Operating system: mac os
Slicer version: 5.6.2
Expected behavior: grow from seed only segments parts of the brain without the background
Actual behavior: grow from seed segments the background in a rectangle form.
Hi!
Segmenting brain CT: painting then using grow from seed. I am surely not putting painted points in the background. And regardless this all, a rectangle appears in the color of one of my segments, or the whole background become part of my segment. Mostly of the darkest segment.
I set the background to -10000 but the issue persists. How could I resolve this issue?
This is a known issue with Grow from Seeds on brain CT, the algorithm leaks into the background because CT background intensities overlap with certain brain regions. Setting background to -10000 alone won’t fix it, the solution involves a specific masking step before running the segmentation.
Completely fixable though. I work with Slicer segmentation professionally you can dm me.
Thank you very much for your offer! I solved the issue by painting(segmenting) the background too, then when I exported the segments as labels, set the background to invisible. It seems successful for my current task for now.
Segmenting part of the image is a designed feature of the module, to reduce memory/computation. Roughly, after you draws the seeds (both target and background), the algorithm computes a bounding box of from those seeds and crop a box out from the original image. It only segment in the cropped image. If the more seeds are added later in the interaction step, the box can be enlarged.
