Can I do two circuits on 12/3 and still have GFCI?

I'm thinking about running a single 12/3 cable to my garage to wires all of the outlets (8 or 9). (This is old construction, with a finished ceiling.) I understand that the black and red wires will create two circuits fed by a double-pole breaker. Will I still be able to install GFCI outlets at the beginning of each wall run? I've read that a GFCI breaker may be needed. I haven't decided if I'll do every other receptacle or the tops of all receptacles on one circuit and the bottoms on the other. By the way, each wall will likely be fed by its own cable, going back to a junction box.