method "GetLogBiasFieldAsImage" missing in N4BiasFieldCorrection c# implementation

Tamar · April 13, 2021, 1:24pm

Hello,
I have the N4BiasFieldCorrectionImageFilter implemented in c# (visual studio) and it is working correctly and improving images.
However, when I attempt to use the method GetLogBiasFieldAsImage() I get the following compilation error:
“‘N4BiasFieldCorrectionImageFilter’ does not contain a definition for ‘GetLogBiasFieldAsImage’ and no accessible extension method…”
I need this method because I need to run the filter with ShrinkFactor higher than 1.
What can cause this method to be missing? and what can I do about it?

Is there another way, besides this method, to obtain the Bias Field?
Thanks!

dzenanz · April 13, 2021, 1:47pm

C++ version of the code has GetLogBiasFieldControlPointLattice():

github.com

InsightSoftwareConsortium/ITK/blob/v5.2.0/Modules/Filtering/BiasCorrection/include/itkN4BiasFieldCorrectionImageFilter.h#L348-L357


/**
 * Typically, a reduced size image is used as input to the N4 filter using
 * something like itkShrinkImageFilter.  Since the output is a corrected
 * version of the input, the user will probably want to apply the bias
 * field correction to the full resolution image.  This can be done by
 * using the LogBiasFieldControlPointLattice to reconstruct the bias field
 * at the full image resolution (using the class
 * BSplineControlPointImageFilter).
 */
itkGetConstObjectMacro(LogBiasFieldControlPointLattice, BiasFieldControlPointLatticeType);

Which version of ITK are you using? Why do you expect GetLogBiasFieldAsImage() to exist?

dzenanz · April 13, 2021, 1:50pm

Maybe you saw it in an example? There is this one:

github.com

InsightSoftwareConsortium/ITKMontage/blob/29707c0920563a2f81d015056a3922ccea3c9310/examples/CompleteMontage.cxx#L155-L219


template <typename PixelType, unsigned Dimension>
typename LogBiasFieldType<Dimension>::Pointer
GetLogBiasField(typename itk::Image<PixelType, Dimension>::Pointer scalarImage,
                std::vector<unsigned>                              iterations = { 20, 10, 5 },
                unsigned                                           shrinkFactor = 4)
{
  using ImageType = itk::Image<PixelType, Dimension>;
  using RealImageType = itk::Image<float, Dimension>;
  typename ImageType::RegionType region = scalarImage->GetLargestPossibleRegion();
  // instantiate N4 and assign variables not exposed to the user
  using CorrecterType = itk::N4BiasFieldCorrectionImageFilter<RealImageType>;
  typename CorrecterType::Pointer correcter = CorrecterType::New();
  correcter->SetSplineOrder(splineOrder);
  correcter->SetWienerFilterNoise(0.01f);
  correcter->SetBiasFieldFullWidthAtHalfMaximum(0.15f);
  correcter->SetConvergenceThreshold(0.00001f);
  typename CorrecterType::VariableSizeArrayType maximumNumberOfIterations(

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Tamar · April 14, 2021, 7:45am

Thank you so much for answering!
I am using simpleITK version 2.0.2 (maybe 2.0.2.0) downloaded from this place (downloaded the zip at the bottom line of this screen capture):

I expected it to have the method GetLogBiasFieldAsImag() because it was listed here:

I realize now that it is not the same version (oops).
What can be done about it? Should I download a newer sitk version? (if yes, which and where from?)
Of course its not that I must use this specific method. Any method that would give me the full-resolution corrected image, through the full-resolution Bias Field or directly, would work for me.
Only it must be available in the C# implementation.
Thanks again!

blowekamp · April 14, 2021, 12:45pm

Hello,

You can download the nightly CSharp binaries for window on the GitHub release tab:
https://simpleitk.readthedocs.io/en/master/gettingStarted.html#latest-binaries

Tamar · April 20, 2021, 1:47pm

Thank you! (both!) I can get the full-resolution Bias Field now, after I downloaded version 2.1.0.dev245.