Update ParameterMap_Recommended.txt

Update ParameterMap_Recommended.txt

Add mind

Update PresetDatabase.json

Add mind

Add mind

Add mind

Update ParameterMap_Mind.txt

Update PresetDatabase.json

Add mind

Add mind

Add mind

Add mind

Update ImpactReg/Uncertainty.yml

Create UncertaintyDVF

Add uncertainty

Add uncertainty

Add uncertainty

Add uncertainty

Add uncertainty

ImpactReg/Uncertainty.yml

@@ -12,9 +12,10 @@ Evaluator:
         groups_dest:
           Uncertainty:
             transforms: 
+              UncertaintyDVF:DVFToNorm: {}
               Variance: {}
               Save:
-                dataset: ./Evaluations/ImpactReg/Output:mha
+                dataset: ./Uncertainties/ImpactReg/Output:mha
                 group: None
     subset: None
     dataset_filenames:

ImpactReg/UncertaintyDVF.py

@@ -0,0 +1,15 @@
+from konfai.data.transform import Transform
+from konfai.utils.dataset import Attribute
+import torch
+
+class DVFToNorm(Transform):
+
+    def __init__(self) -> None:
+        super().__init__()
+
+    def __call__(self, name: str, tensors: torch.Tensor, cache_attribute: Attribute) -> torch.Tensor:
+        cache_attribute["Origin"] = cache_attribute.pop_np_array("Origin")[:tensors.dim()-2]
+        cache_attribute["Spacing"] = cache_attribute.pop_np_array("Spacing")[:tensors.dim()-2]
+        cache_attribute.pop("Direction")
+        cache_attribute["Direction"] = torch.eye(tensors.dim()-2).flatten()
+        return torch.linalg.norm(tensors, dim=-1)

ParameterMap_SynthRad2025_MRI_HN.txt → ParameterMap_Mind.txt

@@ -1,138 +1,132 @@
-(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")
+(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

@@ -2,7 +2,7 @@
 (Metric "Impact")
 (Metric0Weight 1)
 
-(ImpactModelsPath0 "/Models/TS/M730_2_Layers.pt")
+(ImpactModelsPath0 "TS/M730_2_Layers.pt")
 (ImpactDimension0 3)
 (ImpactNumberOfChannels0 1)
 (ImpactPatchSize0 11 11 11)
@@ -13,7 +13,7 @@
 (ImpactDistance0 "L2")
 (ImpactLayersWeight0 1)
 
-(ImpactModelsPath1 "/Models/TS/M258_2_Layers.pt")
+(ImpactModelsPath1 "TS/M730_2_Layers.pt")
 (ImpactDimension1 3)
 (ImpactNumberOfChannels1 1)
 (ImpactPatchSize1 11 11 11)
@@ -24,7 +24,7 @@
 (ImpactDistance1 "L2")
 (ImpactLayersWeight1 1)
 
-(ImpactModelsPath2 "/Models/TS/M258_2_Layers.pt")
+(ImpactModelsPath2 "TS/M730_2_Layers.pt")
 (ImpactDimension2 3)
 (ImpactNumberOfChannels2 1)
 (ImpactPatchSize2 11 11 11)
@@ -35,7 +35,7 @@
 (ImpactDistance2 "L2")
 (ImpactLayersWeight2 1)
 
-(ImpactModelsPath3 "/Models/TS/M258_2_Layers.pt")
+(ImpactModelsPath3 "TS/M730_2_Layers.pt")
 (ImpactDimension3 3)
 (ImpactNumberOfChannels3 1)
 (ImpactPatchSize3 11 11 11)
@@ -56,7 +56,7 @@
 (NumberOfSpatialSamples 2000)
 (Transform "RecursiveBSplineTransform")
 (NumberOfResolutions 4)
-(FinalGridSpacingInPhysicalUnits 8)
+(FinalGridSpacingInPhysicalUnits 10)
 (FixedImagePyramid "FixedSmoothingImagePyramid")
 (MovingImagePyramid "MovingSmoothingImagePyramid")
 (GridSpacingSchedule 10.000000 5.000000 2.000000 1.000000)
@@ -130,4 +130,5 @@
 (DefaultPixelValue -1024)
 (ResultImageFormat "mha")
 
-(ITKTransformOutputFileNameExtension "itk.txt")
+(ITKTransformOutputFileNameExtension "itk.txt")
+(WriteITKCompositeTransform "true")

PresetDatabase.json

@@ -24,7 +24,7 @@
       "description": "This preset performs rigid alignment using an Euler transform optimized with Adaptive Stochastic Gradient Descent. It uses a 4-level multi-resolution strategy and Mattes mutual information as similarity metric. Initial alignment based on image centers are enabled to ensure robust convergence for multimodal images."
     },
     {
-      "display_name": "IMPACT BSpline M730",
+      "display_name": "IMPACT BSpline jacobian M730",
       "parameter_maps": [
           "ParameterMap_Recommended.txt"
       ],
@@ -34,7 +34,21 @@
       "preprocess_function": "Preprocess:standardize_MRI",
       "iterations": 1900,
       "short_description": "IMPACT-based multimodal BSpline registration with deep semantic features (M730)",
-      "description": "A deformable BSpline registration using the IMPACT metric to align semantic features extracted from pretrained models (MIND + M730). The method uses 4 resolution levels."  
+      "description": "A deformable BSpline registration using the IMPACT metric to align semantic features extracted from pretrained models (M730). The method uses 4 resolution levels."  
+    },
+    {
+      "display_name": "IMPACT MIND",
+      "parameter_maps": [
+          "ParameterMap_Mind.txt"
+      ],
+      "models": [
+          "VBoussot/impact-torchscript-models:MIND/R1D2.pt"
+      ],
+      "preprocess_function": "Preprocess:standardize_MRI",
+      "iterations": 900,
+      "short_description": "IMPACT-based multimodal BSpline registration with MIND",
+      "description": "A deformable BSpline registration using the IMPACT metric to align semantic features extracted from pretrained models MIND. The method uses 4 resolution levels."  
     }
+
   ]
 }