Magnetic resonance (MR) methods are widely available on medicine and physiology. The combination of magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) allow the noninvasive investigation of anatomy, physiology and biochemical processes in living animals and humans. Examples of the 3-nitropropionic acid-intoxicated animal model are given to demonstrate the application of MR methods for the investigation of neurodegenerative disease. The MR methods demonstrated here can also be applied for the diagnosis of many neurological diseases, and provide possible therapeutic strategies in the future.