LR rotation transform reduces axial resolution

Development
1

Hi,

I performed an LR rotation transform using an angle and this matrix:
self.transform = np.array([
[1, 0, 0, 0],
[0, cos_angle, sin_angle, 0],
[0, -sin_angle, cos_angle, 0],
[0, 0, 0, 1]
])
From what I understand, it should only effect the sagittal plane, but it changes the spacing of the axial plane - from ~0.2 to ~2mm slices!
Why does it do that?

Thanks for any help in advance

2

anyone? I could really use the help.
When I do it manually there is no problem…

3

If you did this in Slicer we’d appreciate if you told us

  • What Slicer version you use
  • What modules you used, what steps did you take exactly
  • What did you expect, what happened instead, how did you found out
  • Preferably include screenshots
4

Thank you for answering!

Yes it is a part of an extension I’m working on in pycharm (2024.1.4)
I am using Slicer 5.6.2, using a linear transform.
I wanted to simply align the scan to a marked line by rotating around the LR axis. Manually, on a single sagittal slice, I marked the angle between the chosen line and the horizontal line using markups module, and put that angle in the LR rotation in the transforms module. Programmatically, the user marks two control points creating a line, and I calculate the projection of the line on the XY plane (I checked that the angle is identical to the manual process). Then I calculate the transform as I wrote in the first post (again, I checked it is the same as the manual transform is shown), and then I apply the transform using this line of code:
targetNode.SetAndObserveTransformNodeID(transformNode.GetID())
where targetNode is the scan volume, and the transformNode is:
self.transform = np.array([
[1, 0, 0, 0],
[0, cos_angle, sin_angle, 0],
[0, -sin_angle, cos_angle, 0],
[0, 0, 0, 1]
])
transformNode = slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLLinearTransformNode”,
“AlignTransform”)
slicer.util.updateTransformMatrixFromArray(transformNode, self.transform)

The transform is done as I expected (only the sagittal changes), but for some reason, the axial slices which were 0.2 mm thin, become 2 mm thin. I found out when I was trying to move on with marking a target point in the axial plane and I scrolled a bit to find I already passed it because each slice was ten-fold larger…
What screenshots could help the debugging?

5

Are you talking about a CT that you loaded from DICOM?

What screenshots could help the debugging?

I think what could help is one actual matrix that you calculate (Transforms module), and the slice views before and after applying the transform.

Thanks!