Question on NN's performance on long & continuous structure

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Harry Zhou

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Jul 8, 2026, 10:18:33 AM (20 hours ago) Jul 8

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Hi everyone,

I am currently working on AAA / aorta segmentation cases and wanted to ask about the recommended workflow for long continuous structures.

I have tried using nnInteractive, and while it is a very impressive tool, I am not sure if I am using it in the best way for this type of task.

The main issue I encounter is that the aorta is a long continuous structure. When I add prompts in the lower part of the vessel, sometimes the upper part changes or even disappears. After several prompts, it also becomes difficult to understand which region has been updated, expanded, or reduced.

At the moment, my practical workflow is to use nnInteractive once to get an initial segmentation, and then continue with manual editing. However, I feel I may be missing a better workflow.

Is this behavior expected for long structures like the aorta? Have others seen similar issues before? Is there a recommended workflow to avoid overwriting or losing previously segmented regions while refining the segmentation?

Any suggestions or workflow advice would be greatly appreciated.

Best,
Harry

Paul Yushkevich

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4:02 AM (2 hours ago) 4:02 AM

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Hi Harry,

I've also noticed that nnInteractive works best for structures that can be segmented in a few clicks. Have you tried using different labels for different parts of the aorta and then merging the different labels into a single segmentation using the 3D scalpel tool?