Index

Amount of information
    Image, 920
Anisotropic data sets, 303

BinaryMask3DMeshSource
    Header, 314
    Instantiation, 314
    SetInput, 315
BSplineInterpolateImageFunction, 560
BSplineTransform, 620
    Instantiation, 607, 616, 618, 620
    New, 607, 616, 618, 620

Casting Images, 90
CenteredTransformInitializer
    GeometryOn(), 428
    MomentsOn(), 428
CenteredTransformInitializer
    GeometryOn(), 399
    MomentsOn(), 399
Complex images
    Instantiation, 32
    Reading, 32
    Writing, 32
CreateStructuringElement()
    itk::BinaryBallStructuringElement, 133, 138

DICOM, 43
    Changing Headers, 62
    Dictionary, 55
    GDCM, 55
    Header, 55, 59
    Introduction, 43
    Printing Tags, 55, 59
    Series, 43
    Standard, 43
    Tags, 55, 59
Dicom
    HIPPA, 52
Distance Map
    itk::SignedDanielssonDistanceMapImageFilter, 236

EllipseSpatialObject
    Instantiation, 668
Entropy
    Images, 920
    What’s wrong in images, 918

GDCM
    Dictionary, 55
GDCMImageIO
    header, 55
GDCMSeriesFileNames
    GetOutputFileNames(), 54
    SetOutputDirectory(), 54
GetMetaDataDictionary()
    ImageIOBase, 56
GroupSpatialObject
    Instantiation, 668

HIPAA
    Dicom, 52
    Privacy, 52

Image
    Amount of information, 920
    Entropy, 920
Image Series
    Reading, 36
    Writing, 36
ImageToSpatialObjectMetric
    GetValue(), 667
ImageFileRead
    Vector images, 30
ImageFileWriter
    Vector images, 28
ImageIO
    GetMetaDataDictionary(), 61
ImageIOBase
    GetMetaDataDictionary(), 56
ImageSeriesWriter
    SetFileNames(), 54
Isosurface extraction
    Mesh, 314
itk::AddImageFilter
    Instantiation, 119
itk::AffineTransform, 441, 548
    Composition, 287
    header, 241, 441
    Image Registration, 472
    Instantiation, 442, 474
    instantiation, 242, 288
    New(), 288, 442
    Pointer, 288, 442
    resampling, 288
    Rotate2D(), 287, 292
    SetIdentity(), 259
    Translate(), 249, 287, 292, 293
itk::AmoebaOptimizer, 590
itk::ANTSNeighborhoodCorrelationImageToImageMetricv4, 584
itk::BilateralImageFilter, 202
    header, 202
    instantiation, 202
    New(), 202
    Pointer, 202
    SetDomainSigma(), 203
    SetRangeSigma(), 203
itk::BinaryThresholdImageFilter
    Header, 70
    Instantiation, 70
    SetInput(), 71
    SetInsideValue(), 71
    SetOutsideValue(), 71
itk::BinaryBallStructuringElement
    CreateStructuringElement(), 133, 138
    SetRadius(), 133, 138
itk::BinaryDilateImageFilter
    header, 132
    New(), 133
    Pointer, 133
    SetDilateValue(), 134
    SetKernel(), 133
    Update(), 134
itk::BinaryErodeImageFilter
    header, 132
    New(), 133
    Pointer, 133
    SetErodeValue(), 134
    SetKernel(), 133
    Update(), 134
itk::BinaryMedianImageFilter, 142
    GetOutput(), 143
    header, 142
    instantiation, 143
    Neighborhood, 143
    New(), 143
    Pointer, 143
    Radius, 143
    SetInput(), 143
itk::BinomialBlurImageFilter, 164
itk::BinomialBlurImageFilter
    header, 164
    instantiation, 164
    New(), 164
    Pointer, 164
    SetInput(), 164
    SetRepetitions(), 164
    Update(), 164
itk::BSplineDeformableTransform, 552
itk::BSplineInterpolateImageFunction, 561
itk::BSplineTransform, 606, 615, 617
    DeformableRegistration, 606, 615, 617
    header, 606, 615, 617
itk::BSplineTransformParametersAdaptor, 615
itk::CannySegmentationLevelSetImageFilter, 819
    GenerateSpeedImage(), 828
    GetSpeedImage(), 828
    SetAdvectionScaling(), 823
itk::CannyEdgeDetectionImageFilter, 87
    header, 87
itk::CastImageFilter, 90
    header, 90
    instantiation, 216, 221
    New(), 91, 216, 221
    Pointer, 91, 216, 221
    SetInput(), 91
    Update(), 91
itk::CenteredRigid2DTransform, 522
itk::CenteredTransformInitializer
    header, 427
    In 3D, 427
    Instantiation, 428
    New(), 428
    SmartPointer, 428
itk::ChangeInformationImageFilter
    CenterImageOn(), 841
itk::ComplexToRealImageFilter, 309
itk::ConfidenceConnectedImageFilter, 710
    header, 710
    SetInitialNeighborhoodRadius(), 713
    SetMultiplier(), 712
    SetNumberOfIterations(), 713
    SetReplaceValue(), 713
    SetSeed(), 713
itk::ConjugateGradientLineSearchOptimizerv4, 590
itk::ConnectedThresholdImageFilter, 688
    header, 688
    SetLower(), 690
    SetReplaceValue(), 690
    SetSeed(), 690
    SetUpper(), 690
itk::CorrelationImageToImageMetricv4, 578
itk::CovariantVector
    Concept, 498
itk::CurvatureAnisotropicDiffusionImageFilter, 183
    header, 183
    instantiation, 183
    New(), 183
    Pointer, 183
    SetConductanceParameter(), 184
    SetNumberOfIterations(), 184
    SetTimeStep(), 184
    Update(), 184
itk::CurvatureFlowImageFilter, 188
    header, 188
    instantiation, 188
    New(), 188
    Pointer, 188
    SetNumberOfIterations(), 189
    SetTimeStep(), 189
    Update(), 189
itk::DanielssonDistanceMapImageFilter
    GetOutput(), 229
    GetVoronoiMap(), 229
    Header, 228
    Instantiation, 228
    instantiation, 228
    New(), 228
    Pointer, 228
    SetInput(), 229
itk::DataObjectDecorator
    Get(), 333
    Use in Registration, 333
itk::DemonsImageToImageMetricv4, 584
itk::DemonsRegistrationFilter, 626
    SetFixedImage(), 627
    SetMovingImage(), 627
    SetNumberOfIterations(), 627
    SetStandardDeviations(), 627
itk::DerivativeImageFilter, 109
    GetOutput(), 110
    header, 109
    instantiation, 109
    New(), 109
    Pointer, 109
    SetDirection(), 109
    SetInput(), 110
    SetOrder(), 109
itk::DiscreteGaussianImageFilter, 159
    header, 159
    instantiation, 160
    New(), 160
    Pointer, 160
    SetMaximumKernelWidth(), 160
    SetVariance(), 160
    Update(), 160
itk::ElasticBodyReciprocalSplineKernelTransform, 555
itk::ElasticBodySplineKernelTransform, 555
itk::EllipseSpatialObject
    header, 665
    SetRadius(), 668
itk::Euler2DTransform, 374, 398, 518
    header, 374, 398
    Instantiation, 374, 399
    New(), 375, 399
    Pointer, 375, 399
    SmartPointer, 399
itk::Euler3DTransform, 539
itk::EventObject
    CheckEvent, 351
itk::ExhaustiveOptimizerv4, 590
itk::ExtractImageFilter
    header, 23
    SetExtractionRegion(), 25
itk::FastMarchingImageFilter
    Multiple seeds, 764, 782
    NodeContainer, 765, 782
    Nodes, 765, 782
    NodeType, 765, 782
    Seed initialization, 765, 782
    SetStoppingValue(), 765
    SetTrialPoints(), 765, 782
itk::FFTWForwardFFTImageFilter, 308, 311
itk::FileImageReader
    GetOutput(), 71, 85, 698
itk::FlipImageFilter, 237
    GetOutput(), 237
    header, 237
    instantiation, 237
    Neighborhood, 237
    New(), 237
    Pointer, 237
    Radius, 237
    SetInput(), 237
itk::FloodFillIterator
    In Region Growing, 688, 710
itk::ForwardFFTImageFilter, 308, 311
itk::GDCMImageIO
    header, 48
itk::GDCMSeriesFileNames
    GetFileNames(), 50
    header, 48
    SetDirectory(), 50
itk::GeodesicActiveContourLevelSetImageFilter
    SetAdvectionScaling(), 797
    SetCurvatureScaling(), 797
    SetPropagationScaling(), 797
itk::GeodesicActiveContourShapePriorLevelSetImageFilter
    Monitoring, 840
    SetAdvectionScaling(), 842
    SetCurvatureScaling(), 842
    SetPropagationScaling(), 842
itk::GradientAnisotropicDiffusionImageFilter, 178
    header, 178
    instantiation, 178
    New(), 178
    Pointer, 178
    SetConductanceParameter(), 179
    SetNumberOfIterations(), 179
    SetTimeStep(), 179
    Update(), 179
itk::GradientDescentLineSearchOptimizerv4, 590
itk::GradientDescentOptimizerv4, 590
itk::GradientDescentOptimizerv4Template
    GetCurrentIteration(), 329
    SetLearningRate(), 327
    SetMinimumStepLength(), 327
    SetNumberOfIterations(), 328
    SetRelaxationFactor(), 327
itk::GradientMagnitudeRecursiveGaussianImageFilter, 104
    header, 104
    Instantiation, 105
    New(), 105
    Pointer, 105
    SetSigma(), 105, 764, 781
    Update(), 106
itk::GradientRecursiveGaussianImageFilter
    header, 28
itk::GradientMagnitudeImageFilter, 100
    header, 100
    instantiation, 101
    New(), 101
    Pointer, 101
    Update(), 101
itk::GrayscaleDilateImageFilter
    header, 137
    New(), 138
    Pointer, 138
    SetKernel(), 138
    Update(), 138
itk::GrayscaleErodeImageFilter
    header, 137
    New(), 138
    Pointer, 138
    SetKernel(), 138
    Update(), 138
itk::GroupSpatialObject
    header, 665
    New(), 669
    Pointer, 669
itk::HistogramMatchingImageFilter, 632
    SetNumberOfHistogramLevels(), 633
    SetNumberOfMatchPoints(), 633
    SetInput(), 633
    SetReferenceImage(), 633
    SetSourceImage(), 633
    ThresholdAtMeanIntensityOn(), 633
itk::HistogramMatchingImageFilter, 609, 626
    SetInput(), 610, 626
    SetNumberOfHistogramLevels(), 610, 626
    SetNumberOfMatchPoints(), 610, 626
    SetReferenceImage(), 610, 626
    SetSourceImage(), 610, 626
    ThresholdAtMeanIntensityOn(), 610, 626
itk::IdentityTransform, 505
itk::Image
    Header, 323
    Instantiation, 323
itk::ImageRegistrationMethod
    Multi-Modality, 356
itk::ImageRegistrationMethodv4
    SetMovingInitialTransform(), 473
    SetNumberOfLevels(), 463
    SetShrinkFactorsPerLevel(), 463
    SetSmoothingSigmasPerLevel(), 463
itk::ImageToImageMetricv4, 570
    GetDerivatives(), 570
    GetValue(), 570
    GetValueAndDerivatives(), 570
itk::ImageToSpatialObjectMetric
    header, 665
    Instantiation, 671
itk::ImageToSpatialObjectRegistrationMethod
    Instantiation, 671
    New(), 671
    Pointer, 671
    SetFixedImage(), 673
    SetInterpolator(), 673
    SetMetric(), 673
    SetMovingSpatialObject(), 673
    SetOptimizer(), 673
    SetTransform(), 673
    Update(), 673, 674
itk::ImageFileRead
    Complex images, 32
    Vector images, 26, 34
itk::ImageFileReader, 3
    header, 3, 15, 18, 38
    Instantiation, 4, 15, 19
    New(), 4, 16, 19, 22, 24, 29, 31, 35
    RGB Image, 17
    SetFileName(), 4, 16, 20, 22, 24, 29, 31, 35
    SmartPointer, 4, 16, 19, 22, 24, 29, 31, 35
itk::ImageFileWrite
    Complex images, 32
    Vector images, 26
itk::ImageFileWriter, 3
    header, 3, 15, 18, 48
    Instantiation, 4, 15, 19, 37
    New(), 4, 16, 19, 22, 24, 29, 31, 35
    RGB Image, 17, 41
    SetFileName(), 4, 16, 20, 22, 24, 29, 31, 35
    SetImageIO(), 16
    SmartPointer, 4, 16, 19, 22, 24, 29, 31, 35
    UseInputMetaDataDictionaryOff(), 47
itk::ImageMaskSpatialObject
    header, 594
    Instantiation, 594
    New, 594
    Pointer, 594
    SetImage(), 595
itk::ImageMomentsCalculator, 398
itk::ImageRegistrationMethod
    DataObjectDecorator, 333
    GetOutput(), 333
    Monitoring, 349
    Pipeline, 333
    Resampling image, 333
itk::ImageRegistrationMethodv4
    AffineTransform, 472
    GetTransform(), 328
    InPlaceOn(), 618
    Multi-Modality, 357, 457, 472, 592
    Multi-Resolution, 457, 472
    Multi-Stage, 472, 487
    Scaling parameter space, 472
    SetInitialTransform(), 618
itk::ImageSeriesReader
    GetMetaDataDictionaryArray(), 55
    header, 36, 48
    Instantiation, 37
    RGB Image, 41
    SetFileNames(), 50
itk::ImageSeriesWriter
    header, 38
    SetMetaDataDictionaryArray(), 55
itk::ImageToImageMetricv4
    SetFixedImageMask(), 595
itk::InterpolateImageFunction, 561
    Evaluate(), 561
    EvaluateAtContinuousIndex(), 561
    IsInsideBuffer(), 561
    SetInputImage(), 561
itk::IsolatedConnectedImageFilter
    AddSeed1(), 724
    AddSeed2(), 724
    GetIsolatedValue(), 724
    header, 723
    SetLower(), 724
    SetReplaceValue(), 724
itk::KernelTransforms, 555
itk::LaplacianSegmentationLevelSetImageFilter, 828
    SetPropagationScaling(), 832
itk::LaplacianRecursiveGaussianImageFilter, 122
    header, 122
    New(), 122
    Pointer, 122
    SetSigma(), 123
    Update(), 123
itk::LBFGS2Optimizer
    header, 615
itk::LBFGS2Optimizerv4, 615
itk::LBFGSOptimizerv4, 590
itk::LBFGSBOptimizerv4, 590
itk::LBFGSBOptimizerv4, 617
    header, 617
itk::LBFGSOptimizerv4, 606
    header, 606
itk::LevelSetMotionRegistrationFilter, 610
    SetFixedImage(), 610
    SetMovingImage(), 610
    SetNumberOfIterations(), 610
    SetStandardDeviations(), 610
itk::LinearInterpolateImageFunction, 561
    header, 666
itk::MaskImageFilter, 311
itk::MattesMutualInformationImageToImageMetricv4, 583
    SetNumberOfHistogramBins(), 357, 583
itk::MeanSquaresImageToImageMetricv4, 573
itk::MeanImageFilter, 124
    GetOutput(), 125
    header, 124
    instantiation, 125
    Neighborhood, 125
    New(), 125
    Pointer, 125
    Radius, 125
    SetInput(), 125
itk::MeanSquaresImageToImageMetricv4
    SetFixedInterpolator(), 325
    SetMovingInterpolator(), 325
itk::MedianImageFilter, 128
    GetOutput(), 129
    header, 128
    instantiation, 129
    Neighborhood, 129
    New(), 129
    Pointer, 129
    Radius, 129
    SetInput(), 129
itk::MinMaxCurvatureFlowImageFilter, 196
    header, 196
    instantiation, 196
    New(), 196
    Pointer, 196
    SetNumberOfIterations(), 197
    SetTimeStep(), 197
    Update(), 197
itk::MultiGradientOptimizerv4, 590
itk::MultiResolutionPyramidImageFilter, 454
    GetSchedule(), 456
    SetNumberOfLevels(), 455
    SetSchedule(), 456
    SetStartingShrinkFactors(), 456
itk::MutualInformationImageToImageMetricv4
    Trade-offs, 360
itk::NearestNeighborInterpolateImageFunction, 561
    header, 241
    instantiation, 242
itk::NeighborhoodConnectedImageFilter
    SetLower(), 706
    SetReplaceValue(), 706
    SetSeed(), 706
    SetUppder(), 706
itk::NormalizeImageFilter, 90
    header, 90
    New(), 91
    Pointer, 91
    SetInput(), 91
    Update(), 91
itk::NormalVariateGenerator
    Initialize(), 593, 672
    New(), 593, 672
    Pointer, 593, 672
itk::NumericSeriesFileNames
    header, 36
itk::ObjectToObjectOptimizer, 585
    GetCurrentPosition(), 590
    SetMetric(), 590
    SetScales(), 590
    SetScalesEstimator(), 590
    StartOptimization(), 590
itk::OnePlusOneEvolutionaryOptimizer
    Instantiation, 671
itk::OnePlusOneEvolutionaryOptimizerv4, 590
itk::OnePlusOneEvolutionaryOptimizer
    Initialize(), 845
    SetEpsilon(), 845
    SetMaximumIteration(), 845
    SetNormalVariateGenerator(), 845
    SetScales(), 845
itk::OnePlusOneEvolutionaryOptimizerv4
    Multi-Modality, 592
itk::Optimizer
    MaximizeOff(), 673
    MaximizeOn(), 673
itk::OtsuThresholdImageFilter
    SetInput(), 698
    SetInsideValue(), 698
    SetOutsideValue(), 698
itk::OtsuMultipleThresholdsCalculator
    GetOutput(), 703
itk::PCAShapeSignedDistanceFunction
    New(), 843
    SetPrincipalComponentStandardDeviations(), 843
    SetMeanImage(), 843
    SetNumberOfPrincipalComponents(), 843
    SetPrincipalComponentsImages(), 843
    SetTransform(), 843
itk::Point
    Concept, 498
itk::PowellOptimizerv4, 590
itk::QuasiNewtonOptimizerv4, 590
itk::QuaternionRigidTransform, 530
itk::RecursiveGaussianImageFilter, 116, 168
    header, 116, 168
    Instantiation, 116, 122, 169
    New(), 116, 169
    Pointer, 116, 169
    SetSigma(), 119, 171
    Update(), 171
itk::RegionOfInterestImageFilter
    header, 20
    SetRegionOfInterest(), 22
itk::RegistrationMethod
    SetTransform(), 616
itk::RegistrationMethodv4
    GetCurrentIteration(), 443
    GetValue(), 443
    SetFixedImage(), 325
    SetMetric(), 325
    SetMovingImage(), 325
    SetMovingInitialTransform(), 326
    SetOptimizer(), 325
    SetTransform(), 442
itk::RegularStepGradientDescentOptimizer
    SetRelaxationFactor(), 359
itk::RegularStepGradientDescentOptimizerv4, 590
itk::ResampleImageFilter, 241, 627
    GetOutput(), 243
    header, 241
    Image internal transform, 258
    instantiation, 242
    New(), 242
    Pointer, 242
    SetDefaultPixelValue(), 243, 255, 259, 286
    SetInput(), 243, 627
    SetInterpolator(), 242, 627
    SetOutputOrigin(), 243, 259, 262, 268, 277, 286, 627
    SetOutputSpacing(), 243, 259, 268, 277, 286, 627
    SetSize(), 243, 262, 268, 277, 286
    SetTransform(), 242, 259
itk::RescaleIntensityImageFilter, 90
    header, 18, 90
    New(), 91
    Pointer, 91
    SetInput(), 91
    SetOutputMaximum(), 19, 91
    SetOutputMinimum(), 19, 91
    Update(), 91
itk::RGBPixel
    header, 916
    Image, 17, 41
    Instantiation, 17, 41
    Statistics, 916
itk::Rigid3DPerspectiveTransform, 545
itk::Sample
    Histogram, 873
    Interfaces, 866
    PointSetToListSampleAdaptor, 872
itk::ScaleLogarithmicTransform, 515
itk::ScaleTransform, 511
itk::SegmentationLevelSetImageFilter
    SetAdvectionScaling(), 797
    SetCurvatureScaling(), 783, 797, 812
    SetMaximumRMSError(), 783
    SetNumberOfIterations(), 783
    SetPropagationScaling(), 783, 797, 812, 832
itk::SegmentationLevelSetImageFilter
    GenerateSpeedImage(), 828
    GetSpeedImage(), 828
    SetAdvectionScaling(), 823
itk::ShapeDetectionLevelSetImageFilter
    SetCurvatureScaling(), 783
    SetMaximumRMSError(), 783
    SetNumberOfIterations(), 783
itk::ShapeDetectionLevelSetImageFilter
    SetPropagationScaling(), 783
itk::ShapePriorSegmentationLevelSetImageFilter
    Monitoring, 840
    SetAdvectionScaling(), 842
    SetCurvatureScaling(), 842
    SetPropagationScaling(), 842
itk::ShapePriorMAPCostFunction
    SetShapeParameterMeans(), 845
    SetShapeParameterStandardDeviations(), 845
    SetWeights(), 844
itk::ShapeSignedDistanceFunction
    SetTransform(), 843
itk::ShiftScaleImageFilter, 90
    header, 90
    New(), 91
    Pointer, 91
    SetInput(), 91
    SetScale(), 91
    SetShift(), 91
    Update(), 91
itk::SigmoidImageFilter
    GetOutput(), 96
    header, 95
    instantiation, 95
    New(), 95
    Pointer, 95
    SetAlpha(), 95
    SetBeta(), 95
    SetInput(), 96
    SetOutputMaximum(), 95
    SetOutputMinimum(), 95
itk::SigmoidImageFilter , 95
itk::SignedDanielssonDistanceMapImageFilter
    Header, 233
    Instantiation, 233
itk::Similarity2DTransform, 526
    header, 292
    instantiation, 293
    New(), 293
    Pointer, 293
    SetAngle(), 293
    SetRotationCenter(), 293
    SetScale(), 293, 294
itk::Similarity3DTransform, 542
itk::Simularity2DTransform, 415
    header, 415
    Instantiation, 415
    Pointer, 416
    SetAngle(), 416
    SetScale(), 416
itk::SingleValuedNonLinearVnlOptimizerv4, 585
itk::SpatialObjectToImageFilter
    header, 665
    Instantiation, 669
itk::SpatialObjectToImageFilter
    New(), 669
    Pointer, 669
    SetInput(), 670
    SetSize(), 670
    Update(), 670
itk::Statistics
    Color Images, 912
itk::Statistics::CovarianceSampleFilter, 890
itk::Statistics::EuclideanDistanceMetric, 901
itk::Statistics::ExpectationMaximizationMixtureModelEstimator, 952
itk::Statistics::GaussianMixtureModelComponent, 952
itk::Statistics::GaussianMembershipFunction, 900, 946
itk::Statistics::HeapSort, 897
itk::Statistics::Histogram
    GetFrequency(), 914
    Iterators, 911
    Size(), 914
itk::Statistics::ImageToListAdaptor, 868
itk::Statistics::ImageToHistogramFilter
    header, 912, 916
    Update(), 913
itk::Statistics::ImageTohistogramFilter
    GetOutput(), 914
itk::Statistics::InsertSort, 897
itk::Statistics::IntrospectiveSort, 897
itk::Statistics::JointDomainImageToListAdaptor, 868
itk::Statistics::KdTree, 886
itk::Statistics::KdTreeBasedKmeansEstimator, 934
itk::Statistics::KdTreeGenerator, 886
itk::Statistics::ListSampleToHistogramFilter, 884, 894
itk::Statistics::ListSampleToHistogramGenerator, 884
    header, 908
itk::Statistics::ListSample, 866
itk::Statistics::MaximumDecisionRule, 903
itk::Statistics::MaximumRatioDecisionRule, 905
itk::Statistics::MeanCalculator, 890
itk::Statistics::MembershipSampleGenerator, 884
itk::Statistics::MembershipSample, 882
itk::Statistics::MinimumDecisionRule, 904
itk::Statistics::NeighborhoodSampler, 884
itk::Statistics::NeighborhoodSampler, 895
itk::Statistics::NormalVariateGenerator, 907, 946
    Initialize(), 845
itk::Statistics::PointSetToListSampleAdaptor, 870
itk::Statistics::QuickSelect, 897
itk::Statistics::SampleToHistogramFilter
    instantiation, 909
itk::Statistics::SampleToHistogramProjectionFilter, 884
itk::Statistics::SampleClassifier, 946
itk::Statistics::ScalarImageToHistogramGenerator
    Compute(), 911
    header, 910, 911
itk::Statistics::ScalarImageToListAdaptor, 868
    header, 908
    instantiation, 909
itk::Statistics::SelectiveSubsampleGenerator, 884
itk::Statistics::Subsample, 879, 897
itk::Statistics::WeightedCentroidKdTreeGenerator, 886
itk::Statistics::WeightedCovarianceCalculator, 892
itk::Statistics::WeightedMeanCalculator, 892
itk::SymmetricForcesDemonsRegistrationFilter, 633
    SetFixedImage(), 633
    SetMovingImage(), 633
    SetNumberOfIterations(), 634
    SetStandardDeviations(), 634
itk::ThinPlateR2LogRSplineKernelTransform, 555
itk::ThinPlateSplineKernelTransform, 555
itk::ThresholdSegmentationLevelSetImageFilter, 806
    SetCurvatureScaling(), 812
    SetPropagationScaling(), 812
itk::ThresholdImageFilter
    Header, 84
    Instantiation, 84
    SetInput(), 85
    SetOutsideValue(), 86
    ThresholdAbove(), 84
    ThresholdBelow(), 84, 86
    ThresholdOutside(), 84
itk::Transform, 495
    GetJacobian(), 504
    SetParameters(), 503
    TransformCovariantVector(), 501
    TransformPoint(), 501
    TransformVector(), 501
itk::TranslationTransform, 508
    GetNumberOfParameters(), 326
    Instantiation, 472
    New(), 473
    Pointer, 473
itk::Vector
    Concept, 498
itk::VectorConfidenceConnectedImageFilter
    SetInitialNeighborhoodRadius(), 732
    SetMultiplier(), 732
    SetNumberOfIterations(), 732
    SetReplaceValue(), 732
    SetSeed(), 732
itk::VectorCurvatureAnisotropicDiffusionImageFilter, 211
    header, 211, 220
    instantiation, 211, 221
    New(), 211, 221
    Pointer, 211, 221
    RGB Images, 220
    SetNumberOfIterations(), 212, 221
    SetTimeStep(), 212, 221
    Update(), 212, 221
itk::VectorGradientAnisotropicDiffusionImageFilter, 206
    header, 206, 215
    instantiation, 207, 216
    New(), 207, 216
    Pointer, 207, 216
    RGB Images, 215
    SetNumberOfIterations(), 207, 216
    SetTimeStep(), 207, 216
    Update(), 207, 216
itk::VectorIndexSelectionCastImageFilter
    header, 34
    Instantiation, 34
    New(), 34
    Pointer, 34
    SetIndex(), 34
itk::Versor
    Definition, 533
itk::VersorRigid3DTransform, 427
    header, 427
    Instantiation, 428
    Pointer, 428
itk::VersorRigid3DTransform, 536
itk::VersorTransform, 533
itk::VersorTransformOptimizer, 533
itk::VnlForwardFFTImageFilter, 308, 311
itk::VolumeSplineKernelTransform, 555
itk::VotingBinaryHoleFillingImageFilter, 149
    GetOutput(), 150
    header, 149
    instantiation, 149
    Neighborhood, 149
    New(), 149
    Pointer, 149
    Radius, 149
    SetBackgroundValue(), 150
    SetForegroundValue(), 150
    SetInput(), 150
    SetMajorityThreshold(), 150
itk::VotingBinaryIterativeHoleFillingImageFilter, 153
    GetOutput(), 154
    header, 153
    instantiation, 153
    Neighborhood, 154
    New(), 153
    Pointer, 153
    Radius, 154
    SetBackgroundValue(), 154
    SetForegroundValue(), 154
    SetInput(), 154
    SetMajorityThreshold(), 154
    SetMaximumNumberOfIterations(), 154
itk::VTKImageIO
    header, 15
    Instantiation, 15
    New(), 16
    SetFileTypeToASCII(), 16
    SmartPointer, 16
itk::WarpImageFilter
    SetInterpolator(), 298
itk::WarpImageFilter, 297, 611, 634
    SetDisplacementField(), 611, 634
    SetInput(), 611, 634
    SetInterpolator(), 611, 634
    SetOutputOrigin(), 611, 634
    SetOutputSpacing(), 611, 634
itk::WindowedSincInterpolateImageFunction, 564
itksys
    MakeDirectory, 54
    SystemTools, 54

Joint Entropy
    Statistics, 924
Joint Histogram
    Statistics, 924

LandmarkDisplacementFieldSource, 619
LaplacianRecursiveGaussianImageFilter
    SetNormalizeAcrossScale(), 123
LinearInterpolateImageFunction, 560

MakeDirectory
    itksys, 54
    SystemTools, 54
Marching Cubes, 314
Medical Errors, 52
Mesh
    Isosurface extraction, 314
MetaDataDictionary, 56, 61
    Begin(), 61
    ConstIterator, 61
    End(), 61
    header, 55
    Iterator, 61
    MetaDataObject, 61
    String entries, 61
MetaDataObject
    GetMetaDataObjectValue(), 57
    header, 55
    Strings, 61
Model to Image Registration
    Observer, 666
Mutual Information
    Statistics, 924

NearestNeighborInterpolateImageFunction, 560

Open Science, 373

RecursiveGaussianImageFilter
    SetDirection(), 117, 169
    SetNormalizeAcrossScale(), 118, 170
    SetOrder(), 117, 169
Registration
    Finite Element-Based, 604
RegularStepGradientDescentOptimizer
    SetLearningRate(), 377
    SetMinimumStepLength(), 377
    SetNumberOfIterations(), 377
    SetRelaxationFactor(), 377
Resampling, 303
RescaleIntensityImageFilter
    Instantiation, 31, 35
    New(), 31, 35
    Pointer, 31, 35
    SetOutputMaximum(), 31, 35
    SetOutputMinimum(), 31, 35
RGB
    reading Image, 17, 41
    writing Image, 17, 41

Series
    Reading, 36
    Writing, 36
SetConductanceParameter()
    itk::CurvatureAnisotropicDiffusionImageFilter, 184
SetDilateValue()
    itk::BinaryDilateImageFilter, 134
SetDomainSigma()
    itk::BilateralImageFilter, 203
SetErodeValue()
    itk::BinaryErodeImageFilter, 134
SetFileName()
    itk::ImageFileReader, 4, 20, 22, 24, 29, 31, 35
    itk::ImageFileWriter, 4, 20, 22, 24, 29, 31, 35
SetInsideValue()
    itk::BinaryThresholdImageFilter, 71
    itk::OtsuThresholdImageFilter, 698
SetKernel()
    itk::BinaryDilateImageFilter, 133
    itk::BinaryErodeImageFilter, 133
    itk::GrayscaleDilateImageFilter, 138
    itk::GrayscaleErodeImageFilter, 138
SetNumberOfIterations()
    itk::CurvatureAnisotropicDiffusionImageFilter, 184
    itk::CurvatureFlowImageFilter, 189
    itk::GradientAnisotropicDiffusionImageFilter, 179
    itk::MinMaxCurvatureFlowImageFilter, 197
    itk::VectorCurvatureAnisotropicDiffusionImageFilter, 212, 221
    itk::VectorGradientAnisotropicDiffusionImageFilter, 207, 216
SetOutputMaximum()
    itk::RescaleIntensityImageFilter, 91
SetOutputMinimum()
    itk::RescaleIntensityImageFilter, 91
SetOutsideValue()
    itk::BinaryThresholdImageFilter, 71
    itk::OtsuThresholdImageFilter, 698
    itk::ThresholdImageFilter, 86
SetRadius()
    itk::BinaryBallStructuringElement, 133, 138
SetRangeSigma()
    itk::BilateralImageFilter, 203
SetScale()
    itk::ShiftScaleImageFilter, 91
SetShift()
    itk::ShiftScaleImageFilter, 91
SetSigma()
    itk::GradientMagnitudeRecursiveGaussianImageFilter, 105
    itk::LaplacianRecursiveGaussianImageFilter, 123
    itk::RecursiveGaussianImageFilter, 119, 171
SetTimeStep()
    itk::CurvatureAnisotropicDiffusionImageFilter, 184
    itk::CurvatureFlowImageFilter, 189
    itk::GradientAnisotropicDiffusionImageFilter, 179
    itk::MinMaxCurvatureFlowImageFilter, 197
    itk::VectorCurvatureAnisotropicDiffusionImageFilter, 212, 221
    itk::VectorGradientAnisotropicDiffusionImageFilter, 207, 216
Statistics
    Bayesian plugin classifier, 946
    Covariance, 890
    Expectation maximization, 952
    Gaussian (normal) probability density function, 900
    Heap sort, 897
    Images, 908
    Importing ListSample to Histogram, 894
    Insert sort, 897
    Introspective sort, 897
    Joint Entropy, 924
    Joint Histogram, 924
    k-means clustering (using k-d tree), 934
    Mean, 890
    Mixture model estimation, 952
    Mutual Information, 924
    Order statistics, 897
    Quick select, 897
    Random number generation
        Normal (Gaussian) distribution, 907
    Sampling measurement vectors using radius, 895
    Sorting, 897
    Weighted covariance, 892
    Weighted mean, 892
Subsampling, 303
Supersampling, 303
Surface Extraction, 313
SystemTools, 54
    MakeDirectory, 54

Vector
    Geometrical Concept, 495
Vector images
    Reading, 26
    Writing, 26
VectorMagnitudeImageFilter
    header, 30
    Instantiation, 31
    New(), 31
    Pointer, 31
Voronoi partitions, 232
    itk::DanielssonDistanceMapImageFilter, 232

WarpImageFilter, 619
Watersheds, 736
    ImageFilter, 746
    Overview, 736
WindowedSincInterpolateImageFunction, 560