Your brain and muscles communicate especially during exercise. During intense exercise, your muscles release markers of muscle damage which travel to the brain. The brain then releases specific signals that increase your feelings of fatigue. This interchange between brain and muscle serves as a protective function so you don't severely damage your muscles.
A recent study found that there are other communication pathways between the brain and muscles which involve emotions. In a sophisticated study, researchers had individuals undergo a functional MRI following different intensities of exercise. A functional MRI allows scientists to determine what areas of the brain are influenced by specific activities. Subjects performed either a low or high intensity exercise regimen followed by a functional MRI. Following low intensity exercise, areas of the brain responsible for cognitive control and attention processing were stimulated – in other words decision making. Following high intensity exercise, different areas of the brain were stimulated – areas responsible for fatigue and affective processing which relate more to emotion.
The bottom line – high intensity exercise increased those brain networks related to emotional processes and also decreased activity networks associated with motor function. Low intensity exercise increased cognitive and attention processing. This was the first study to relate exercise intensity to differential effects on the brain.