Comments (4)
Did you have a look at the example notebooks yet?
In case of masks, example 3 might be helpful.
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Did you have a look at the example notebooks yet?
In case of masks, example 3 might be helpful.
I did refer to example 3, but the log still said both fMask and mMask were unspecified. Here's my code.
elastix_object = itk.ElastixRegistrationMethod.New(fixed_image, moving_image)
elastix_object.SetFixedMask(mask)
elastix_object.SetMovingMask(mask)
elastix_object.SetParameterObject(parameter_object)
elastix_object.SetLogToConsole(True)
elastix_object.UpdateLargestPossibleRegion()
result_image = elastix_object.GetOutput()
result_transform_parameters = elastix_object.GetTransformParameterObject()
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Can you also show the part of the code that loads the mask?
And why would you want to use the same mask for both the fixed and the moving mask?
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The empty BufferedRegion seems to be caused by not setting WriteResultImage
to True
(as reported in #157).
However, I am not sure if the masks are not read. Indeed, the log indicates:
ELASTIX version: 5.1.0
Command line options from ElastixBase:
-fMask unspecified, so no fixed mask used
-mMask unspecified, so no moving mask used
but later it also reports:
Setting the fixed masks took: 0 ms.
Setting the moving masks took: 1 ms.
So, I assume the masks are being used.. cc. @N-Dekker
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Related Issues (20)
- SWIG build warning for `itk::ElastixLogLevel` HOT 3
- Notebook test failures
- Latest ITKElastix crashes HOT 6
- How to minimise non-rigid distortion when using groupwise registration HOT 3
- pip install itk-elastix does not work HOT 3
- register these two dicom file HOT 1
- Extraction deformation field after 3D registration.
- Error loading initial transform and applying mask
- Error when multiprocessing coregistration HOT 1
- Groupwise registration of 4D objects and registration with mask
- Applying series of registrations to moving image label map HOT 4
- Reset random seed for deterministic registration HOT 7
- Data format differs from the example HOT 1
- Data format differs from the example HOT 1
- itk.ParameterObject -> seg fault in fresh env HOT 5
- Issue with image format HOT 1
- Elastix Model Zoo site cannot be opened HOT 1
- Inverse transform HOT 10
- ErodeMask and dilating mask
- GroupwiseRegistration notebook: ERROR: the direction cosines matrix of the fixed image is invalid! HOT 1
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