Muscle functional magnetic resonance imaging (MRI) refers to changes in the contrast properties of certain MR images that occur in exercising muscles. In part, these changes result indirectly from increased rates of cellular energy metabolism, which alter the image contrast properties by increasing the water content and by decreasing the intracellular pH. Also, increases in blood oxygen extraction cause a rapidly evolving, small, and negative contribution to signal. Together, these changes produce a complex time course of contrast changes during exercise. Analysis of this time course may provide insight into the physiology of exercising muscles. These contrast changes also provide a non-invasive method for determining the spatial pattern of muscle activation.