I’m working with MR images of Fricke gel jars and trying to isolate each jar for analysis. I’m currently using the Crop Volume module in 3D Slicer, but it only lets me define a rectangular ROI. Since the jars are cylindrical, I’d like to crop each one using a circular (or cylindrical) ROI instead, to more accurately capture the region of interest and minimize background noise.
Is there a way to crop a volume in a circular shape, or apply a cylindrical mask for this purpose? I’ve attached a screenshot showing what I’m currently working with.
You can mask-out everything outside a cylinder with the following steps:
Install extension “Extra segment editor effects” using the Extensions Manager
Create a segmentation node for your volume in the Segment Editor module
Create a new segment
Use the “Draw tube” effect, and create a point at the top and another one at the bottom of the cylinder visible on your CT. Adjust the radius to cover the cylinder. Click apply.
Use “Mask volume” effect. Select “Fill outside”. Set fill value as “-1024”. Click apply
Check out that you should have a newer CT volume that only contains your cylinder
