# SlicerNNInteractive: segmenting one structure erases part of an adjacent, already-completed segment

**URL:** <https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792>\
**Category:** Support\
**Tags:** extensions-manager\
**Created:** [August 3, 2026, 7:32am UTC](https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792 "2026-08-03T07:32:06Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Jean\_Pinson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jean_pinson/32/79053_2.png) [@Jean\_Pinson](https://discourse.slicer.org/u/Jean_Pinson)\
**Post date:** [August 3, 2026, 7:32am UTC](https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792/1 "2026-08-03T07:32:06Z")

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Hi everyone,

The new version of nninteractive in 3D slicer is huge !!! I’m using it on local on my desktop PC but I’ve now an issue that I hadn’t before where several structures are directly adjacent (e.g., bladder and rectum).

**Issue:** When I finish segmenting structure A, then start prompting on adjacent structure B, any voxels where B’s segmentation slightly overlaps A get erased from A — with no way to recover them via Ctrl+Z (which only undoes the last nnInteractive prompt, not the erasure of the other segment).

my Segment Editor masking settings are “Modify other segments” → “Allow overlap”

Neither prevented the overlap-erase behavior. This suggests nnInteractive writes directly to the shared labelmap layer rather than going through Slicer’s standard masking pipeline ? The only solution I’ve find for the moment is to create a new segmentation to segment the other structure…

But sometimes, I succeed to get an overlap, and I doesn’t know why !

Is this expected behavior, or a bug? Is there a recommended workflow for segmenting adjacent structures without risking overwriting completed work ? Can I freeze one segment so it dosent change ?

my setup Slicer 5.12.2, Windows, RTX 5080

Thanks!

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [August 3, 2026, 10:10am UTC](https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792/2 "2026-08-03T10:10:42Z")

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I am not familiar with the implementation of this effect, but this sounds like a bug that it does not respect the masking settings (I suppose it outputs a normal labelmap without overlaps and inserts it to the layer in the segmentation).

Until this is fixed I’d probably do the following: clone the segmentation just before starting using NNInteractive, create the new segment, then drag&drop that segment into your original segmentation, finally delete the clone.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 3, 2026, 4:36pm UTC](https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792/3 "2026-08-03T16:36:34Z")

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I agree that this is a subtle bug (that should not be too difficult to fix). Please let the developers know by submitting an issue to [Issues · coendevente/SlicerNNInteractive · GitHub](https://github.com/coendevente/SlicerNNInteractive/issues)

To get latest updates, you need to use the latest Slicer Stable Release (currently Slicer-5.12.3).

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**Author:** ![Jean\_Pinson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jean_pinson/32/79053_2.png) [@Jean\_Pinson](https://discourse.slicer.org/u/Jean_Pinson)\
**Post date:** [August 9, 2026, 3:28am UTC](https://discourse.slicer.org/t/slicernninteractive-segmenting-one-structure-erases-part-of-an-adjacent-already-completed-segment/47792/4 "2026-08-09T03:28:55Z")

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Thanks @cpinter For your suggestion, I will do that until it’s fixed. And thanks @lassoan, I’m going to submit this issue