Unfortunately, this is a common image acquisition problem. See for example this discussion. Maybe imaging techs don’t know that such scans are not well suited for 3D reconstruction or high-resolution 3D reconstruction is not a priority.
Anyway, you can address this by forcing the segmentation’s internal labelmap representation to have isotropic voxel spacing.
Example: Bone segmentation with thresholding. 3D surface representation is created with surface smoothing disabled, master volume’s interpolation is disabled to see voxel boundaries more clearly.
Using the master volume’s spacing (0.7 x 0.7 x 2.5):
Enable “Isotropic spacing” in the segmentation geometry window (resulting spacing: 0.7 x 0.7 x 0.7) and then re-thresholding (see how blocky the master volume is and how smooth the segmentation(:
After applying Smoothing effect (method: Closing; Kernel size: 5x5x5 pixels) and enabling surface smoothing (factor=0.5):