We have a blank segmentation template with 8 segments. Some of the organisms we segment will have all 8 of these distinct structures, and some other will only a subset of it. When I save my segmentation, say with 6 structures (e.g., 3 and 4 is missing), and reload the segmentation back into slicer as a volume (since that’s what we ultimately need), I see segments 5, 6, 7, and 8 are shifted to 3, 4, 5, and 6. Not only we lost the ability to tell the segments are missing, they are now also mapped to incorrect structures. It does not suffer from this problem if the data is loaded as a segmentation.
If this is intentional, I would argue it is a bug. Same segmentation exported as a label map doesn’t suffer from this (e.g., loaded volume has indices 1,2, 5, 6, 7, 8). While saving the output as label map fixes my issue, I think the behavior should be the same for segmentations too.
This is with Slicer r28896 on windows 10.