I was able to get a crash using the Slicer 4.4 release. I'll attach a screenshot of the stacktrace.

It dies in:

itk::ImageToImageMetricv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double> >::SetMovingImageMask(itk::SpatialObject<3u> const*)

I tested again with a debug build and got basically the same stack trace but with some extra detail.

Here's the code it dies on:

if ( m_Pointer ) { m_Pointer->Register(); }

so m_Pointer is nonzero, but corrupt.

(lldb) bt

• thread 0000003: tid = 0xcbe0a, 0x00000001339ad141 libBRAINSFitLib.dylib`itk::SmartPointer<itk::SpatialObject<3u> const>::Register(this=0x0000000125874d18) + 49 at itkSmartPointer.h:164, stop reason = EXC_BAD_ACCESS (code=EXC_I386_GPFLT)
  • frame #0: 0x00000001339ad141 libBRAINSFitLib.dylibitk::SmartPointer<itk::SpatialObject<3u> const>::Register(this=0x0000000125874d18) + 49 at itkSmartPointer.h:164 frame 0000001: 0x0000000133c8f0a3 libBRAINSFitLib.dylibitk::SmartPointer<itk::SpatialObject<3u> const>::SmartPointer(this=0x0000000125874d18, p=0x00007ffca743b580) + 35 at itkSmartPointer.h:70
    frame 0000002: 0x000000013396561d libBRAINSFitLib.dylibitk::SmartPointer<itk::SpatialObject<3u> const>::SmartPointer(this=0x0000000125874d18, p=0x00007ffca743b580) + 29 at itkSmartPointer.h:70 frame 0000003: 0x0000000133b1eb08 libBRAINSFitLib.dylibitk::SmartPointer<itk::SpatialObject<3u> const>::operator=(this=0x00007ffca727a038, r=0x00007ffca743b580) + 40 at itkSmartPointer.h:130
    frame 0000004: 0x0000000133bc40de libBRAINSFitLib.dylibitk::ImageToImageMetricv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double> >::SetMovingImageMask(this=0x00007ffca7279ed0, _arg=0x00007ffca743b580) + 2030 at itkImageToImageMetricv4.h:380 frame 0000005: 0x00000001339920c6 libBRAINSFitLib.dylibitk::BRAINSFitHelperTemplate<itk::Image<float, 3u>, itk::Image<float, 3u> >::Update(this=0x00007ffcb4d9a2b0) + 42166 at BRAINSFitHelperTemplate.hxx:1420
    frame 0000006: 0x0000000133968707 libBRAINSFitLib.dylibvoid itk::BRAINSFitHelper::RunRegistration<itk::MattesMutualInformationImageToImageMetricv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double, itk::DefaultImageToImageMetricTraitsv4<itk::Image<float, 3u>, itk::Image<float, 3u>, itk::Image<float, 3u>, double> > >(this=0x00007ffcb4bdbcd0) + 391 at BRAINSFitHelper.h:446 frame 0000007: 0x00000001339603b4 libBRAINSFitLib.dylibitk::BRAINSFitHelper::Update(this=0x00007ffcb4bdbcd0) + 8228 at BRAINSFitHelper.cxx:323
    frame 0000008: 0x0000000133572474 libBRAINSFitLib.dylibModuleEntryPoint(argc=94, argv=0x00007ffca6fc08b0) + 189076 at BRAINSFit.cxx:485 frame 0000009: 0x0000000105559216 libqSlicerBaseQTCLI.dylibvtkSlicerCLIModuleLogic::ApplyTask(this=0x00007ffcbb834f50, clientdata=0x00007ffcbb2f0ad0) + 116102 at vtkSlicerCLIModuleLogic.cxx:2100
    frame 0000010: 0x0000000108875def libSlicerBaseLogic.dylibvtkSlicerTask::Execute(this=0x00007ffcb4b644e0) + 175 at vtkSlicerTask.cxx:36 frame 0000011: 0x000000010883c9d1 libSlicerBaseLogic.dylibvtkSlicerApplicationLogic::ProcessProcessingTasks(this=0x00007ffcb4f4c980) + 705 at vtkSlicerApplicationLogic.cxx:462
    frame 0000012: 0x000000010883c19e libSlicerBaseLogic.dylibvtkSlicerApplicationLogic::ProcessingThreaderCallback(arg=0x00007ffcb9832890) + 78 at vtkSlicerApplicationLogic.cxx:420 frame 0000013: 0x00007fff8981f2fc libsystem_pthread.dylib_pthread_body + 131
    frame 0000014: 0x00007fff8981f279 libsystem_pthread.dylib_pthread_start + 176 frame 0000015: 0x00007fff8981d4b1 libsystem_pthread.dylibthread_start + 13

CLI options:

slicer:0x120fa6bf0 --processinformationaddress 0x135253890 --fixedVolume slicer:0x10e2a72b0#vtkMRMLScalarVolumeNode2 --movingVolume slicer:0x10e2a72b0#vtkMRMLScalarVolumeNode6 --outputVolume slicer:0x10e2a72b0#vtkMRMLScalarVolumeNode5 --initializeTransformMode useCenterOfROIAlign --samplingPercentage 0.002 --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --useBSpline --splineGridSize 5,5,5 --numberOfIterations 1500 --maskProcessingMode ROI --fixedBinaryVolume slicer:0x10e2a72b0#vtkMRMLScalarVolumeNode1 --movingBinaryVolume slicer:0x10e2a72b0#vtkMRMLScalarVolumeNode3 --outputVolumePixelType float --backgroundFillValue 0 --maskInferiorCutOffFromCenter 1000 --interpolationMode Linear --minimumStepLength 0.001 --translationScale 1000 --reproportionScale 1 --skewScale 1 --maxBSplineDisplacement 0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --numberOfSamples 0 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --removeIntensityOutliers 0 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --ROIAutoDilateSize 0 --ROIAutoClosingSize 9 --relaxationFactor 0.5 --maximumStepLength 0.05 --failureExitCode -1 --numberOfThreads -1 --forceMINumberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 2e+13 --projectedGradientTolerance 1e-05 --maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random --costMetric MMI --metricSeed 21474836

This one crashes for me:

0000004 Slicer-build $ ./lib/Slicer-4.4/cli-modules/BRAINSFit --fixedVolume ~/data/3913-brainsfit-crash/Day01_axial.nrrd --movingVolume ~/data/3913-brainsfit-crash/Day42_axial.nrrd --outputVolume /tmp/out.nrrd --initializeTransformMode useCenterOfROIAlign --samplingPercentage 0.002 --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --useBSpline --splineGridSize 5,5,5 --numberOfIterations 1500 --maskProcessingMode ROI --fixedBinaryVolume ~/data/3913-brainsfit-crash/Day01_axial-label.nrrd --movingBinaryVolume ~/data/3913-brainsfit-crash/Day42_axial-label.nrrd --outputVolumePixelType float --backgroundFillValue 0 --maskInferiorCutOffFromCenter 1000 --interpolationMode Linear --minimumStepLength 0.001 --translationScale 1000 --reproportionScale 1 --skewScale 1 --maxBSplineDisplacement 0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --numberOfSamples 0 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --removeIntensityOutliers 0 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --ROIAutoDilateSize 0 --ROIAutoClosingSize 9 --relaxationFactor 0.5 --maximumStepLength 0.05 --failureExitCode -1 --numberOfThreads -1 --forceMINumberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 2e+13 --projectedGradientTolerance 1e-05 --maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random --costMetric MMI --metricSeed 21474836

Here's an easier way to replicate. You can use this with the attached 3913-brainsfit-crash.tar.gz file and just update your data path.

datadir=~/data/3913-brainsfit-crash

./lib/Slicer-4.4/cli-modules/BRAINSFit \
--fixedVolume ${datadir}/Day01_axial.nrrd \
--movingVolume ${datadir}/Day42_axial.nrrd \
--outputVolume /tmp/out.nrrd \
--initializeTransformMode useCenterOfROIAlign \
--samplingPercentage 0.002 \
--useRigid \
--useScaleVersor3D \
--useScaleSkewVersor3D \
--useAffine \
--useBSpline \
--splineGridSize 5,5,5 \
--numberOfIterations 1500 \
--maskProcessingMode ROI \
--fixedBinaryVolume ${datadir}/Day01_axial-label.nrrd \
--movingBinaryVolume ${datadir}/Day42_axial-label.nrrd \
--outputVolumePixelType float \
--backgroundFillValue 0 \
--maskInferiorCutOffFromCenter 1000 \
--interpolationMode Linear \
--minimumStepLength 0.001 \
--translationScale 1000 \
--reproportionScale 1 \
--skewScale 1 \
--maxBSplineDisplacement 0 \
--numberOfHistogramBins 50 \
--numberOfMatchPoints 10 \
--numberOfSamples 0 \
--fixedVolumeTimeIndex 0 \
--movingVolumeTimeIndex 0 \
--medianFilterSize 0,0,0 \
--removeIntensityOutliers 0 \
--useCachingOfBSplineWeightsMode ON \
--useExplicitPDFDerivativesMode AUTO \
--ROIAutoDilateSize 0 \
--ROIAutoClosingSize 9 \
--relaxationFactor 0.5 \
--maximumStepLength 0.05 \
--failureExitCode -1 \
--numberOfThreads -1 \
--forceMINumberOfThreads -1 \
--debugLevel 0 \
--costFunctionConvergenceFactor 2e+13 \
--projectedGradientTolerance 1e-05 \
--maximumNumberOfEvaluations 900 \
--maximumNumberOfCorrections 25 \
--metricSamplingStrategy Random \
--costMetric MMI \
--metricSeed 21474836

Once BRAINSTools was updated to recent version, Bradley Lowekamp confirmed that this issue was resolved.