Hello,
I am trying to compare two airway segmentations in 3D Slicer: a Bronchus segmentation generated by one algorithm and an airway segmentation generated by TotalSegmentator.
The TotalSegmentator segmentation loads and is visible correctly in 3D Slicer. However, although the Bronchus segmentation appears to load, I cannot see it in the 2D slice views or the 3D view.
Could this issue be caused by differences in image geometry, such as spacing, origin, orientation, or coordinate system? Are there specific settings or checks I should use to determine why the Bronchus segmentation is not displaying?
Both segmentations are intended to correspond to the same patient CT scan.
Thank you for your help.
Hi Tien,
I haven’t used TotalSegmentator specifically, but I’ve run into similar “loads but doesn’t display” issues with vascular segmentations, so a couple of things worth checking:
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First, the simplest thing — double check that the segment’s visibility (eye icon) is actually toggled on in the Segmentations module, both for the 2D slice views and the 3D view separately. Sometimes only one of the two gets left off.
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If visibility is on and it’s still not showing, I’d look at whether the Bronchus segmentation and the TotalSegmentator segmentation actually share the same reference geometry (origin, spacing, and especially orientation/IJK-to-RAS matrix). If the Bronchus segmentation was generated by a different algorithm/pipeline than TotalSegmentator, it’s possible it was built on a volume with a different coordinate system, so the segmentation technically exists but sits outside the geometry currently being displayed.
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You can check this in Slicer by loading the Bronchus segmentation’s source volume (if you have it) into the scene and seeing whether it aligns with your CT — if it doesn’t overlap, that would confirm a geometry mismatch rather than a visibility setting issue.
Hope one of these points you in the right direction — let us know what you find.