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SuperElastix / SimpleElastix

Multi-lingual medical image registration library
http://simpleelastix.github.io
Apache License 2.0
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Problems to get the Displacement Field using TransformixImageFilter #466

Open RivettiLuciano opened 2 years ago

RivettiLuciano commented 2 years ago

I had some problems to get the displacement field of a registration. The registration work well but when I use TransformixImageFilter to get the displacement field I get an error. Below the code I'm using:

CT = sitk.ReadImage('',sitk.sitkFloat32)
CBCT = sitk.ReadImage('',sitk.sitkFloat32)

elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.LogToFileOff()
elastixImageFilter.LogToConsoleOff()
elastixImageFilter.SetOutputDirectory(ElastixOutputFile)
elastixImageFilter.SetFixedImage(CBCT)
parametermap = elastixImageFilter.ReadParameterFile(Parameter_File)
elastixImageFilter.SetParameterMap(parametermap)
elastixImageFilter.SetMovingImage(CT)
elastixImageFilter.Execute()

transformixImageFilter = sitk.TransformixImageFilter()
transformixImageFilter.SetTransformParameterMap(elastixImageFilter.GetTransformParameterMap())
transformixImageFilter.ComputeDeformationFieldOn()
transformixImageFilter.Execute()

The Parameter_File I used can be found here

Error:

RuntimeError: Exception thrown in SimpleITK TransformixImageFilter_Execute: /mnt/Luco/Modules/Elastix/SimpleElastix/Code/Elastix/src/sitkTransformixImageFilterImpl.cxx:116: sitk::ERROR: itk::ExceptionObject (0x564e638b7190) Location: "unknown" File: /mnt/Luco/Modules/Elastix/Build/ITK-prefix/include/ITK-5.1/itkImageBase.hxx Line: 184 Description: itk::ERROR: Image(0x564e63aa0300): Bad direction, determinant is 0. Direction is 1 0 0 0