Can’t visualize my liver segmentation in 3D after cropping (Scalar Range shows 0–2 but nothing displays)

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1

Hello everyone.
I am working on a liver surgery simulation project. I have:

  • Pre-operative MRI resampled to isotropic (preop_n4_iso)

  • Liver segmentation exported as labelmap (liver_full_seg)

What I did:

  1. Resampled the segmentation with NearestNeighbor using preop_n4_iso as reference → got liver_full_seg_iso

  2. Cropped MRI (preop_n4_iso_crop, Linear) and mask (liver_full_seg_iso_crop, NearestNeighbor) with the same ROI

  3. In Volumes → Information:

    • liver_full_seg_iso_crop shows Scalar Range = 0–2, valid dimensions and spacing (1 mm)

    • So it is not empty

  4. When I Import labelmap to Segmentation, I get Segment_1 and Segment_2, but neither looks like the full liver in 2D or 3D. ( There is no 3D liver at all is just showing a small thing

  5. Clicking Show 3D shows nothing

My question:

  • Why doesn’t the liver appear in 3D even though Scalar Range = 0–2?

  • Did I crop incorrectly, or is my export wrong?

  • Should I re-export my liver segmentation as a binary (0/1) labelmap before resampling/cropping?

I have attached screenshots showing the Volumes Information panel and the empty 3D view.

Any help to understand what I am doing wrong would be greatly appreciated, because Ive been doing the same things for more than 3 days and cannot find the solution.

Thank you!

2

To facilitate the process I suggest that you at the least make some relevant screenshots, but if the issue can be reproduced with a saved MRB scene, even better (only anonymized data please). Thank you!

3

MRB file - Google Drive you can find it here at this link