Best way to flip entire scene

Support
1

Hello,

I am having some trouble with incorrect orientations of a scan.

We received a CT scan of the upper body in .IMA format (unfortunately not DICOM). Therefore to load the CT data I converted to .nrrd in ImageJ, then loaded in Slicer.

I noticed that the left and right axes are flipped in the scan - I assume it has to do with something going wrong in the IJK to RAS transformation because the scan was “upside down”, ie when I load it in slicer, superior and inferior are also flipped.

In my original image volume the transform is as follows which seems to be the standard IFK to RAS.
IJKToRASDirections:
-1 0 0
0 -1 0
0 0 1

Maybe the image was already in RAS and that caused the issues?

Since the last axis is not flipped in the IJK to RAS transform, I created a linear transform and applied it to everything in the scene:

image
image1503×445 8.05 KB

This gives me the correct orientations for superior inferior, left right etc, and the bones are not mirrored incorrectly anymore.

I just wanted to confirm:
-Do you recommend applying the transform to everything in the scene and continuing working on that scene? Or exporting the transformed image and segmentation data and importing into a new scene?

I already did some segmentation so would like to avoid re-starting from scratch.

Should I also transform the camera or no?

Thank you,
Eva

2

Applying and hardening the transform would make sense, because by hardening you permanently fix the position/orientation of the objects.

You don’t have to transform the camera or modify views - they are all good, just the pose of the objects were incorrect.

3

Thank you so much Andras.

Best,
Eva

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