After changing battery in my 2007 Toyota Sienna many of the features of the car no longer work. Help?

If the car starts then the battery is hooked up correctly. This is what you need to do. Turn the key to the on position (not start) and input the code into the radio. Once the code is accepted it will restore all other functions. The car comes equipped with a anti-theft system when power is lost to the radio or another component the car think it is being stolen and won't move. This type of anti-theft system is called an immobilizer