Functional neuroimaging technologies are increasingly being used to predict cognitive/behavioral outcomes after the initiation of clinical interventions such as resective surgery or cognitive rehabilitation. We provide a conceptual model and a case example to explain how the results from various neuroimaging techniques can be integrated to answer important questions about clinical recovery such as whether neural reorganization has occurred and, if so, the type of adaptive cognitive mechanism driving this reorganization. This proposed framework and its use in interpreting neuroimaging outcomes studies should help uncover the principles that govern neural reorganization, and be of use to any patient for whom the risk, or potential benefit, of brain-based interventions is unknown.