the way my doc explained it was a bone scan shows you where, the CT scan shows what.
thats to say the bone scan simply shows where your body is reproducing bone. helpful with stress fractures. i had one to show WHERE to get the CT scan of my back
a bone scan will probably not diagnose you, but I suppose it could in the case of stress fractures. instead, it will tell your dr where to do the CT (mine didn't want to CT my whole lumbar spine)
the CT scan gives more of a 3D view of your bones. for example, after my friend broke her neck, they did CTs every month or so to see if the vertebrae was still tilted.
neither one is in the least bit painful.