Your brain stem is the lower part of your brain that connects to your spinal cord.MRI stands for magnetic resonance imaging. It uses strong magnets and radio waves to take pictures of the inside of your body. Doctors often use MRI to look at the brain and spine. In this case, the doctor is using MRI to take a picture of the brain stem without any dye. Dye is sometimes used during MRI to help make the images clearer. But in this case, the doctor wants to take a picture of the brain stem without dye.