I have currently been using 3D slicer to segment sarcopenia from CT scans. I use the tissue type segmentation task on Total Segmentator Extension and look at the skeletal muscle. I was able to figure out how to calculate the volume of the segmentations in 3D slicer using Segment statistics, but I was wondering if there was a way to capture the volume statistics of the segmentation at a single slice/scene of the CT scan on 3D slicer? As I am looking at sarcopenia, I’m trying to find the volume of segmentation at a particular area of the CT scan (L3). If anyone has any suggestions or solutions or questions, I will gladly elaborate on them, and it will be greatly appreciated!
Thank you so much! I downloaded the extension and I see the segment cross section area chart display but how do I get the CT scan slices displayed in the left top corner of your image? Also, by using this module, will I be able to save a singular slice with the segmentation and be to calculate the volume from that single slice?
Click the eye icon on the side view controller (buttons at the top of slice views).
It is much better than that. You get all the slice cross-sectional areas in a table (git can see it in Tables module or save the scene and open the table in Excel). To get the volume you multiply the surface area with the slice spacing.
