Binary labelmaps approximate the shape at a given resolution. When you build a 3D representation it will look more spherical. If it’s not high enough resolution you can increase the resolution of the segmentation (Segment editor — 3D Slicer documentation). If you really want precise spheres or circles you could try some kind of parametric technique but usually that isn’t the best approach.
Also note that you can segment these spheres or tubes fully automatically by using
- Threshold effect, followed by
- Islands effect → Split islands to segments
Thanks for your help!