I’m tasked with creating a model of the airways, down to the smallest possible viewing distance. The initial study is an HRCT of the lungs. I used the “Lung CT Segmenter” tool with the “Airway segmentation,” “Use AI,” and “High detail” options. As a result, I achieved very good segmentation of the airways, but with the lungs included. I’ve attached a preview of the model with transparency enabled. How can I “remove the lungs” from this model while retaining the airways? Is there a way to do this in Slicer, or do I need to find another tool? Any ideas on how to do this?
In this 3D rendering it looks like that you have a lung segment and an airways segment, both yellow. You can delete the lung segment if you don’t need it.
If you only have one segment then this rendering is very misleading. Attach a few screenshot of the slice views. If you have multiple segments then make sure each has a distinct color.
Unfortunately, this is just one segment, so there’s nothing to subtract
I’ll anonymize the data and share the entire project; maybe you’ll figure out how to do it correctly.
I can use other tools to create the airways, but I can’t get any further than the lobar bronchi. The Lung Segmenter can go deeper, but it connects the lungs to the airways.
You can’t really remove the lungs, because they are part of the segmentation. (you can try to further threshold the lowest range, but i suspect you will also loose details).
If you want to make the internal branches more prominent without altering the segmentation so that they are not occluded by lungs, then I think you want to explore Colorize Volume module in the Sandbox extension, which gives you more control over visualizations than surface based rendering in the segment editor.
Does this look more similar to what you want to do? I also probably use a slightly darker color than this light blue. You will probably have bit more contrast that way.
@lassoan I also encountered this error in the Colorize Volume. So we are limited to 16 segments max?
Links failed: ERROR: Implementation limit of 16 active fragment shader samplers (e.g., maximum number of supported image units) exceeded, fragment shader uses 18 samplers
Thanks for the tip, but I’m not interested in the visualization you can get with the colorization module. I can do that, and I’m familiar with this solution (very useful, by the way). The problem is that my surgeons are very insistent on creating a model with as many airway branches as possible, even down to the level of the segmental bronchi. While segmenting and modeling down to the level of the lobar bronchi is easy, I still can’t segment. Only in the Lung CT module… do I see further branches, but they’re connected to the lungs. And that’s a problem that needs to be solved.
Excuse my English, I work with a translator and sometimes write nonsense
