When running the N4 filter as part of my (c#) code, I see that if the input image has only 1 slice I get an error, even if I set ShrinkFactor=1. The error message is:
Exception thrown in SimpleITK N4BiasFieldCorrectionImageFilter_Execute: d:\a\1\sitk-build\itk-prefix\include\itk-5.2\itkImageBase.hxx:165:
ITK ERROR: Image(00000218C297CE70): A spacing of 0 is not allowed: Spacing is [0, 123, 123]
With 2 slices or more, I don’t get an error (as long as the shrink factor is 1).
Will be glad for any advice - thank you!
This is strange. When you read a single 3D slice you should have an image of size [x,y,1] and spacing [dx,dy,1.0]. Not sure how a spacing of zero happens in your case.
Possibly a manually created image and not one read from disk?
I get the same error also when trying to run the N4 filter from within the “Slicer” application when input-ing a single dicom slice extracted from a 3d dicom image.
How would it matter if the image is "“manually created” vs read from the disk?
When working with a 3D “slice”, with a dimension of size 1, frequently the image needs to be reduced to 2D.
The ExtractImageFilter can be used to convert a 3D image into a 2D image. When the extraction size has a “0” value for a dimension then that dimension will be collapsed and the output dimension reduced by 1.
