Recent advances in MRI have provided the opportunity to map changes in hemodynamics that correspond to cognitive and sensory operations. These advances in noninvasive, low-risk, imaging environments have extended the traditional role of medical imaging into new domains that include investigations into the interplay between brain anatomy, physiology, and function. This interplay is mandatory for examination of the complex effects of diffuse damage caused by traumatic brain injury. Functional MRI (fMRI) provides relatively high-resolution indirect assessment of neuronal activity. Three main factors interact to affect the quality of fMRI data that is acquired: (1) MRI hardware, (2) the paradigm (or experimental) design, and (3) subject cooperation. This article focuses on paradigm design and subject cooperation.