetInput( movingImage ); warpFilter->SetOutputSpacing( fixedImage->GetSpacing() ); warpFilter->SetOutputOrigin( fixedImage->GetOrigin() ); warpFilter->SetDeformationField( vectorField ); warpFilter->Update(); ImageType::ConstPointerdeformedImage = warpFilter->GetOutput(); Lecture 20

  22. Demons Registration Demons Registration Lecture 20

  23. Demons Registration Demons is a Family of Algorithms Lecture 20

  24. Demons Registration Demons Type 0 Lecture 20

  25. Demons Registration: Type 0 Transform Scene Model Lecture 20

  26. Demons Registration: Type 0 Transform Scene Gradients Model Lecture 20

  27. Demons Registration: Type 0 Transform Scene Forces Model Lecture 20

  28. Demons Registration Demons Type 1 Lecture 20

  29. Demons Registration: Type 1 Transform Scene Vector Field Model Lecture 20

  30. Demons Registration: Type 1 Transform Scene Vector Field Model Lecture 20

  31. Demons Registration: Type 1 Transform Scene Vector Field Model Lecture 20

  32. Demons Registration: Type 1 Transform Scene Vector Field Model Lecture 20

  33. Demons Registration: Type 1 Gradient Scene Lecture 20

  34. Demons Registration: Type 1 Current Estimation Intensity Space Gradient Desired Displacement Scene Lecture 20

  35. Demons Registration: Type 1 Transform Scene Vector Field Model Lecture 20

  36. Demons Registration: Type 1 Scene Lecture 20

  37. Incremental Field Next Field Demons Registration: Type 1 Iterations Previous Field Gaussian Smoothing Lecture 20

  38. Demons Registration: Type 1 ( s – m ) . Grad(s) V = Grad(s)2 ( s – m ) . Grad(s) V = Grad(s)2 + (s-m)2 K Lecture 20

  39. Image Registration Framework FixedImage Increment Computation PDE Solver MovingImage Interpolator DeformationField Transform Lecture 20

  40. Demons Registration: Type 1 #include "itkImage.h" #include "itkDemonsRegistrationFilter.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointerfixedImage = GetFixedImage(); ImageType::ConstPointermovingImage = GetMovingImage(); typedef itk::Vector< float, 2 > VectorType; typedef itk::Image< VectorType , 2 > VectorFieldType; typedef itk::DemonsRegistrationFilter< ImageType, ImageType, VectorFieldType > DemonsType; DemonsType::Pointerdemons = DemonsType::New(); Lecture 20

  41. Demons Registration: Type 1 demons->SetFixedImage( fixedImage ); demons->SetMovingImage( movingImage ); demons->SetNumberOfIterations( 200 ); demons->SetStandardDeviations( 1.0 ); demons->Update(); ImageType::ConstPointervectorField = demons->GetOutput(); Lecture 20

  42. Demons Registration: Type 1 Scene Lecture 20

  43. Demons Registration: Type 1 Model Lecture 20

  44. Demons Registration: Type 1 After Registration Lecture 20

  45. Demons Registration: Type 1 Scene Lecture 20

  46. Demons Registration: Type 1 Scene Lecture 20

  47. Requirements Fixed and Moving images should have the same intensity distribution ! Lecture 20

  48. Eventual Preprocessing - Histogram Matching Filter- Anisotropic Diffusion Filtering Lecture 20

  49. Image Registration Framework FixedImage Increment Computation PDE Solver MovingImage Interpolator DeformationField Transform Resampler MovingRegistered Lecture 20

  50. End Enjoy ITK ! Lecture 20

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