ga / wa

Q:Kibun wa do desu ka? A:Atama ga itai desu. Do questions use the topic particle instead of the subject particle? Would "Atama wa itai desu" sound odd?

In this situation, it should be "ga". Because up until this person mentions "atama", they were not talking ABOUT the head. They are talking ABOUT "how he/she's feeling." For you information, "wa" is the topic particle and "ga" is the subject particle. :D