I’m trying to segment the upper airway but having difficulties as the thresholds I’ve been trying out either a) don’t capture all the air (as in the picture of the nasal cavity in green), or b) capture too much of the surrounding tissue (picture in yellow).
I’ve tried increasing the spacing using crop volume, and different methods of segmenting (starting with air and using operators to extract, and wrapsolidify to get the internal surface of the surrounding tissue).
Anything i can do to more accurately capture the air ?
Maybe you can try to add the regions you need with “Use for Masking”, in the Threshold effect, adding the value you need to obtain, activating the Sphere Brush, and simply paint those little spaces. Is an easy way to do fine work just painting over. It will only let you paint the values you need and nothing else.
Hello
I would recommend changing the approach to the following instead of using thresholds.
Change the volume to Air. So you get a more clear image of air and tissue. There are two presets, lung and air. I would prefer air.
Resampling if needed. For this case, Linear is somewhat more practical. However, others may recommend using a different interpolation. I wouldn’t go anything less than 0.5 and somewhere from 0.5 to .75 seems okay. Try to crop the image to save time and reduce RAM space.
Chest Imaging Platform. You can use CIP to get a segment of tissue and air.
Please consider the fact that if you are resampling, CIP doesn’t work properly and you need to run a linear transform to overlap your segment and image.
If you only need the nasal cavity, use TotalSegmentator. If you have a CUDA-enabled system, consider using it. It will save you lots of time.
Please let me know if you need more help with any of these steps.
Thanks so much, this is really helpful ! I tried this, and it does a pretty good job, but still not capturing only the airway. Maybe i’m using the wrong segmentation tool under the CIP ? (Interactive lobe segmentation, where i placed fiduciaries for one fissure and then ran the script).
You can see the result in the picture below. The red arrows show to some of the walls inside the nasal cavity that shouldn’t be part of the segment and this blank band in a circle that is somehow missed a few times during the segmentation. Appreciate any tips on this !
Hello
In the CIP, please use the Simple Lung Mask.
Consider this that most probably the segments you receive will not overlap with your image and you need to use to a Transform to overlap these two. These has already been addressed to @lassoan
Just one more thing to add. Getting a very high detail segment of the airway requiring no adjustments is close to impossible. Using these modules and extensions will speed up your process. This from my experience but others might have a solution to this.
