Lung segmentation - extra segment outsize the body mass

[stergioc]

Dear @JoHof,

thanks for sharing this work. I am posting this issue just because it seems like a simple fix that can increase the robustness of the whole pipeline. While checking the performance on some scans I figured than in some cases, the model produced an additional segment outside of the body mass along with the left/right labels. I found cases with both 1 and 2 as label for this extra segment. Here is an example:

I would guess that a simple counting of the connected components in the final segmentation could fix this issue.

[JoHof]

Hi,

thanks for reporting this. That's weird, post-processing should take care of this. Are you eventually using an older version? Otherwise this is a bug. Could you eventually share such a case?

[stergioc]

Hello, I am indeed using the latest version lungmask==0.2.3. Looking a bit closer to the intermediate results it seems that the problem can be identified after this line:

lungmask/lungmask/utils.py

Line 200 in 1018e41

regionmask = skimage.measure.label(label_image > 0)

in the case that the left/right lung are touching then they both belong to the same label mask and therefore the second largest region is outside of the lung region.

I hope this helps.

[JoHof]

Absolutely! Thank you so much! Will fix that shortly...

[JoHof]

Should be fixed. Let me know if there are any other issues...

[stergioc]

Indeed it is fixed for the examples I checked. Cool 👌