Gap between segments in 3D view

[jamesobutler (James Butler)]

Statistics is based on the segmentation labelmap as you are seeing in the 2D slice view. What you’re showing in the 3D view is the segmentation with a smoothing factor applied for display purposes only. It is not removing actual features in the segmentation.

See the below post from another thread

What's the different between show3D smooth and the segment's smooth?

Surface smoothing is required for reconstructing a continuous surface mesh from discrete samples stored in a labelmap volume. This smoothing does not remove any details from the segmentation. If you set surface smoothing to 0 then you will see the discrete samples instead of the reconstructed surface (each voxel of the labelmap will appear as a cube). Smoothing effect is for removing irrelevant details (i.e., surface noise, speckled, small holes) from the segmentation.