By hands? Yes. You can compile rom for gateway even if you have only unpacked game resources. But this compiled rom will have nothing in common with the original cartridge dump.you can convert CIA to 3DS for GW, just there's no easy way to since its not common or something. CIA is an entirely different format, not just a "cutted" .3ds
.cia is different format, of course, but .cia files converted from .3ds cartridge dumps is just a cut off.