Problematic registration cases

Also see notes from the cases: https://docs.google.com/document/d/1Zj4WgKUXvm98pAU66UiamUJz6oBKFrk_AYhHu0Yc_vg/edit?ts=56fd2bed

Case377-20160321

Reference image

Initialization results

Slicer3

Slicer4

Rigid results

Slicer3

Slicer4

Afffine results

Slicer3

Slicer4

B-spline results

Slicer3

Slicer4

Slicer3 log

https://gist.github.com/fedorov/d59e60ba1a31c0107573

Slicer4 log

Command line:

slicer:0x7f96da72e1f0 --processinformationaddress 0x718a090 
--fixedVolume slicer:0x2049380#vtkMRMLScalarVolumeNode2 
--movingVolume slicer:0x2049380#vtkMRMLScalarVolumeNode1 
--samplingPercentage 0.002 --splineGridSize 3,3,3 
--outputVolume slicer:0x2049380#vtkMRMLScalarVolumeNode3 
--initializeTransformMode useCenterOfROIAlign --useRigid --useAffine --useBSpline 
--maskProcessingMode ROI --fixedBinaryVolume slicer:0x2049380#vtkMRMLLabelMapVolumeNode1 
--movingBinaryVolume slicer:0x2049380#vtkMRMLLabelMapVolumeNode2 --medianFilterSize 0,0,0 
--removeIntensityOutliers 0 --outputVolumePixelType float --backgroundFillValue 0 
--interpolationMode Linear --numberOfIterations 1500 --maximumStepLength 0.05 
--minimumStepLength 0.001 --relaxationFactor 0.5 --translationScale 1000 
--reproportionScale 1 --skewScale 1 --maxBSplineDisplacement 0 --fixedVolumeTimeIndex 0 
--movingVolumeTimeIndex 0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --costMetric MMI 
--maskInferiorCutOffFromCenter 1000 --ROIAutoDilateSize 0 --ROIAutoClosingSize 9 
--numberOfSamples 0 --failureExitCode -1 --numberOfThreads -1 --debugLevel 0 
--costFunctionConvergenceFactor 2e+13 --projectedGradientTolerance 1e-05 
--maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random

https://gist.github.com/fedorov/f52e4ce299b0b660d8b5

Slicer4 log (Christian Laptop)

Command line (rigid):

/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/BRAINSFit --fixedVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeB.nrrd --movingVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeD.nrrd --samplingPercentage 0.002 --splineGridSize 14,10,12 --outputVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeE.nrrd --initializeTransformMode useCenterOfROIAlign --useRigid --maskProcessingMode ROI --fixedBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeB.nrrd --movingBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeC.nrrd --medianFilterSize 0,0,0 --removeIntensityOutliers 0.0 --outputVolumePixelType float --backgroundFillValue 0.0 --interpolationMode Linear --numberOfIterations 1500 --maximumStepLength 0.05 --minimumStepLength 0.001 --relaxationFactor 0.5 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --maxBSplineDisplacement 0.0 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --costMetric MMI --maskInferiorCutOffFromCenter 1000.0 --ROIAutoDilateSize 0.0 --ROIAutoClosingSize 9.0 --numberOfSamples 0 --outputTransform /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLinearTransformNodeE.h5 --failureExitCode -1 --numberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 2e+13 --projectedGradientTolerance 1e-5 --maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random 

Command line (affine):

/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/BRAINSFit --fixedVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeB.nrrd --movingVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeD.nrrd --samplingPercentage 0.002 --splineGridSize 14,10,12 --outputVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeF.nrrd --initialTransform /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLinearTransformNodeE.h5 --initializeTransformMode Off --useAffine --maskProcessingMode ROI --fixedBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeB.nrrd --movingBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeC.nrrd --medianFilterSize 0,0,0 --removeIntensityOutliers 0.0 --outputVolumePixelType float --backgroundFillValue 0.0 --interpolationMode Linear --numberOfIterations 1500 --maximumStepLength 0.05 --minimumStepLength 0.001 --relaxationFactor 0.5 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --maxBSplineDisplacement 0.0 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --costMetric MMI --maskInferiorCutOffFromCenter 1000.0 --ROIAutoDilateSize 0.0 --ROIAutoClosingSize 9.0 --numberOfSamples 0 --outputTransform /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLinearTransformNodeF.h5 --failureExitCode -1 --numberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 2e+13 --projectedGradientTolerance 1e-5 --maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random 

Command line (bSpline):

/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/BRAINSFit 
--fixedVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeB.nrrd 
--movingVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeD.nrrd 
--samplingPercentage 0.002 --splineGridSize 3,3,3 --bsplineTransform /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLBSplineTransformNodeB.h5 
--outputVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLScalarVolumeNodeG.nrrd 
--initialTransform /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLinearTransformNodeF.h5 
--initializeTransformMode Off --useBSpline --maskProcessingMode ROI 
--fixedBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeB.nrrd 
--movingBinaryVolume /var/folders/68/sjc6zmyd7px1kwsrggw3lbmc0000gn/T/Slicer/JIABF_vtkMRMLLabelMapVolumeNodeC.nrrd 
--useROIBSpline --medianFilterSize 0,0,0 --removeIntensityOutliers 0.0 --outputVolumePixelType float 
--backgroundFillValue 0.0 --interpolationMode Linear --numberOfIterations 1500 --maximumStepLength 0.2 
--minimumStepLength 0.005 --relaxationFactor 0.5 --translationScale 1000.0 --reproportionScale 1.0 
--skewScale 1.0 --maxBSplineDisplacement 0.0 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 
--numberOfHistogramBins 50 --numberOfMatchPoints 10 --costMetric MMI --maskInferiorCutOffFromCenter 1000.0 
--ROIAutoDilateSize 0.0 --ROIAutoClosingSize 9.0 --numberOfSamples 0 --failureExitCode -1 
--numberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 1.00E+09 --projectedGradientTolerance 1e-5 
--maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random 

https://gist.github.com/fedorov/5d67fc29b1a537954336