Hi Soo Hyun,

Adding on a little here with some more suggestions:

1. Attaching labels to volumes. Besides copying labels from one dataset to another, you can also make new labeltables with @MakeLabelTable. The labels can be a little more complicated with centers associated with regions and available through whereami with @Atlasize. You only need a text file with index numbers and region labels.
2. Surface to volume irregularities. Consider the @surf_to_vol_spackle program. The process of projecting from the surface to the volume can leave holes in the volume because the projection occurs over line segments (either between surfaces or from normal vectors). This program will iteratively fill a mask volume to patch the remaining holes.
3. Boundary edges. If the problem is just edges of the regions when you are viewing the overlay grid over a different underlay grid, e.g. if the datasets have different resolutions, then that might come about from the overlay interpolation. NN (nearest neighbor) interpolation usually works well, but there might be subtle differences between grids. Try the linear interpolation instead, but that will give you interpolated ROI values on the edges.