When a transform is applied to more than one volume, and you then go to the Transforms module and edit it, weird things happen. When switching the presentation between the views, the transform (as applied to the volumes) changes (without changing in the module).
I did the following actions:
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Open Slicer 5.12.4
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Open the “Sample Data” module
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Click “MRHead” and “MRBrainTumor1”. MRBrainTumor1 is presented in the slices.
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Go To “Data” module
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Right click on the right side of MRHead (the transform context menu), and pick “create new transform”
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Move to the “Transform Hierarchy” tab, and drag MRBrainTumor1 under the transform
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Go to the “Transforms” module. Using the “Rotation” scrollbar “IS”, rotate by 45°. The MRBrainTumor1 volume is rotated as expected.
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Go back to the “Data” module. Click the MRHead eye to make it visible. Result:
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Going back to the Transforms module, it still shows the 45°:
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Now, clicking “Identity” to reset the transform:
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And finally, “compare volumes”:
If you now return to the “conventional” view, you get the head in 45° again.
This last move seems to imply that the problem is mostly in the slice views, but that does not make it “just presentation” or “cosmetic”, because the transform is edited based on this presentation – leading to wrong transformation matrices being selected.