The simplest thing would be to input a set of slices filled with zeros that will fill the gap between the two half-brains. If the gap is an integral multiple of the slice thickness, this is not too hard (e.g., if you have 5 mm slices and a 15 mm gap, you need 3 all-zero slices to fill in). If not (e.g., 5 mm slices but a 16 mm gap), then it is also possible, but requires more work. Please provide more details about your particular case, including the format of your data and sample filenames, and I'll be able to help get you going.
AFNI is set up to deal with data defined over a single rectangular grid.
bob cox
