How to easily turn a hollow segmentation into a solid (blood pool) segmentation

Operating system: macOS Catalina 10.15.7
Slicer version: 4.11 20200930


I’m aware that it is possible to turn a hollow segmentation (e.g artery) into a solid (blood pool) version. This is done using the following:

  • Logical operators effect, Invert operation => Apply
  • Islands effect, Keep largest island => Apply

If I erase parts of my original segment, this technique no longer works, because the “invert” tool will still appliy over the original segment volume, meaning that the inverted segment will not be an isoltated island that can be removed using the “keep largest island” tool.

I want to know how to control the target volume of the “invert” tool. How can I adjust it so that it matches my modified segmentation which no longer has the same volume as it originally had?

I would recommend to delete the “bridges” at the opening of the vessel to isolate the vessel lumen from the background. You can use Paint or Scissors effect for this.

Hi Iassoan, could you clarify what you mean by “bridges”? Once I’ve inverted my model it becomes very hard to find the section I need to delete. Since my vessel is curved, I’m forced to make the modifications in the 3D window to be accurate.

You can make the segmentation semi-transparent so that you can clearly see all the vessel endpoints in the 3D view and you can snip the ends with Scissors effect.