Connect to project MONAI

[mstaring]

Investigate the connection with project MONAI

[Spenhouet]

Just to note this here. This issue is directly linked to this one (https://github.com/InsightSoftwareConsortium/ITKElastix/issues/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

[thewtex]

@aylward @hjmjohnson

[aylward]

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 wenqil@nvidia.com

[thewtex]

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