Comments (4)
Just to note this here. This issue is directly linked to this one (#145) since this tries to use ITKs registration via MONAI.
I currently suspect the following issues to exist:
- Orientation
- ITK uses LPS orientation for images and transforms
- Monai/Nibabel uses RAS orientation for images and transforms
- Center of Rotation
- ITK provides the used center of rotation
- Monai implicitly assumes the center of rotation to be the center of the image
- World space vs. Index space.
- All transforms and points from ITK are in world space.
- Monai seems to operate directly on the image.
- (0, 0, 0) Corner - ITK and Monai seem to use the opposit corner for coordinates - e.g. in a 4x4x4 image, position (0, 0, 0) in ITK is position (3, 3, 3) in Monai.
This is also tracked via this SO question: https://stackoverflow.com/questions/71529039/how-to-factor-the-itk-centerofrotationpoint-in-a-affine-transformation-matrix
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Here is a proposal to improve transforms in MONAI:
https://drive.google.com/file/d/1odXYUpQeoaMpjqzkeLnQK64eYRfd01YB/view
A good point of contact at MONAI is Wenqi Li [email protected]
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Once Elastix has more complete itk::Transform support (in memory Python interface support via itk-elastix), this package will enable an elegant interface with MONAI: https://github.com/InsightSoftwareConsortium/itk-torch-transform-bridge
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Related Issues (20)
- Order of transformparameter files when computing inverse HOT 1
- Method visibility issue with Apple M1 install HOT 1
- Segmentation fault on Apple M2 HOT 4
- Use saved registration to apply for new images HOT 2
- python can't find itk-elastix on arm64 Mac HOT 3
- macOS arm packages missing for 0.18.0 HOT 3
- Update documentation
- External initial transform causes a failure in ConvertToItkTransform HOT 16
- How to convert ITK transform into Elastix transform parameters file? HOT 14
- Saving and Loading Paramter files to reapply transfomr HOT 2
- Histology image registration HOT 5
- `itkwasm-elastix` Site Feedback
- `itk.elastix_registration_method` sometimes crashes silently HOT 2
- Make `itk.ParameterObject` and parameter maps serializable HOT 5
- Segmentation fault on Ubuntu 20.04.6 LTS, x86_64, Python 3.9-3.11 HOT 13
- CORS on loading 3D data HOT 2
- 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
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