Density and surface area of a segment on a single axial cut

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1

Hello everyone!

I am new to the 3d slicer software and its powerful features.

I am currently planning a research project and have been successful in running totalsegmentator to segment tissues I am interested in. I have now to get the density and surface area of the segmented tissues I generate on a single axial cut. Can anyone please provide with simple, beginner-level, instructions on how to do so?

Thanks in advance!

2

Hi! You can run “Segment Statistics” for your quantification based on label maps, the corresponding Scalar Volume and Closed Surface.
documentation: Segment statistics — 3D Slicer documentation
Hope this help.

3

Hello!

Thank you so much for your reply!
It really means a lot.

I checked the link and the segment statistics extension. However, it gives values for the whole segment, while what I need are surface area and density for the segment on a single axial slice.

To note, the link mentions, Segment Cross-Section Area module in Sandbox extension for the cross sectional area of a segment on axial images, which is fair because I tried it and it works. However, is there any similar thing for the density?

Thanks in advance.

4

Hello, you can try SementGeometry mudule(which also has cross-sectional area included) to compute Mean brightness of each slice of a segmentation.

5

Thank you again for your reply!

The issue with SegmentGeometry is that it generates the information for each segment alone. Is there a way to generate the density for multiple segments at once (like in the Segment Cross-Section area module)?

6

Hi, don’t know if there is such a module that meets your needs. The method I can think of is to merge all the segments into one (using the Logical Operators tool in the Segment Editor) , or, if possible, do some Python programming to perform the measurement.