[ITK] itk::N4BiasFieldCorrectionImageFilter ; Inputs do not occupy the same physical space

[P. Pieperhoff]

Dear ITK-Users,

I want to use the bias field correction filter itk::N4BiasFieldCorrectionImageFilter with a mask, that indicates the voxels where the intensities shall be corrected.

I have attached the code of my filter implementation. The program is called as

N4_test inputimage.nii mask.nii output.nii


However, the program crashes with the following error message:

>>>>>
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /develop/ITK/ITK-4.8.0/InsightToolkit-4.8.0/Modules/Core/Common/include/itkImageToImageFilter.hxx:248:
itk::ERROR: N4BiasFieldCorrectionImageFilter(0x299f3d0): Inputs do not occupy the same physical space!
InputImage Origin: [8.7000000e+01, 1.2300000e+02, -1.6400000e+02], InputImage_1 Origin: [0.0000000e+00, 0.0000000e+00, 0.0000000e+00]
        Tolerance: 1.0000000e-06
InputImage Direction: -1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 -1.0000000e+00 0.0000000e+00
0.0000000e+00 0.0000000e+00 1.0000000e+00
, InputImage_1 Direction: 1.0000000e+00 0.0000000e+00 0.0000000e+00
0.0000000e+00 1.0000000e+00 0.0000000e+00
0.0000000e+00 0.0000000e+00 1.0000000e+00

        Tolerance: 1.0000000e-06

Aborted


<<<<<<


But the sizes, origins and the direction matrices of the input image and mask are definitively identical.
Below is the debug information of the input and mask image, before the program crashes.


I'm using ITK version 4.8.0 on Debian-Linux.

Please could anyone help me to get the program running?
Thanks a lot in advance!

Peter




(gdb) p *pInputImage
$82 = {<itk::ImageBase<3u>> = {<itk::DataObject> = {<itk::Object> = {<itk::LightObject> = {_vptr.LightObject = 0xeaa810 <vtable for itk::Image<float, 3u>+16>, m_ReferenceCount = {m_Object = 1}}, m_Debug = false, m_MTime = {m_ModifiedTime = 196}, static m_GlobalWarningDisplay = true, m_SubjectImplementation = 0x0, m_MetaDataDictionary = 0x19fbc80, m_ObjectName = ""}, m_Source = {m_Pointer = 0x19f0dd0}, m_SourceOutputName = "Primary", m_UpdateMTime = {m_ModifiedTime = 197}, m_RealTimeStamp = {m_Seconds = 0, m_MicroSeconds = 0}, m_ReleaseDataFlag = false, m_DataReleased = false, m_PipelineMTime = 52, static m_GlobalReleaseDataFlag = false}, m_Spacing = {<itk::FixedArray<double, 3u>> = {m_InternalArray = {1, 1, 1}}, <No data fields>}, m_Origin = {<itk::FixedArray<double, 3u>> = {m_InternalArray = {87, 123, -164}}, <No data fields>}, m_Direction = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_InverseDirection = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_IndexToPhysicalPoint = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_PhysicalPointToIndex = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_OffsetTable = {1, 176, 40832, 10452992}, m_LargestPossibleRegion = {<itk::Region> = {_vptr.Region = 0xeaad90 <vtable for itk::ImageRegion<3u>+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}, m_RequestedRegion = {<itk::Region> = {_vptr.Region = 0xeaad90 <vtable for itk::ImageRegion<3u>+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}, m_BufferedRegion = {<itk::Region> = {_vptr.Region = 0xeaad90 <vtable for itk::ImageRegion<3u>+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}}, m_Buffer = {m_Pointer = 0x19f57c0}}
(gdb) p *pMaskL
$83 = {<itk::ImageBase<3u>> = {<itk::DataObject> = {<itk::Object> = {<itk::LightObject> = {_vptr.LightObject = 0x19faaf0, m_ReferenceCount = {m_Object = 27248080}}, m_Debug = false, m_MTime = {m_ModifiedTime = 360}, static m_GlobalWarningDisplay = true, m_SubjectImplementation = 0x0, m_MetaDataDictionary = 0x1a05140, m_ObjectName = ""}, m_Source = {m_Pointer = 0x0}, m_SourceOutputName = "", m_UpdateMTime = {m_ModifiedTime = 359}, m_RealTimeStamp = {m_Seconds = 0, m_MicroSeconds = 0}, m_ReleaseDataFlag = false, m_DataReleased = false, m_PipelineMTime = 214, static m_GlobalReleaseDataFlag = false}, m_Spacing = {<itk::FixedArray<double, 3u>> = {m_InternalArray = {1, 1, 1}}, <No data fields>}, m_Origin = {<itk::FixedArray<double, 3u>> = {m_InternalArray = {87, 123, -164}}, <No data fields>}, m_Direction = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_InverseDirection = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_IndexToPhysicalPoint = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_PhysicalPointToIndex = {m_Matrix = {data_ = {{-1, 0, 0}, {0, -1, 0}, {0, 0, 1}}}}, m_OffsetTable = {1, 176, 40832, 10452992}, m_LargestPossibleRegion = {<itk::Region> = {_vptr.Region = 0xec0310 <vtable for itk::Region+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}, m_RequestedRegion = {<itk::Region> = {_vptr.Region = 0xec0310 <vtable for itk::Region+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}, m_BufferedRegion = {<itk::Region> = {_vptr.Region = 0xec0310 <vtable for itk::Region+16>}, m_Index = {m_Index = {0, 0, 0}}, m_Size = {m_Size = {176, 232, 256}}}}, m_Buffer = {m_Pointer = 0x290}}



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