Cleanup repository by removing unnecessary files

ParameterMap_Mind.txt

@@ -1,132 +0,0 @@
-(MaximumNumberOfIterations 300 300 300 300)
-(NumberOfSpatialSamples 2048)
-(Transform "RecursiveBSplineTransform")
-(NumberOfResolutions 4)
-(FinalGridSpacingInPhysicalUnits 16)
-(FixedImagePyramid "FixedRecursiveImagePyramid")
-(MovingImagePyramid "MovingRecursiveImagePyramid")
-
-(ImpactModelsPath0 "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 "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 "MIND/R1D2.pt")
-(ImpactDimension2 3)
-(ImpactNumberOfChannels2 1)
-(ImpactPatchSize2 0 0 0)
-(ImpactVoxelSize2 1.5 1.5 1.5)
-(ImpactLayersMask2 "1")
-(ImpactSubsetFeatures2 32)
-(ImpactPCA2 0)
-(ImpactDistance2 "L1")
-(ImpactLayersWeight2 1)
-
-(ImpactModelsPath3 "MIND/R1D2.pt")
-(ImpactDimension3 3)
-(ImpactNumberOfChannels3 1)
-(ImpactPatchSize3 0 0 0)
-(ImpactVoxelSize3 1 1 1)
-(ImpactLayersMask3 "1")
-(ImpactSubsetFeatures3 32)
-(ImpactPCA3 0)
-(ImpactDistance3 "L1")
-(ImpactLayersWeight3 1)
-
-(ImpactUseMixedPrecision "true")
-(ImpactFeaturesMapUpdateInterval -1)
-(ImpactWriteFeatureMaps "./Features/")
-(ImpactMode "Static")
-(ImpactGPU 0)
-
-(Metric "Impact")
-(Metric0Weight 1)
-
-// 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 -1024)
-(ResultImageFormat "mha")
-
-(ITKTransformOutputFileNameExtension "itk.txt")
-(WriteITKCompositeTransform "true")

ParameterMap_Recommended.txt

@@ -1,134 +0,0 @@
-// IMPACT metric
-(Metric "Impact")
-(Metric0Weight 1)
-
-(ImpactModelsPath0 "TS/M730_2_Layers.pt")
-(ImpactDimension0 3)
-(ImpactNumberOfChannels0 1)
-(ImpactPatchSize0 11 11 11)
-(ImpactVoxelSize0 6 6 6)
-(ImpactLayersMask0 "01")
-(ImpactPCA0 0)
-(ImpactSubsetFeatures0 64)
-(ImpactDistance0 "L2")
-(ImpactLayersWeight0 1)
-
-(ImpactModelsPath1 "TS/M730_2_Layers.pt")
-(ImpactDimension1 3)
-(ImpactNumberOfChannels1 1)
-(ImpactPatchSize1 11 11 11)
-(ImpactVoxelSize1 3 3 3)
-(ImpactLayersMask1 "01")
-(ImpactPCA1 0)
-(ImpactSubsetFeatures1 64)
-(ImpactDistance1 "L2")
-(ImpactLayersWeight1 1)
-
-(ImpactModelsPath2 "TS/M730_2_Layers.pt")
-(ImpactDimension2 3)
-(ImpactNumberOfChannels2 1)
-(ImpactPatchSize2 11 11 11)
-(ImpactVoxelSize2 1.5 1.5 1.5)
-(ImpactLayersMask2 "01")
-(ImpactPCA2 0)
-(ImpactSubsetFeatures2 64)
-(ImpactDistance2 "L2")
-(ImpactLayersWeight2 1)
-
-(ImpactModelsPath3 "TS/M730_2_Layers.pt")
-(ImpactDimension3 3)
-(ImpactNumberOfChannels3 1)
-(ImpactPatchSize3 11 11 11)
-(ImpactVoxelSize3 1 1 1)
-(ImpactLayersMask3 "01")
-(ImpactPCA3 0)
-(ImpactSubsetFeatures3 64)
-(ImpactDistance3 "L2")
-(ImpactLayersWeight3 1)
-
-(ImpactMode "Jacobian")
-(ImpactGPU 0)
-(ImpactFeaturesMapUpdateInterval -1)
-(ImpactWriteFeatureMaps "false")
-
-
-(MaximumNumberOfIterations 500)
-(NumberOfSpatialSamples 2000)
-(Transform "RecursiveBSplineTransform")
-(NumberOfResolutions 4)
-(FinalGridSpacingInPhysicalUnits 10)
-(FixedImagePyramid "FixedSmoothingImagePyramid")
-(MovingImagePyramid "MovingSmoothingImagePyramid")
-(GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
-
-// 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 -1024)
-(ResultImageFormat "mha")
-
-(ITKTransformOutputFileNameExtension "itk.txt")
-(WriteITKCompositeTransform "true")

ParameterMap_SynthRad2023_CBCT_brain.txt

@@ -1,150 +0,0 @@
-(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

@@ -1,150 +0,0 @@
-(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

@@ -1,149 +0,0 @@
-(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

@@ -1,150 +0,0 @@
-(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

@@ -1,138 +0,0 @@
-(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

@@ -1,138 +0,0 @@
-(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

@@ -1,154 +0,0 @@
-(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 "TS/M730_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 "TS/M730_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 "TS/M730_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 "TS/M730_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 "TS/M730_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 "mha")
-
-
-(ITKTransformOutputFileNameExtension "itk.txt")
-(WriteITKCompositeTransform "true")

ParameterMap_SynthRad2025_MRI_TH.txt

@@ -1,138 +0,0 @@
-(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

@@ -1,138 +0,0 @@
-(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

@@ -1,150 +0,0 @@
-(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")

Preprocess.py

@@ -1,26 +0,0 @@
-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