Get into the car (using the key), put the key in the ignition, turn the ignition halfway, to the point where you can turn on some of the electronics in the car, but one level before where the engine starts to turn over. While the ignition is in that state, press the button on your remote fob that is usually used to unlock the car. This should synchronise the remote's frequency with the car (which was cleared when the battery went dead). If you have two remotes, you will need to do this with both remotes.