good morning, I’m trying the alpaca tutorial from this link: "Tutorials/MALPACA/K-means_templates_selection.md at main · chz31/Tutorials · GitHub "
unfortunately I can’t get past the second step, I attach screenshot to show the settings:
I’ve tried with two different pc’s with two different slicer versions:
Macbook M1 (2020) - Slicer ver. 5.7.0
ROG Zephyrus G14 - Slicer ver. 5.6.1
both generate a series of errors that I’m struggling to interpret, as I don’t have adequate knowledge of Phyton.
It seems strange to me that the errors are generated by the dataset entered for the tutorial.
I attach the log files for both:
Mac →
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.568655630649662
Voxel Size is 0.499821448191199
Scaling factor is 0.997153434640227
movingMeshPoints.shape (5021, 3)
movingMeshPointNormals.shape (5021, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2093 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.16982989736096482
Best Fitness without Scaling 1.0 RMSE is 0.16982989736096482
RANSAC Duraction 28.829017877578735
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.16982989736096482
Refinement took 13 iterations
After Inlier = 1.0 RMSE = 0.18650660487674556
949
87529
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.31930086628061
Voxel Size is 0.499821448191199
Scaling factor is 1.0062548739834791
movingMeshPoints.shape (5182, 3)
movingMeshPointNormals.shape (5182, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2145 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.1902918489735167
Best Fitness without Scaling 1.0 RMSE is 0.1902918489735167
RANSAC Duraction 28.968416929244995
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.1902918489735167
Refinement took 29 iterations
After Inlier = 1.0 RMSE = 0.18982818128750228
949
88274
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 26.10924972657576
Voxel Size is 0.499821448191199
Scaling factor is 1.0528904483430859
movingMeshPoints.shape (5036, 3)
movingMeshPointNormals.shape (5036, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2045 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.21646823614800612
Best Fitness without Scaling 1.0 RMSE is 0.21646823614800612
RANSAC Duraction 28.901240825653076
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.21646823614800612
Refinement took 16 iterations
After Inlier = 1.0 RMSE = 0.20428705018420934
949
77369
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 24.775053388285006
Voxel Size is 0.499821448191199
Scaling factor is 1.1095911366840807
movingMeshPoints.shape (4852, 3)
movingMeshPointNormals.shape (4852, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2008 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.23794131463500012
Best Fitness without Scaling 1.0 RMSE is 0.23794131463500012
RANSAC Duraction 29.535005807876587
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.23794131463500012
Refinement took 15 iterations
After Inlier = 1.0 RMSE = 0.21661549368439323
949
67249
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 25.38223905335343
Voxel Size is 0.499821448191199
Scaling factor is 1.0830478584939502
movingMeshPoints.shape (5281, 3)
movingMeshPointNormals.shape (5281, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2128 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.2990313731952503
Best Fitness without Scaling 1.0 RMSE is 0.2990313731952503
RANSAC Duraction 30.21252417564392
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9897746638894149 RMSE = 0.2937590511021508
Refinement took 18 iterations
After Inlier = 0.9992425676955122 RMSE = 0.29918747735529544
949
73873
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 28.374627250030027
Voxel Size is 0.499821448191199
Scaling factor is 0.9688296310742497
movingMeshPoints.shape (5012, 3)
movingMeshPointNormals.shape (5012, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2070 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.19843935184564565
Best Fitness without Scaling 1.0 RMSE is 0.19843935184564565
RANSAC Duraction 30.628879070281982
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.19843935184564565
Refinement took 14 iterations
After Inlier = 1.0 RMSE = 0.2047550117656061
949
94689
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.801588154001653
Voxel Size is 0.499821448191199
Scaling factor is 0.9887988951652431
movingMeshPoints.shape (4844, 3)
movingMeshPointNormals.shape (4844, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2065 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.16601349812887392
Best Fitness without Scaling 1.0 RMSE is 0.16601349812887392
RANSAC Duraction 30.84484887123108
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.16601349812887392
Refinement took 11 iterations
After Inlier = 1.0 RMSE = 0.1833367014098634
949
89572
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 25.937013625507507
Voxel Size is 0.499821448191199
Scaling factor is 1.0598822226580855
movingMeshPoints.shape (5008, 3)
movingMeshPointNormals.shape (5008, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2063 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.2449635437235649
Best Fitness without Scaling 1.0 RMSE is 0.2449635437235649
RANSAC Duraction 30.988171100616455
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9988019169329073 RMSE = 0.2443334550313174
Refinement took 16 iterations
After Inlier = 0.9996006389776357 RMSE = 0.2514258931977246
949
74891
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 26.717470935935047
Voxel Size is 0.499821448191199
Scaling factor is 1.0289214767533106
movingMeshPoints.shape (4956, 3)
movingMeshPointNormals.shape (4956, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2082 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.26616004232244184
Best Fitness without Scaling 1.0 RMSE is 0.26616004232244184
RANSAC Duraction 33.98073410987854
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9993946731234867 RMSE = 0.26584822688560517
Refinement took 17 iterations
After Inlier = 1.0 RMSE = 0.2700731472736678
949
79906
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 24.344602529639285
Voxel Size is 0.499821448191199
Scaling factor is 1.1292104529965914
movingMeshPoints.shape (5020, 3)
movingMeshPointNormals.shape (5020, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 1037, in onMatchingPointsButton
template_density, matchedPoints, indices, files = logic.matchingPCD(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 3167, in matchingPCD
) = self.runSubsample(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 2856, in runSubsample
source_fpfh = self.get_fpfh_feature(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 2747, in get_fpfh_feature
fpfh.ComputeFPFHFeature(pointset, normalset, float(radius), int(neighbors))
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/itk/itkPointFeaturePython.py”, line 632, in ComputeFPFHFeature
return _itkPointFeaturePython.itkPointFeatureMF3MF3_ComputeFPFHFeature(self, input, input_normals, radius, neighbors)
RuntimeError: /Users/svc-dashboard/D/P/ITKPythonPackage/ITK-source/ITK/Modules/Core/Common/include/itkPointSet.hxx:190:
ITK ERROR: PointSet(0x600001854fc0): Point id doesn’t exist: 18446744073709551615
[VTK] Generic Warning: In vtkMath.cxx, line 799
[VTK] vtkMath::Jacobi: Error extracting eigenfunctions
Zephyrus -
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.568655630649662
Voxel Size is 0.499821448191199
Scaling factor is 0.997153434640227
movingMeshPoints.shape (5021, 3)
movingMeshPointNormals.shape (5021, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2093 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.16982989736096482
Best Fitness without Scaling 1.0 RMSE is 0.16982989736096482
RANSAC Duraction 28.829017877578735
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.16982989736096482
Refinement took 13 iterations
After Inlier = 1.0 RMSE = 0.18650660487674556
949
87529
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.31930086628061
Voxel Size is 0.499821448191199
Scaling factor is 1.0062548739834791
movingMeshPoints.shape (5182, 3)
movingMeshPointNormals.shape (5182, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2145 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.1902918489735167
Best Fitness without Scaling 1.0 RMSE is 0.1902918489735167
RANSAC Duraction 28.968416929244995
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.1902918489735167
Refinement took 29 iterations
After Inlier = 1.0 RMSE = 0.18982818128750228
949
88274
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 26.10924972657576
Voxel Size is 0.499821448191199
Scaling factor is 1.0528904483430859
movingMeshPoints.shape (5036, 3)
movingMeshPointNormals.shape (5036, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2045 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.21646823614800612
Best Fitness without Scaling 1.0 RMSE is 0.21646823614800612
RANSAC Duraction 28.901240825653076
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.21646823614800612
Refinement took 16 iterations
After Inlier = 1.0 RMSE = 0.20428705018420934
949
77369
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 24.775053388285006
Voxel Size is 0.499821448191199
Scaling factor is 1.1095911366840807
movingMeshPoints.shape (4852, 3)
movingMeshPointNormals.shape (4852, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2008 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.23794131463500012
Best Fitness without Scaling 1.0 RMSE is 0.23794131463500012
RANSAC Duraction 29.535005807876587
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.23794131463500012
Refinement took 15 iterations
After Inlier = 1.0 RMSE = 0.21661549368439323
949
67249
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 25.38223905335343
Voxel Size is 0.499821448191199
Scaling factor is 1.0830478584939502
movingMeshPoints.shape (5281, 3)
movingMeshPointNormals.shape (5281, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2128 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.2990313731952503
Best Fitness without Scaling 1.0 RMSE is 0.2990313731952503
RANSAC Duraction 30.21252417564392
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9897746638894149 RMSE = 0.2937590511021508
Refinement took 18 iterations
After Inlier = 0.9992425676955122 RMSE = 0.29918747735529544
949
73873
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 28.374627250030027
Voxel Size is 0.499821448191199
Scaling factor is 0.9688296310742497
movingMeshPoints.shape (5012, 3)
movingMeshPointNormals.shape (5012, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2070 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.19843935184564565
Best Fitness without Scaling 1.0 RMSE is 0.19843935184564565
RANSAC Duraction 30.628879070281982
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.19843935184564565
Refinement took 14 iterations
After Inlier = 1.0 RMSE = 0.2047550117656061
949
94689
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 27.801588154001653
Voxel Size is 0.499821448191199
Scaling factor is 0.9887988951652431
movingMeshPoints.shape (4844, 3)
movingMeshPointNormals.shape (4844, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2065 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.16601349812887392
Best Fitness without Scaling 1.0 RMSE is 0.16601349812887392
RANSAC Duraction 30.84484887123108
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 1.0 RMSE = 0.16601349812887392
Refinement took 11 iterations
After Inlier = 1.0 RMSE = 0.1833367014098634
949
89572
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 25.937013625507507
Voxel Size is 0.499821448191199
Scaling factor is 1.0598822226580855
movingMeshPoints.shape (5008, 3)
movingMeshPointNormals.shape (5008, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2063 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.2449635437235649
Best Fitness without Scaling 1.0 RMSE is 0.2449635437235649
RANSAC Duraction 30.988171100616455
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9988019169329073 RMSE = 0.2443334550313174
Refinement took 16 iterations
After Inlier = 0.9996006389776357 RMSE = 0.2514258931977246
949
74891
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 26.717470935935047
Voxel Size is 0.499821448191199
Scaling factor is 1.0289214767533106
movingMeshPoints.shape (4956, 3)
movingMeshPointNormals.shape (4956, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
FPFH generates 2082 putative correspondences.
Rigid Reg, no scaling
Non-Scaling Attempt = 0 Fitness = 1.0 RMSE is 0.26616004232244184
Best Fitness without Scaling 1.0 RMSE is 0.26616004232244184
RANSAC Duraction 33.98073410987854
Best Fitness after scaling 1.0
{‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
Starting Rigid Refinement
Before Inlier = 0.9993946731234867 RMSE = 0.26584822688560517
Refinement took 17 iterations
After Inlier = 1.0 RMSE = 0.2700731472736678
949
79906
parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}
:: Loading point clouds and downsampling
Scale length are 27.490179650515945 24.344602529639285
Voxel Size is 0.499821448191199
Scaling factor is 1.1292104529965914
movingMeshPoints.shape (5020, 3)
movingMeshPointNormals.shape (5020, 3)
fixedMeshPoints.shape (4924, 3)
fixedMeshPointNormals.shape (4924, 3)
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 1037, in onMatchingPointsButton
template_density, matchedPoints, indices, files = logic.matchingPCD(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 3167, in matchingPCD
) = self.runSubsample(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 2856, in runSubsample
source_fpfh = self.get_fpfh_feature(
File “/Applications/Slicer.app/Contents/Extensions-33123/SlicerMorph/lib/Slicer-5.7/qt-scripted-modules/ALPACA.py”, line 2747, in get_fpfh_feature
fpfh.ComputeFPFHFeature(pointset, normalset, float(radius), int(neighbors))
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/itk/itkPointFeaturePython.py”, line 632, in ComputeFPFHFeature
return _itkPointFeaturePython.itkPointFeatureMF3MF3_ComputeFPFHFeature(self, input, input_normals, radius, neighbors)
RuntimeError: /Users/svc-dashboard/D/P/ITKPythonPackage/ITK-source/ITK/Modules/Core/Common/include/itkPointSet.hxx:190:
ITK ERROR: PointSet(0x600001854fc0): Point id doesn’t exist: 18446744073709551615
[VTK] Generic Warning: In vtkMath.cxx, line 799
[VTK] vtkMath::Jacobi: Error extracting eigenfunctions