search

wasserth / TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images
Apache License 2.0
1.42k stars 239 forks source link

Segmentation noise #230

Closed lvonasek closed 10 months ago

lvonasek commented 10 months ago

Hello, I tried to overlap the segmentations over the original images but it contains noise: 24

Are there any plans to improve the ML model on this topic? In 3D the noise is not visible because it is inside of the organs.

The script+data I used: https://github.com/lvonasek/Dicom2ColoredOBJ

wasserth commented 10 months ago

Can you share the dataset where this happens so I can try to reproduce the issue?

lvonasek commented 10 months ago

Of course https://github.com/lvonasek/Dicom2ColoredOBJ/tree/main/demo_data

wasserth commented 10 months ago

When running TotalSegmentator -i demo_data -o seg I get good segmentations without any holes. Is it maybe a problem with how you display the masks?

lvonasek commented 10 months ago

That is possible. I will take a deeper look into it over the weekend.

lvonasek commented 10 months ago

You were right, the problem was on my side (fixed by https://github.com/lvonasek/Dicom2ColoredOBJ/commit/5dd52a6a033951a59794c8e0892a23667bd14964).

Now the output looks like this: 24