ITK Deformable Registration Demons Methods

Deformable Registration

Deformable Transforms

Deformable Transformation y y Transform x x Fixed Image Moving Image

Deformable Transformation y y Transform x x Fixed Image Moving Image

Deformable Transformation y y Transform x x Fixed Image Moving Image

Image Resampling Interpolator Fixed Image Resample Image Moving Image Filter Moving Image Deformed Image Transform

Image Resampling Fixed Image Interpolator Resample Image Filter Moving Image Orthogonal Basis Explicit Vector Field Splines High Order Polynomials Deformed Image Transform

Kernel Splines Transforms Target Landmarks Source Landmarks Interpolated Values Displacement Vectors

Kernel Spline Transforms Thin Plates Thin Plates R2 log R Elastic Body Elastic Body Reciprocal Volume

Kernel Spline Transforms InsightApplications / ThinPlateSplines

Resampling: Kernel Spline Transform #include "itkImage.h" #include "itkResampleImageFilter.h" #include "itkLinearInterpolateImageFunction.h" #include "itkElasticBodySplineKernelTransform.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointer fixedImage = GetFixedImage(); ImageType::ConstPointer movingImage = GetMovingImage(); typedef itk::LinearInterpolateImageFunction< ImageType, double > InterpolatorType; InterpolatorType::Pointer interpolator = InterpolatorType::New(); typedef itk::ResampleImageFilter< ImageType, ImageType > FilterType; FilterType::Pointer resampler = FilterType::New();

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

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

Resampling: Kernel Spline Transform sources->Reserve( numberOfLandmarks ); targets->Reserve( numberOfLandmarks ); typedef PointSetType::PointType PointType; PointType source; PointType target; 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::ConstPointer deformedImage = resampler->GetOutput();

Kernel Spline Transforms VolView : ITK Plugin

Kernel Spline Transforms VolView : ITK Plugin

Deformable Transforms Deformation Fields

Deformation Vector Field ParaView: http://www.paraview.org

Warp Image Filter #include "itkImage.h" #include "itkWarpImageFilter.h" #include "itkLinearInterpolateImageFunction.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointer fixedImage = GetFixedImage(); ImageType::ConstPointer movingImage = GetMovingImage(); typedef itk::LinearInterpolateImageFunction< ImageType, double > InterpolatorType; InterpolatorType::Pointer interpolator = InterpolatorType::New(); typedef itk::Vector< float, 2 > VectorType; typedef itk::Image< VectorType , 2 > VectorFieldType; VectorFieldType::Pointer vectorField = GetVectorField();

Warp Image Filter typedef itk::WarpImageFilter< ImageType, VectorFieldType > WarpFilterType; WarpFilterType::Pointer warpFilter = WarpFilterType::New(); warpFilter->SetInterpolator( interpolator ); warpFilter->SetInput( movingImage ); warpFilter->SetOutputSpacing( fixedImage->GetSpacing() ); warpFilter->SetOutputOrigin( fixedImage->GetOrigin() ); warpFilter->SetDeformationField( vectorField ); warpFilter->Update(); ImageType::ConstPointer deformedImage = warpFilter->GetOutput();

Demons Registration Demons Registration

Demons is a Family of Algorithms Demons Registration Demons is a Family of Algorithms

Demons Registration Demons Type 0

Demons Registration: Type 0 Transform Scene Model

Demons Registration: Type 0 Transform Scene Gradients Model

Demons Registration: Type 0 Transform Scene Forces Model

Demons Registration Demons Type 1

Demons Registration: Type 1 Transform Scene Vector Field Model

Demons Registration: Type 1 Transform Scene Vector Field Model

Demons Registration: Type 1 Transform Scene Vector Field Model

Demons Registration: Type 1 Transform Scene Vector Field Model

Demons Registration: Type 1 Gradient Scene

Demons Registration: Type 1 Current Estimation Intensity Space Gradient Desired Displacement Scene

Demons Registration: Type 1 Transform Scene Vector Field Model

Demons Registration: Type 1 Scene

Demons Registration: Type 1 Iterations Incremental Field Next Field Previous Field Gaussian Smoothing

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

Image Registration Framework Fixed Image Increment Computation PDE Solver Moving Image Interpolator Deformation Field Transform

Demons Registration: Type 1 #include "itkImage.h" #include "itkDemonsRegistrationFilter.h" typedef itk::Image< char, 2 > ImageType; ImageType::ConstPointer fixedImage = GetFixedImage(); ImageType::ConstPointer movingImage = GetMovingImage(); typedef itk::Vector< float, 2 > VectorType; typedef itk::Image< VectorType , 2 > VectorFieldType; typedef itk::DemonsRegistrationFilter< ImageType, VectorFieldType > DemonsType; DemonsType::Pointer demons = DemonsType::New();

Demons Registration: Type 1 demons->SetFixedImage( fixedImage ); demons->SetMovingImage( movingImage ); demons->SetNumberOfIterations( 200 ); demons->SetStandardDeviations( 1.0 ); demons->Update(); ImageType::ConstPointer vectorField = demons->GetOutput();

Demons Registration: Type 1 Scene

Demons Registration: Type 1 Model

Demons Registration: Type 1 After Registration

Demons Registration: Type 1 Scene

Demons Registration: Type 1 Scene

Fixed and Moving images should have the same intensity distribution ! Requirements Fixed and Moving images should have the same intensity distribution !

Eventual Preprocessing - Histogram Matching Filter - Anisotropic Diffusion Filtering

Image Registration Framework Fixed Image Increment Computation PDE Solver Moving Image Interpolator Deformation Field Transform Resampler Moving Registered

Enjoy ITK !