Following error message dialog appears when using the GFA method for file I_should_be_coloured_not_black.qbi:

An error occurred. You should save all data and quit the program to prevent possible data loss.
See the error log for details.

/Volumes/FastDrive/Developer/MITK/bin/itk4/MITK-superbuild/ITK-src/Modules/Core/Common/src/itkMultiThreader.cxx:359:
itk::ERROR: MultiThreader(0x7ff81cb3f200): Exception occurred during SingleMethodExecute
/Volumes/FastDrive/Developer/MITK/bin/itk4/MITK-superbuild/ITK-src/Modules/Core/Common/include/itkImageSource.hxx:295:
itk::ERROR: DiffusionQballGeneralizedFaImageFilter(0x7ff8259c35a0): Subclass should override this method!!!
The signature of ThreadedGenerateData() has been changed in ITK v4 to use the new ThreadIdType.
DiffusionQballGeneralizedFaImageFilter::ThreadedGenerateData() might need to be updated to used it.

So it seems like this is an itk4-Issue...