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| using | CompositeTransformType = typename Superclass::CompositeTransformType |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer |
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| using | DecoratedOutputTransformType = typename Superclass::DecoratedOutputTransformType |
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| using | DerivativeType = typename OutputTransformType::DerivativeType |
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| using | DerivativeValueType = typename DerivativeType::ValueType |
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| using | DisplacementFieldPointer = typename DisplacementFieldType::Pointer |
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| using | DisplacementFieldTransformPointer = typename DisplacementFieldTransformType::Pointer |
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| using | DisplacementFieldTransformType = DisplacementFieldTransform< RealType, ImageDimension > |
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| using | DisplacementFieldType = typename OutputTransformType::DisplacementFieldType |
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| using | DisplacementVectorType = typename DisplacementFieldType::PixelType |
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| using | FixedImageMasksContainerType = typename Superclass::FixedImageMasksContainerType |
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| using | FixedImageMaskType = typename Superclass::FixedImageMaskType |
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| using | FixedImagePointer = typename FixedImageType::Pointer |
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| using | FixedImagesContainerType = typename Superclass::FixedImagesContainerType |
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| using | FixedImageType = TFixedImage |
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| using | FixedMaskImageType = typename ImageMaskSpatialObjectType::ImageType |
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| using | ImageMaskSpatialObjectType = ImageMaskSpatialObject< ImageDimension > |
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| using | ImageMetricPointer = typename ImageMetricType::Pointer |
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| using | ImageMetricType = typename Superclass::ImageMetricType |
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| using | InitialTransformType = typename Superclass::InitialTransformType |
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| using | MeasureType = typename ImageMetricType::MeasureType |
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| using | MetricPointer = typename MetricType::Pointer |
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| using | MetricType = typename Superclass::MetricType |
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| using | MovingImageMasksContainerType = typename Superclass::MovingImageMasksContainerType |
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| using | MovingImageMaskType = typename Superclass::MovingImageMaskType |
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| using | MovingImagePointer = typename MovingImageType::Pointer |
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| using | MovingImagesContainerType = typename Superclass::MovingImagesContainerType |
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| using | MovingImageType = TMovingImage |
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| using | MovingMaskImageType = typename ImageMaskSpatialObjectType::ImageType |
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| using | MultiMetricType = typename Superclass::MultiMetricType |
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| using | NumberOfIterationsArrayType = Array< SizeValueType > |
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| using | OutputTransformPointer = typename OutputTransformType::Pointer |
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| using | OutputTransformType = TOutputTransform |
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| using | Pointer = SmartPointer< Self > |
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| using | PointSetMetricType = typename Superclass::PointSetMetricType |
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| using | PointSetPointer = typename PointSetType::Pointer |
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| using | PointSetsContainerType = typename Superclass::PointSetsContainerType |
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| using | PointSetType = typename Superclass::PointSetType |
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| using | RealType = typename OutputTransformType::ScalarType |
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| using | Self = SyNImageRegistrationMethod |
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| using | Superclass = ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet > |
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| using | TransformBaseType = typename CompositeTransformType::TransformType |
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| using | VirtualImageBaseConstPointer = typename Superclass::VirtualImageBaseConstPointer |
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| using | VirtualImageBaseType = typename Superclass::VirtualImageBaseType |
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| using | VirtualImageType = typename Superclass::VirtualImageType |
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| using | CompositeTransformPointer = typename CompositeTransformType::Pointer |
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| using | CompositeTransformType = CompositeTransform< RealType, ImageDimension > |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | DecoratedInitialTransformPointer = typename DecoratedInitialTransformType::Pointer |
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| using | DecoratedInitialTransformType = DataObjectDecorator< InitialTransformType > |
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| using | DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer |
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| using | DecoratedOutputTransformType = DataObjectDecorator< OutputTransformType > |
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| using | DerivativeType = typename OutputTransformType::DerivativeType |
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| using | DerivativeValueType = typename DerivativeType::ValueType |
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| using | FixedImageConstPointer = typename FixedImageType::ConstPointer |
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| using | FixedImageMaskConstPointer = typename FixedImageMaskType::ConstPointer |
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| using | FixedImageMasksContainerType = std::vector< FixedImageMaskConstPointer > |
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| using | FixedImageMaskType = typename ImageMetricType::FixedImageMaskType |
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| using | FixedImagePointer = typename FixedImageType::Pointer |
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| using | FixedImagesContainerType = std::vector< FixedImageConstPointer > |
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| using | FixedImageType = TFixedImage |
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| using | ImageMetricType = ImageToImageMetricv4< FixedImageType, MovingImageType, VirtualImageType, RealType > |
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| using | InitialTransformPointer = typename InitialTransformType::Pointer |
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| using | InitialTransformType = Transform< RealType, ImageDimension, ImageDimension > |
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| using | MetricPointer = typename MetricType::Pointer |
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| using | MetricSamplePointSetType = typename ImageMetricType::FixedSampledPointSetType |
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| using | MetricSamplingPercentageArrayType = Array< RealType > |
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| using | MetricSamplingStrategyEnum = ImageRegistrationMethodv4Enums::MetricSamplingStrategy |
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| using | MetricType = ObjectToObjectMetricBaseTemplate< RealType > |
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| using | MovingImageConstPointer = typename MovingImageType::ConstPointer |
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| using | MovingImageMaskConstPointer = typename MovingImageMaskType::ConstPointer |
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| using | MovingImageMasksContainerType = std::vector< MovingImageMaskConstPointer > |
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| using | MovingImageMaskType = typename ImageMetricType::MovingImageMaskType |
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| using | MovingImagePointer = typename MovingImageType::Pointer |
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| using | MovingImagesContainerType = std::vector< MovingImageConstPointer > |
| |
| using | MovingImageType = TMovingImage |
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| using | MultiMetricType = ObjectToObjectMultiMetricv4< ImageDimension, ImageDimension, VirtualImageType, RealType > |
| |
| using | OptimizerPointer = typename OptimizerType::Pointer |
| |
| using | OptimizerType = ObjectToObjectOptimizerBaseTemplate< RealType > |
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| using | OptimizerWeightsType = typename OptimizerType::ScalesType |
| |
| using | OutputTransformPointer = typename OutputTransformType::Pointer |
| |
| using | OutputTransformType = TOutputTransform |
| |
| using | Pointer = SmartPointer< Self > |
| |
| using | PointSetConstPointer = typename PointSetType::ConstPointer |
| |
| using | PointSetMetricType = PointSetToPointSetMetricWithIndexv4< PointSetType, PointSetType, RealType > |
| |
| using | PointSetsContainerType = std::vector< PointSetConstPointer > |
| |
| using | PointSetType = TPointSet |
| |
| using | RealType = typename OutputTransformType::ScalarType |
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| using | Self = ImageRegistrationMethodv4 |
| |
| using | ShrinkFactorsArrayType = Array< SizeValueType > |
| |
| using | ShrinkFactorsPerDimensionContainerType = typename ShrinkFilterType::ShrinkFactorsType |
| |
| using | ShrinkFilterType = ShrinkImageFilter< FixedImageType, VirtualImageType > |
| |
| using | SmoothingSigmasArrayType = Array< RealType > |
| |
| using | Superclass = ProcessObject |
| |
| using | TransformParametersAdaptorPointer = typename TransformParametersAdaptorType::Pointer |
| |
| using | TransformParametersAdaptorsContainerType = std::vector< TransformParametersAdaptorPointer > |
| |
| using | TransformParametersAdaptorType = TransformParametersAdaptorBase< InitialTransformType > |
| |
| using | VectorType = Vector< RealType, ImageDimension > |
| |
| using | VirtualImageBaseConstPointer = typename VirtualImageBaseType::ConstPointer |
| |
| using | VirtualImageBaseType = ImageBase< ImageDimension > |
| |
| using | VirtualImagePointer = typename VirtualImageType::Pointer |
| |
| using | VirtualImageType = TVirtualImage |
| |
| using | DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType |
| |
| using | ConstPointer = SmartPointer< const Self > |
| |
| using | DataObjectIdentifierType = DataObject::DataObjectIdentifierType |
| |
| using | DataObjectPointer = DataObject::Pointer |
| |
| using | DataObjectPointerArray = std::vector< DataObjectPointer > |
| |
| using | DataObjectPointerArraySizeType = DataObjectPointerArray::size_type |
| |
| using | MultiThreaderType = MultiThreaderBase |
| |
| using | NameArray = std::vector< DataObjectIdentifierType > |
| |
| using | Pointer = SmartPointer< Self > |
| |
| using | Self = ProcessObject |
| |
| using | Superclass = Object |
| |
| using | ConstPointer = SmartPointer< const Self > |
| |
| using | Pointer = SmartPointer< Self > |
| |
| using | Self = Object |
| |
| using | Superclass = LightObject |
| |
| using | ConstPointer = SmartPointer< const Self > |
| |
| using | Pointer = SmartPointer< Self > |
| |
| using | Self = LightObject |
| |
|
| static constexpr unsigned int | ImageDimension = TFixedImage::ImageDimension |
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| static constexpr unsigned int | ImageDimension = TFixedImage::ImageDimension |
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| RealType | m_LearningRate { 0.25 } |
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| OutputTransformPointer | m_MovingToMiddleTransform { nullptr } |
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| OutputTransformPointer | m_FixedToMiddleTransform { nullptr } |
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| RealType | m_ConvergenceThreshold { static_cast<RealType>(1.0e-6) } |
| |
| unsigned int | m_ConvergenceWindowSize { 10 } |
| |
| NumberOfIterationsArrayType | m_NumberOfIterationsPerLevel |
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| bool | m_DownsampleImagesForMetricDerivatives { true } |
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| bool | m_AverageMidPointGradients { false } |
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| RealType | m_GaussianSmoothingVarianceForTheUpdateField { 3.0 } |
| |
| RealType | m_GaussianSmoothingVarianceForTheTotalField { 0.5 } |
| |
| virtual void | SetLearningRate (RealType _arg) |
| |
| virtual RealType | GetLearningRate () const |
| |
| virtual void | SetNumberOfIterationsPerLevel (NumberOfIterationsArrayType _arg) |
| |
| virtual NumberOfIterationsArrayType | GetNumberOfIterationsPerLevel () const |
| |
| virtual void | SetConvergenceThreshold (RealType _arg) |
| |
| virtual RealType | GetConvergenceThreshold () const |
| |
| virtual void | SetConvergenceWindowSize (unsigned int _arg) |
| |
| virtual unsigned int | GetConvergenceWindowSize () const |
| |
| virtual void | SetDownsampleImagesForMetricDerivatives (bool _arg) |
| |
| virtual bool | GetDownsampleImagesForMetricDerivatives () const |
| |
| virtual void | SetAverageMidPointGradients (bool _arg) |
| |
| virtual bool | GetAverageMidPointGradients () const |
| |
| virtual void | SetGaussianSmoothingVarianceForTheUpdateField (RealType _arg) |
| |
| virtual const RealType & | GetGaussianSmoothingVarianceForTheUpdateField () const |
| |
| virtual void | SetGaussianSmoothingVarianceForTheTotalField (RealType _arg) |
| |
| virtual const RealType & | GetGaussianSmoothingVarianceForTheTotalField () const |
| |
| virtual OutputTransformType * | GetModifiableFixedToMiddleTransform () |
| |
| virtual const OutputTransformType * | GetFixedToMiddleTransform () const |
| |
| virtual OutputTransformType * | GetModifiableMovingToMiddleTransform () |
| |
| virtual const OutputTransformType * | GetMovingToMiddleTransform () const |
| |
| virtual void | SetFixedToMiddleTransform (OutputTransformType *_arg) |
| |
| virtual void | SetMovingToMiddleTransform (OutputTransformType *_arg) |
| |
| | SyNImageRegistrationMethod () |
| |
| | ~SyNImageRegistrationMethod () override=default |
| |
| void | PrintSelf (std::ostream &os, Indent indent) const override |
| |
| void | GenerateData () override |
| |
| virtual void | StartOptimization () |
| |
| void | InitializeRegistrationAtEachLevel (const SizeValueType) override |
| |
| virtual DisplacementFieldPointer | ComputeUpdateField (const FixedImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const MovingImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const FixedImageMasksContainerType, const MovingImageMasksContainerType, MeasureType &) |
| |
| virtual DisplacementFieldPointer | ComputeMetricGradientField (const FixedImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const MovingImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const FixedImageMasksContainerType, const MovingImageMasksContainerType, MeasureType &) |
| |
| virtual DisplacementFieldPointer | ScaleUpdateField (const DisplacementFieldType *) |
| |
| virtual DisplacementFieldPointer | GaussianSmoothDisplacementField (const DisplacementFieldType *, const RealType) |
| |
| virtual DisplacementFieldPointer | InvertDisplacementField (const DisplacementFieldType *, const DisplacementFieldType *=nullptr) |
| |
template<typename TFixedImage, typename TMovingImage, typename TOutputTransform = DisplacementFieldTransform<double, TFixedImage::ImageDimension>, typename TVirtualImage = TFixedImage, typename TPointSet = PointSet<unsigned int, TFixedImage::ImageDimension>>
class itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet >
Interface method for the performing greedy SyN image registration.
For greedy SyN we use m_Transform to map the time-parameterized middle image to the fixed image (and vice versa using m_Transform->GetInverseDisplacementField() ). We employ another ivar, m_InverseTransform, to map the time-parameterized middle image to the moving image.
Output: The output is the updated transform which has been added to the composite transform.
This implementation is based on the source code in Advanced Normalization Tools (ANTs)
Avants, B. B.; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A. & Gee, J. C. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, Penn Image Computing and Science Laboratory, University of Pennsylvania, 2011, 54, 2033-2044
The original paper discussing the method is here:
Avants, B. B.; Epstein, C. L.; Grossman, M. & Gee, J. C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal, Department of Radiology, University of Pennsylvania, 2008, 12, 26-41
The method evolved since that time with crucial contributions from Gang Song and Nick Tustison. Though similar in spirit, this implementation is not identical.
- Todo:
- Need to allow the fixed image to have a composite transform.
- Author
- Nick Tustison
-
Brian Avants
Definition at line 71 of file itkSyNImageRegistrationMethod.h.
Inheritance diagram for itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet >:
1.8.16
