Segmentation issue

Support
1

Operating system: Windows 10
Slicer version: 4.1120200903
Expected behavior: segmentation
Actual behavior:

I have a CT scan with contrast. The scanning has been performed as a bolus tracking scan to maximize interaterial contrast. I want to segment bones, aterial vessels and kidneys in the abdominal region.
I start with defining one segment R_kidney. I then use segmentation = (threshold, smooting and keep largest part) to isolate the above organs. I the define a new box segment around the kidney using scissors. I the try to use logical operation intersect to select the kidney. But this operation just cuts out the kidney or actual the whole box area of the R_kidney. My next approach was to use the scissors to cut out the R_kidney. Then I define the L_kidney segment and do the above segmentation again. But when I cut out the left kidney, the R_kidney segment is also cleared.
Next approach was to do each segment once at at time and the convert into volumes. I the succeded to create R_kidney, L_kidney and bone. I now want to subtract theese volumes from the last segment aterial vessels, to get the vessels only. But I cannot select the volumes in the logical operations?
So my question is how can I do this? And I suspect there must be an easier way to do this than my somewhat cumbersome method above? I would love to hear suggestions.
Best
Carl_Slicer

2

If you want to reassign a part of an existing segment to a new segment, you can use Scissors effect with these settings:

  • Operation -> “Fill inside” (to not erase but paint instead)
  • Masking / Editable area -> Inside all segments (to not paint solid blocks but to keep the shape of already existing segments)

There are many other approaches, which may be even better. For example, using Grow from seeds effect and masking with editable intensity range, as described in this segmentation recipe: https://lassoan.github.io/SlicerSegmentationRecipes/AortaMaskedGrowFromSeeds/ (you can add more seeds, e.g., one for for each kidney).

3

Thanks a lot for a very fast reply to my question. I have tried the suggested approach, which is much faster than my previous approach. You answer also deepened my understanding of how 3D slicer works.
Thanks
Jesper

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