afni.nimh.nih.gov

It seems to me you can do something more along the lines of Rick's suggestion then; smooth then with some program and only use the values for the holes. 3dmerge allows custom filters with "-1filter_expr" where you could compose a filter that does not include the voxel itself. It may be simpler to use a median filter, just replacing the hole voxels with the median value in the neighborhood. See "3dmerge -1filter_winsor", "3dLocalstat -stat median".