Initial upload

ParameterMap_SynthRad2023_CBCT_brain.txt

@@ -0,0 +1,150 @@
+(MaximumNumberOfIterations 300  300 200 200 150)
+(NumberOfSpatialSamples 2000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+
+(ImpactModelsPath0 "/Data/Model/TS/M732_2_Layers.pt")
+(ImpactDimension0 3)
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 6 6 6)
+(ImpactLayersMask0 "01")
+(ImpactSubsetFeatures0 64)
+(ImpactPCA0 0)
+(ImpactDistance0 "L1")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/TS/M731_2_Layers.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "01")
+(ImpactSubsetFeatures1 64)
+(ImpactPCA1 0)
+(ImpactDistance1 "L1")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/TS/M731_2_Layers.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 3 3 3)
+(ImpactLayersMask2 "01")
+(ImpactSubsetFeatures2 64)
+(ImpactPCA2 0)
+(ImpactDistance2 "L1")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/TS/M730_2_Layers.pt")
+(ImpactDimension3 3)
+(ImpactNumberOfChannels3 1)
+(ImpactPatchSize3 0 0 0)
+(ImpactVoxelSize3 2 2 3)
+(ImpactLayersMask3 "01")
+(ImpactSubsetFeatures3 64)
+(ImpactPCA3 0)
+(ImpactDistance3 "L1")
+(ImpactLayersWeight3 1)
+
+(ImpactModelsPath4 "/Data/Model/TS/M730_2_Layers.pt")
+(ImpactDimension4 3)
+(ImpactNumberOfChannels4 1)
+(ImpactPatchSize4 0 0 0)
+(ImpactVoxelSize4 2 2 3)
+(ImpactLayersMask4 "01")
+(ImpactSubsetFeatures4 64)
+(ImpactPCA4 0)
+(ImpactDistance4 "L1")
+(ImpactLayersWeight4 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.65)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_CBCT_generic1.txt

@@ -0,0 +1,150 @@
+(MaximumNumberOfIterations 350 250 200 150 100)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+
+(ImpactModelsPath0 "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension0 3)
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 3 3 3)
+(ImpactLayersMask0 "01000001")
+(ImpactSubsetFeatures0 64 64)
+(ImpactPCA0 0 0)
+(ImpactDistance0 "L1" "Dice")
+(ImpactLayersWeight0 0.1 0.9)
+
+(ImpactModelsPath1 "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "01000001")
+(ImpactSubsetFeatures1 64 64)
+(ImpactPCA1 0 0)
+(ImpactDistance1 "L1" "Dice")
+(ImpactLayersWeight1 0.2 0.8)
+
+(ImpactModelsPath2 "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "01000001")
+(ImpactSubsetFeatures2 64 64)
+(ImpactPCA2 0 0)
+(ImpactDistance2 "L1" "Dice")
+(ImpactLayersWeight2 0.3 0.7)
+
+(ImpactModelsPath3 "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension3 3)
+(ImpactNumberOfChannels3 1)
+(ImpactPatchSize3 0 0 0)
+(ImpactVoxelSize3 2 2 3)
+(ImpactLayersMask3 "01000001")
+(ImpactSubsetFeatures3 64 64)
+(ImpactPCA3 0 0)
+(ImpactDistance3 "L1" "Dice")
+(ImpactLayersWeight3 0.5 0.5)
+
+(ImpactModelsPath4 "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension4 3)
+(ImpactNumberOfChannels4 1)
+(ImpactPatchSize4 0 0 0)
+(ImpactVoxelSize4 2 2 3)
+(ImpactLayersMask4 "01000001")
+(ImpactSubsetFeatures4 64 64)
+(ImpactPCA4 0 0)
+(ImpactDistance4 "L1" "Dice")
+(ImpactLayersWeight4 0.7 0.3)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_CBCT_generic2.txt

@@ -0,0 +1,149 @@
+(MaximumNumberOfIterations 400 300 300 300 300)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+
+(ImpactModelsPath0 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension0 3)
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 3 3 3)
+(ImpactLayersMask0 "01000001")
+(ImpactSubsetFeatures0 64 64)
+(ImpactPCA0 0 0)
+(ImpactDistance0 "L1" "Dice")
+(ImpactLayersWeight0 1 1)
+
+(ImpactModelsPath1 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "01000001")
+(ImpactSubsetFeatures1 64 64)
+(ImpactPCA1 0 0)
+(ImpactDistance1 "L1" "Dice")
+(ImpactLayersWeight1 1 1)
+
+(ImpactModelsPath2 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "01000001")
+(ImpactSubsetFeatures2 64 64)
+(ImpactPCA2 0 0)
+(ImpactDistance2 "L1" "Dice")
+(ImpactLayersWeight2 1 1)
+
+(ImpactModelsPath3 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension3 3)
+(ImpactNumberOfChannels3 1)
+(ImpactPatchSize3 0 0 0)
+(ImpactVoxelSize3 2 2 3)
+(ImpactLayersMask3 "01000001")
+(ImpactSubsetFeatures3 64 64)
+(ImpactPCA3 0 0)
+(ImpactDistance3 "L1" "Dice")
+(ImpactLayersWeight3 1 1)
+
+(ImpactModelsPath4 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension4 3)
+(ImpactNumberOfChannels4 1)
+(ImpactPatchSize4 0 0 0)
+(ImpactVoxelSize4 2 2 3)
+(ImpactLayersMask4 "01000001")
+(ImpactSubsetFeatures4 64 64)
+(ImpactPCA4 0 0)
+(ImpactDistance4 "L1" "Dice")
+(ImpactLayersWeight4 1 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_CBCT_pelvisV2.txt

@@ -0,0 +1,150 @@
+(MaximumNumberOfIterations 200 150 150 100 50)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension0 3 3)
+(ImpactNumberOfChannels0 1 1)
+(ImpactPatchSize0 0 0 0 0 0 0)
+(ImpactVoxelSize0 3 3 3 3 3 3)
+(ImpactLayersMask0 "1" "00000001")
+(ImpactSubsetFeatures0 32 64)
+(ImpactPCA0 0 0)
+(ImpactDistance0 "L1" "Dice")
+(ImpactLayersWeight0 0.2 0.8)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension1 3 3)
+(ImpactNumberOfChannels1 1 1)
+(ImpactPatchSize1 0 0 0 0 0 0)  
+(ImpactVoxelSize1 3 3 3 3 3 3)
+(ImpactLayersMask1 "1" "00000001")
+(ImpactSubsetFeatures1 32 64)
+(ImpactPCA1 0 0)
+(ImpactDistance1 "L1" "Dice")
+(ImpactLayersWeight1 0.3 0.7)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension2 3 3)
+(ImpactNumberOfChannels2 1 1)
+(ImpactPatchSize2 0 0 0 0 0 0)
+(ImpactVoxelSize2 3 3 3 3 3 3)
+(ImpactLayersMask2 "1"  "00000001")
+(ImpactSubsetFeatures2 32 64)
+(ImpactPCA2 0 0)
+(ImpactDistance2 "L1" "Dice")
+(ImpactLayersWeight2 0.4 0.6)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 2 2 3 2 2 3)
+(ImpactLayersMask3 "1"  "00000001")
+(ImpactSubsetFeatures3 32 64)
+(ImpactPCA3 0 0)
+(ImpactDistance3 "L1" "Dice")
+(ImpactLayersWeight3 0.5 0.5)
+
+
+(ImpactModelsPath4 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension4 3 3)
+(ImpactNumberOfChannels4 1 1)
+(ImpactPatchSize4 0 0 0 0 0 0)
+(ImpactVoxelSize4 2 2 3 2 2 3)
+(ImpactLayersMask4 "1"  "00000001")
+(ImpactSubsetFeatures4 32 64)
+(ImpactPCA4 0 0)
+(ImpactDistance4 "L1" "Dice")
+(ImpactLayersWeight4 0.5 0.5)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.5)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_MRI_Brain.txt

@@ -0,0 +1,138 @@
+(MaximumNumberOfIterations 400 300 300 300)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 4)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension0 3 )
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 6 6 6)
+(ImpactLayersMask0 "1")
+(ImpactSubsetFeatures0 32)
+(ImpactPCA0 0)
+(ImpactDistance0 "L1")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "1")
+(ImpactSubsetFeatures1 32)
+(ImpactPCA1 0)
+(ImpactDistance1 "L1")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "1")
+(ImpactSubsetFeatures2 32)
+(ImpactPCA2 0)
+(ImpactDistance2 "L1")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 1 1 3)
+(ImpactLayersMask3 "1")
+(ImpactSubsetFeatures3 32)
+(ImpactPCA3 0)
+(ImpactDistance3 "L1")
+(ImpactLayersWeight3 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 50)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_MRI_pelvis.txt

@@ -0,0 +1,138 @@
+(MaximumNumberOfIterations 500 400 300 200)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 4)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension0 3 3)
+(ImpactNumberOfChannels0 1 1)
+(ImpactPatchSize0 0 0 0 0 0 0)
+(ImpactVoxelSize0 6 6 6 6 6 6)
+(ImpactLayersMask0 "1" "00000001")
+(ImpactSubsetFeatures0 32 64)
+(ImpactPCA0 0 0)
+(ImpactDistance0 "L1" "Dice")
+(ImpactLayersWeight0 0.2 0.8)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension1 3 3)
+(ImpactNumberOfChannels1 1 1)
+(ImpactPatchSize1 0 0 0 0 0 0)  
+(ImpactVoxelSize1 3 3 3 3 3 3)
+(ImpactLayersMask1 "1" "00000001")
+(ImpactSubsetFeatures1 32 64)
+(ImpactPCA1 0 0)
+(ImpactDistance1 "L1" "Dice")
+(ImpactLayersWeight1 0.3 0.7)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension2 3 3)
+(ImpactNumberOfChannels2 1 1)
+(ImpactPatchSize2 0 0 0 0 0 0)
+(ImpactVoxelSize2 2 2 3 2 2 3)
+(ImpactLayersMask2 "1"  "00000001")
+(ImpactSubsetFeatures2 32 64)
+(ImpactPCA2 0 0)
+(ImpactDistance2 "L1" "Dice")
+(ImpactLayersWeight2 0.6 0.4)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 2 2 3 2 2 3)
+(ImpactLayersMask3 "1"  "00000001")
+(ImpactSubsetFeatures3 32 64)
+(ImpactPCA3 0 0)
+(ImpactDistance3 "L1" "Dice")
+(ImpactLayersWeight3 0.7 0.3)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2023_MRI_pelvisV3.txt

@@ -0,0 +1,150 @@
+(MaximumNumberOfIterations 500 500 400 300 200)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+
+(ImpactModelsPath0 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension0 3)
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 3 3 3)
+(ImpactLayersMask0 "00000001")
+(ImpactSubsetFeatures0 64)
+(ImpactPCA0 0)
+(ImpactDistance0 "Dice")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "00000001")
+(ImpactSubsetFeatures1 64)
+(ImpactPCA1 0)
+(ImpactDistance1 "Dice")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "00000001")
+(ImpactSubsetFeatures2 64)
+(ImpactPCA2 0)
+(ImpactDistance2 "Dice")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension3 3)
+(ImpactNumberOfChannels3 1)
+(ImpactPatchSize3 0 0 0)
+(ImpactVoxelSize3 2 2 3)
+(ImpactLayersMask3 "00000001")
+(ImpactSubsetFeatures3 64)
+(ImpactPCA3 0)
+(ImpactDistance3 "Dice")
+(ImpactLayersWeight3 1)
+
+(ImpactModelsPath4 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension4 3)
+(ImpactNumberOfChannels4 1)
+(ImpactPatchSize4 0 0 0)
+(ImpactVoxelSize4 2 2 3)
+(ImpactLayersMask4 "00000001")
+(ImpactSubsetFeatures4 64)
+(ImpactPCA4 0)
+(ImpactDistance4 "Dice")
+(ImpactLayersWeight4 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedNormalizedCorrelation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.2)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2025_MRI_HN.txt

@@ -0,0 +1,138 @@
+(MaximumNumberOfIterations 400 300 200 100)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 4)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension0 3 )
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 6 6 6)
+(ImpactLayersMask0 "1")
+(ImpactSubsetFeatures0 32)
+(ImpactPCA0 0)
+(ImpactDistance0 "L1")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "1")
+(ImpactSubsetFeatures1 32)
+(ImpactPCA1 0)
+(ImpactDistance1 "L1")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "1")
+(ImpactSubsetFeatures2 32)
+(ImpactPCA2 0)
+(ImpactDistance2 "L1")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 1 1 3)
+(ImpactLayersMask3 "1")
+(ImpactSubsetFeatures3 32)
+(ImpactPCA3 0)
+(ImpactDistance3 "L1")
+(ImpactLayersWeight3 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 50)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2025_MRI_TH.txt

@@ -0,0 +1,138 @@
+(MaximumNumberOfIterations 400 300 200 100)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 4)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension0 3 3)
+(ImpactNumberOfChannels0 1 1)
+(ImpactPatchSize0 0 0 0 0 0 0)
+(ImpactVoxelSize0 6 6 6 6 6 6)
+(ImpactLayersMask0 "1" "00000001")
+(ImpactSubsetFeatures0 32 64)
+(ImpactPCA0 0 0)
+(ImpactDistance0 "L1" "Dice")
+(ImpactLayersWeight0 0.2 0.8)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension1 3 3)
+(ImpactNumberOfChannels1 1 1)
+(ImpactPatchSize1 0 0 0 0 0 0)  
+(ImpactVoxelSize1 3 3 3 3 3 3)
+(ImpactLayersMask1 "1" "00000001")
+(ImpactSubsetFeatures1 32 64)
+(ImpactPCA1 0 0)
+(ImpactDistance1 "L1" "Dice")
+(ImpactLayersWeight1 0.3 0.7)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension2 3 3)
+(ImpactNumberOfChannels2 1 1)
+(ImpactPatchSize2 0 0 0 0 0 0)
+(ImpactVoxelSize2 2 2 3 2 2 3)
+(ImpactLayersMask2 "1"  "00000001")
+(ImpactSubsetFeatures2 32 64)
+(ImpactPCA2 0 0)
+(ImpactDistance2 "L1" "Dice")
+(ImpactLayersWeight2 0.7 0.3)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt" "/Data/Model/TS/MRSegmentator_8_Layers.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 2 2 3 2 2 3)
+(ImpactLayersMask3 "1"  "00000001")
+(ImpactSubsetFeatures3 32 64)
+(ImpactPCA3 0 0)
+(ImpactDistance3 "L1" "Dice")
+(ImpactLayersWeight3 0.7 0.3)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2025_MRI_THA.txt

@@ -0,0 +1,138 @@
+(MaximumNumberOfIterations 400 300 200 100)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 4)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+(ImpactModelsPath0 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension0 3 )
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 6 6 6)
+(ImpactLayersMask0 "1")
+(ImpactSubsetFeatures0 32)
+(ImpactPCA0 0)
+(ImpactDistance0 "L1")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "1")
+(ImpactSubsetFeatures1 32)
+(ImpactPCA1 0)
+(ImpactDistance1 "L1")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "1")
+(ImpactSubsetFeatures2 32)
+(ImpactPCA2 0)
+(ImpactDistance2 "L1")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/MIND/R1D2.pt")
+(ImpactDimension3 3 3)
+(ImpactNumberOfChannels3 1 1)
+(ImpactPatchSize3 0 0 0 0 0 0)
+(ImpactVoxelSize3 1 1 3)
+(ImpactLayersMask3 "1")
+(ImpactSubsetFeatures3 32)
+(ImpactPCA3 0)
+(ImpactDistance3 "L1")
+(ImpactLayersWeight3 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.3)
+(Metric2Weight 50)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

ParameterMap_SynthRad2025_MRI_pelvis.txt

@@ -0,0 +1,150 @@
+(MaximumNumberOfIterations 500 500 400 300 200)
+(NumberOfSpatialSamples 3000)
+(Transform "RecursiveBSplineTransform")
+(NumberOfResolutions 5)
+(FinalGridSpacingInPhysicalUnits 10)
+(FixedImagePyramid "FixedGenericImagePyramid")
+(MovingImagePyramid "MovingGenericImagePyramid")
+(FixedImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+(MovingImagePyramidRescaleSchedule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1)
+// (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
+
+
+
+(ImpactModelsPath0 "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension0 3)
+(ImpactNumberOfChannels0 1)
+(ImpactPatchSize0 0 0 0)
+(ImpactVoxelSize0 3 3 3)
+(ImpactLayersMask0 "00000001")
+(ImpactSubsetFeatures0 64)
+(ImpactPCA0 0)
+(ImpactDistance0 "Dice")
+(ImpactLayersWeight0 1)
+
+(ImpactModelsPath1 "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension1 3)
+(ImpactNumberOfChannels1 1)
+(ImpactPatchSize1 0 0 0)  
+(ImpactVoxelSize1 3 3 3)
+(ImpactLayersMask1 "00000001")
+(ImpactSubsetFeatures1 64)
+(ImpactPCA1 0)
+(ImpactDistance1 "Dice")
+(ImpactLayersWeight1 1)
+
+(ImpactModelsPath2 "/Data/Model/TS/M731_8_Layers.pt")
+(ImpactDimension2 3)
+(ImpactNumberOfChannels2 1)
+(ImpactPatchSize2 0 0 0)
+(ImpactVoxelSize2 2 2 3)
+(ImpactLayersMask2 "00000001")
+(ImpactSubsetFeatures2 64)
+(ImpactPCA2 0)
+(ImpactDistance2 "Dice")
+(ImpactLayersWeight2 1)
+
+(ImpactModelsPath3 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension3 3)
+(ImpactNumberOfChannels3 1)
+(ImpactPatchSize3 0 0 0)
+(ImpactVoxelSize3 2 2 3)
+(ImpactLayersMask3 "00000001")
+(ImpactSubsetFeatures3 64)
+(ImpactPCA3 0)
+(ImpactDistance3 "Dice")
+(ImpactLayersWeight3 1)
+
+(ImpactModelsPath4 "/Data/Model/TS/M850_8_Layers.pt")
+(ImpactDimension4 3)
+(ImpactNumberOfChannels4 1)
+(ImpactPatchSize4 0 0 0)
+(ImpactVoxelSize4 2 2 3)
+(ImpactLayersMask4 "00000001")
+(ImpactSubsetFeatures4 64)
+(ImpactPCA4 0)
+(ImpactDistance4 "Dice")
+(ImpactLayersWeight4 1)
+
+
+(ImpactUseMixedPrecision "true")
+(ImpactFeaturesMapUpdateInterval -1)
+(ImpactWriteFeatureMaps "false")
+(ImpactMode "Static")
+(ImpactGPU 0)
+
+
+(Metric "Impact" "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
+(Metric0Weight 1)
+(Metric1Weight 0.7)
+(Metric2Weight 10)
+
+// imageTypes
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// components
+(Registration "MultiMetricMultiResolutionRegistration")
+(BSplineTransformSplineOrder 3)
+(UseCyclicTransform "false")
+
+// transform
+(AutomaticTransformInitialization "false")
+(AutomaticTransformInitializationMethod "GeometricalCenter")
+(AutomaticScalesEstimation "true")
+(HowToCombineTransforms "Compose")
+
+
+// optimizer
+(Optimizer "AdaptiveStochasticGradientDescent")
+(MaximumNumberOfSamplingAttempts 8)
+(UseAdaptiveStepSizes "true")
+(UseMultiThreadingForMetrics "true")
+(ASGDParameterEstimationMethod "DisplacementDistribution")
+//(MaximumStepLength 0.6602)
+(SigmoidInitialTime 0.0)
+(NoiseCompensation "true")
+(NumberOfSamplesForExactGradient 4096)
+
+// automatic
+(AutomaticParameterEstimation "true")
+//(SP_alpha 1)
+//(SP_A 20.0)
+//(SP a 400)
+//(SigmoidMax 1.0)
+//(SigmoidMin -0.8)
+//(SigmoidScale 0.00000001)
+//(NumberOfGradientMeasurements 10)
+//(NumberOfJacobianMeasurements 1000)
+
+(FixedKernelBSplineOrder 3)
+(MovingKernelBSplineOrder 3)
+(CheckNumberOfSamples "true")
+(UseRelativeWeights "false")
+
+
+// several
+(WriteTransformParametersEachIteration "false")
+(WriteTransformParametersEachResolution "false")
+(ShowExactMetricValue "false")
+(ErodeFixedMask "false")
+(ErodeMovingMask "false")
+(UseBinaryFormatForTransformationParameters "false")
+
+// imageSampler
+(Interpolator "BSplineInterpolator")
+(ImageSampler "RandomCoordinate")
+(NewSamplesEveryIteration "true")
+(UseRandomSampleRegion "false")
+
+
+// interpolator and resampler
+(ResampleInterpolator "FinalBSplineInterpolator")
+(FinalBSplineInterpolationOrder 3)
+(BSplineInterpolationOrder 3)
+(Resampler "DefaultResampler")
+(WriteIterationInfo "false")
+(WriteResultImage "false")
+(DefaultPixelValue 0)
+(ResultImageFormat "nii.gz")

Parameters_BSpline.txt

@@ -0,0 +1,159 @@
+// Example parameter file for B-spline registration
+// C-style comments: //
+
+// The internal pixel type, used for internal computations
+// Leave to float in general. 
+// NB: this is not the type of the input images! The pixel 
+// type of the input images is automatically read from the 
+// images themselves.
+// This setting can be changed to "short" to save some memory
+// in case of very large 3D images.
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+
+// **************** Main Components **************************
+
+// The following components should usually be left as they are:
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+
+// These may be changed to Fixed/MovingSmoothingImagePyramid.
+// See the manual.
+(FixedImagePyramid "FixedRecursiveImagePyramid")
+(MovingImagePyramid "MovingRecursiveImagePyramid")
+
+// The following components are most important:
+// The optimizer AdaptiveStochasticGradientDescent (ASGD) works
+// quite ok in general. The Transform and Metric are important
+// and need to be chosen careful for each application. See manual.
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "BSplineTransform")
+(Metric "AdvancedMattesMutualInformation")
+
+// ***************** Transformation **************************
+
+// The control point spacing of the bspline transformation in 
+// the finest resolution level. Can be specified for each 
+// dimension differently. Unit: mm.
+// The lower this value, the more flexible the deformation.
+// Low values may improve the accuracy, but may also cause
+// unrealistic deformations. This is a very important setting!
+// We recommend tuning it for every specific application. It is
+// difficult to come up with a good 'default' value.
+(FinalGridSpacingInPhysicalUnits 16)
+
+// Alternatively, the grid spacing can be specified in voxel units.
+// To do that, uncomment the following line and comment/remove
+// the FinalGridSpacingInPhysicalUnits definition.
+//(FinalGridSpacingInVoxels 16)
+
+// By default the grid spacing is halved after every resolution,
+// such that the final grid spacing is obtained in the last 
+// resolution level. You can also specify your own schedule,
+// if you uncomment the following line:
+//(GridSpacingSchedule 4.0 4.0 2.0 1.0)
+// This setting can also be supplied per dimension.
+
+// Whether transforms are combined by composition or by addition.
+// In generally, Compose is the best option in most cases.
+// It does not influence the results very much.
+(HowToCombineTransforms "Compose")
+
+//Save composite ITK transform
+(ITKTransformOutputFileNameExtension "h5")
+(WriteITKCompositeTransform "true")
+
+// ******************* Similarity measure *********************
+
+// Number of grey level bins in each resolution level,
+// for the mutual information. 16 or 32 usually works fine.
+// You could also employ a hierarchical strategy:
+//(NumberOfHistogramBins 16 32 64)
+(NumberOfHistogramBins 32)
+
+// If you use a mask, this option is important. 
+// If the mask serves as region of interest, set it to false.
+// If the mask indicates which pixels are valid, then set it to true.
+// If you do not use a mask, the option doesn't matter.
+(ErodeMask "false")
+
+// ******************** Multiresolution **********************
+
+// The number of resolutions. 1 Is only enough if the expected
+// deformations are small. 3 or 4 mostly works fine. For large
+// images and large deformations, 5 or 6 may even be useful.
+(NumberOfResolutions 4)
+
+// The downsampling/blurring factors for the image pyramids.
+// By default, the images are downsampled by a factor of 2
+// compared to the next resolution.
+// So, in 2D, with 4 resolutions, the following schedule is used:
+//(ImagePyramidSchedule 8 8  4 4  2 2  1 1 )
+// And in 3D:
+//(ImagePyramidSchedule 8 8 8  4 4 4  2 2 2  1 1 1 )
+// You can specify any schedule, for example:
+//(ImagePyramidSchedule 4 4  4 3  2 1  1 1 )
+// Make sure that the number of elements equals the number
+// of resolutions times the image dimension.
+
+// ******************* Optimizer ****************************
+
+// Maximum number of iterations in each resolution level:
+// 200-2000 works usually fine for nonrigid registration.
+// The more, the better, but the longer computation time.
+// This is an important parameter!
+(MaximumNumberOfIterations 500)
+
+// The step size of the optimizer, in mm. By default the voxel size is used.
+// which usually works well. In case of unusual high-resolution images
+// (eg histology) it is necessary to increase this value a bit, to the size
+// of the "smallest visible structure" in the image:
+//(MaximumStepLength 1.0)
+
+// **************** Image sampling **********************
+
+// Number of spatial samples used to compute the mutual
+// information (and its derivative) in each iteration.
+// With an AdaptiveStochasticGradientDescent optimizer,
+// in combination with the two options below, around 2000
+// samples may already suffice.
+(NumberOfSpatialSamples 2048)
+
+// Refresh these spatial samples in every iteration, and select
+// them randomly. See the manual for information on other sampling
+// strategies.
+(NewSamplesEveryIteration "true")
+(ImageSampler "Random")
+
+// ************* Interpolation and Resampling ****************
+
+// Order of B-Spline interpolation used during registration/optimisation.
+// It may improve accuracy if you set this to 3. Never use 0.
+// An order of 1 gives linear interpolation. This is in most 
+// applications a good choice.
+(BSplineInterpolationOrder 1)
+
+// Order of B-Spline interpolation used for applying the final
+// deformation.
+// 3 gives good accuracy; recommended in most cases.
+// 1 gives worse accuracy (linear interpolation)
+// 0 gives worst accuracy, but is appropriate for binary images
+// (masks, segmentations); equivalent to nearest neighbor interpolation.
+(FinalBSplineInterpolationOrder 3)
+
+//Default pixel value for pixels that come from outside the picture:
+(DefaultPixelValue 0)
+
+// Choose whether to generate the deformed moving image.
+// You can save some time by setting this to false, if you are
+// not interested in the final deformed moving image, but only
+// want to analyze the deformation field for example.
+(WriteResultImage "true")
+
+// The pixel type and format of the resulting deformed moving image
+(ResultImagePixelType "short")
+(ResultImageFormat "mhd")
+
+

Parameters_Rigid.txt

@@ -0,0 +1,145 @@
+// Example parameter file for rotation registration
+// C-style comments: //
+
+// The internal pixel type, used for internal computations
+// Leave to float in general. 
+// NB: this is not the type of the input images! The pixel 
+// type of the input images is automatically read from the 
+// images themselves.
+// This setting can be changed to "short" to save some memory
+// in case of very large 3D images.
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+
+// **************** Main Components **************************
+
+// The following components should usually be left as they are:
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+
+// These may be changed to Fixed/MovingSmoothingImagePyramid.
+// See the manual.
+(FixedImagePyramid "FixedRecursiveImagePyramid")
+(MovingImagePyramid "MovingRecursiveImagePyramid")
+
+// The following components are most important:
+// The optimizer AdaptiveStochasticGradientDescent (ASGD) works
+// quite ok in general. The Transform and Metric are important
+// and need to be chosen careful for each application. See manual.
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "EulerTransform")
+(Metric "AdvancedMattesMutualInformation")
+
+// ***************** Transformation **************************
+
+// Scales the rotations compared to the translations, to make
+// sure they are in the same range. In general, it's best to  
+// use automatic scales estimation:
+(AutomaticScalesEstimation "true")
+
+// Automatically guess an initial translation by aligning the
+// geometric centers of the fixed and moving.
+(AutomaticTransformInitialization "true")
+
+// Whether transforms are combined by composition or by addition.
+// In generally, Compose is the best option in most cases.
+// It does not influence the results very much.
+(HowToCombineTransforms "Compose")
+
+//Save composite ITK transform
+(ITKTransformOutputFileNameExtension "h5")
+(WriteITKCompositeTransform "true")
+
+// ******************* Similarity measure *********************
+
+// Number of grey level bins in each resolution level,
+// for the mutual information. 16 or 32 usually works fine.
+// You could also employ a hierarchical strategy:
+//(NumberOfHistogramBins 16 32 64)
+(NumberOfHistogramBins 32)
+
+// If you use a mask, this option is important. 
+// If the mask serves as region of interest, set it to false.
+// If the mask indicates which pixels are valid, then set it to true.
+// If you do not use a mask, the option doesn't matter.
+(ErodeMask "false")
+
+// ******************** Multiresolution **********************
+
+// The number of resolutions. 1 Is only enough if the expected
+// deformations are small. 3 or 4 mostly works fine. For large
+// images and large deformations, 5 or 6 may even be useful.
+(NumberOfResolutions 4)
+
+// The downsampling/blurring factors for the image pyramids.
+// By default, the images are downsampled by a factor of 2
+// compared to the next resolution.
+// So, in 2D, with 4 resolutions, the following schedule is used:
+//(ImagePyramidSchedule 8 8  4 4  2 2  1 1 )
+// And in 3D:
+//(ImagePyramidSchedule 8 8 8  4 4 4  2 2 2  1 1 1 )
+// You can specify any schedule, for example:
+//(ImagePyramidSchedule 4 4  4 3  2 1  1 1 )
+// Make sure that the number of elements equals the number
+// of resolutions times the image dimension.
+
+// ******************* Optimizer ****************************
+
+// Maximum number of iterations in each resolution level:
+// 200-500 works usually fine for rigid registration.
+// For more robustness, you may increase this to 1000-2000.
+(MaximumNumberOfIterations 250)
+
+// The step size of the optimizer, in mm. By default the voxel size is used.
+// which usually works well. In case of unusual high-resolution images
+// (eg histology) it is necessary to increase this value a bit, to the size
+// of the "smallest visible structure" in the image:
+//(MaximumStepLength 1.0)
+
+// **************** Image sampling **********************
+
+// Number of spatial samples used to compute the mutual
+// information (and its derivative) in each iteration.
+// With an AdaptiveStochasticGradientDescent optimizer,
+// in combination with the two options below, around 2000
+// samples may already suffice.
+(NumberOfSpatialSamples 2048)
+
+// Refresh these spatial samples in every iteration, and select
+// them randomly. See the manual for information on other sampling
+// strategies.
+(NewSamplesEveryIteration "true")
+(ImageSampler "Random")
+
+// ************* Interpolation and Resampling ****************
+
+// Order of B-Spline interpolation used during registration/optimisation.
+// It may improve accuracy if you set this to 3. Never use 0.
+// An order of 1 gives linear interpolation. This is in most 
+// applications a good choice.
+(BSplineInterpolationOrder 1)
+
+// Order of B-Spline interpolation used for applying the final
+// deformation.
+// 3 gives good accuracy; recommended in most cases.
+// 1 gives worse accuracy (linear interpolation)
+// 0 gives worst accuracy, but is appropriate for binary images
+// (masks, segmentations); equivalent to nearest neighbor interpolation.
+(FinalBSplineInterpolationOrder 3)
+
+//Default pixel value for pixels that come from outside the picture:
+(DefaultPixelValue 0)
+
+// Choose whether to generate the deformed moving image.
+// You can save some time by setting this to false, if you are
+// only interested in the final (nonrigidly) deformed moving image
+// for example.
+(WriteResultImage "true")
+
+// The pixel type and format of the resulting deformed moving image
+(ResultImagePixelType "short")
+(ResultImageFormat "mhd")
+
+

Preprocess.py

@@ -0,0 +1,26 @@
+import SimpleITK as sitk
+import numpy as np
+
+def standardize_MRI(image: sitk.Image) -> sitk.Image:    
+    data = sitk.GetArrayFromImage(image)
+    data = (data-data.mean())/data.std()
+    result = sitk.GetImageFromArray(data)
+    result.CopyInformation(image)
+    return result
+
+def clip_and_standardize_CT(image: sitk.Image) -> sitk.Image:    
+    data = sitk.GetArrayFromImage(image)
+    data[data < -1024] = -1024
+    data[data > 276.0] = 276
+    data = (data-(-370.00039267657144))/436.5998675471528
+    result = sitk.GetImageFromArray(data)
+    result.CopyInformation(image)
+    return result
+
+def standardize_ImageNet(image: sitk.Image) -> sitk.Image:
+    data = sitk.GetArrayFromImage(image)
+    data = (data-np.min(data))/(np.max(data)-np.min(data))
+    data = (data-0.485)/0.229
+    result = sitk.GetImageFromArray(data)
+    result.CopyInformation(image)
+    return result

PresetDatabase.json

@@ -0,0 +1,33 @@
+{
+  "presets": [
+    {
+        "GENERIC_MI": {
+            "display_name": "Generic",
+            "parameter_maps":  [
+                "Parameters_Rigid.txt",
+                "Parameters_BSpline.txt"
+            ],
+            "models": [],
+            "preprocess_function": "",
+            "iterations": 3000,
+            "short_description": "Generic image registration elastix.",
+            "description": "blablabla"
+        }
+    },
+    {
+        "IMPACT_M850_bspline": {
+            "display_name": "M850 bspline",
+            "parameter_maps": [
+                "ParameterMap_SynthRad2023_MRI_pelvisV3.txt"
+            ],
+            "models": [
+                "TS/M850_8_Layers.pt"
+            ],
+            "preprocess_function": "Preprocess:standardize_MRI",
+            "iterations": 1900,
+            "short_description": "Synthrad 2023.",
+            "description": "blablabla1"
+        }
+    }
+  ]
+}