This is caused by a bug in BrainsFit in BRAINSTools\BRAINSCommonLib\BRAINSFitHelperTemplate.hxx. If the splineGridSize parameter vector has less than 3 components then an invalid memory access occurs here (SpaceDimension==3; m_SplineGridSize.size()==1):

  // Initialize the BSpline transform
  // Using BSplineTransformInitializer
  //
  BSplineTransformType::MeshSizeType    meshSize;
  for( unsigned int i=0; i< SpaceDimension; i++ )
    {
    meshSize[i] = m_SplineGridSize[i];
    }

This should crash on all platforms. It is surprising why it does not crash on Linux.

It is easy to fix the problem by adding checks and/or use the same parameters for all dimension if only one parameter is specified, but the fix has to be done in BRAINS.

Reported the problem at the BRAINS bugtracker:
https://github.com/BRAINSia/BRAINSTools/issues/166

I thought this was the bug tracker for BRIANS tools :)

Example command-line options to reproduce the problem:

C:/Program Files/Slicer 4.4.0/lib/Slicer-4.4/cli-modules/BRAINSFit.exe --fixedVolume C:/Users/Andras/AppData/Local/Temp/Slicer/HEEI_vtkMRMLScalarVolumeNodeC.nrrd --movingVolume C:/Users/Andras/AppData/Local/Temp/Slicer/HEEI_vtkMRMLScalarVolumeNodeE.nrrd --bsplineTransform C:/Users/Andras/AppData/Local/Temp/Slicer/HEEI_vtkMRMLBSplineTransformNodeB.h5 --initializeTransformMode Off --samplingPercentage 0.002 --useBSpline --splineGridSize 6 --numberOfIterations 1500 --maskProcessingMode NOMASK --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+013 --projectedGradientTolerance 1e-005 --maximumNumberOfEvaluations 900 --maximumNumberOfCorrections 25 --metricSamplingStrategy Random --costMetric MMI --metricSeed 21474836

Changing this one parameter the registration completes successfully:
--splineGridSize 6,6,6

lassoan,

Thank you for tracking this down. We are making several other changes to BRAINSTools and will work over the holiday season to upgrade Slicer.

Hans

Great, thank you!

This version of BRAINSTools was updated during NAMIC Winter project week 2015.

commit 38c2198c44c8f2dbd405654c2465f2991a637999
Merge: 19fa37d cce8056
Author: Ali Ghayoor <ali-ghayoor@uiowa.edu>
Date: Tue Dec 23 10:56:24 2014 -0600

Merge pull request 0000167 from aghayoor/BFitBSplineGridSize

BUG: Fix BFit crash when only one value is set for splineGridSize