Recent neuroscientific findings suggest that functional magnetic resonance imaging (fMRI)-based brain–computer interfaces may be a viable strategy for detecting covert awareness in patients clinically diagnosed as being in a vegetative state. This research may open a promising new avenue for developing neuroimaging techniques that provide prognostic and diagnostic information that complements current behavioral tests for assessing disorders of consciousness, thereby increasing the effectiveness of diagnostic screening. These techniques may also permit patients who are behaviorally nonresponsive yet retain high levels of preserved cognition to meaningfully engage in clinical decision making. Before this application can occur, certain ethical issues associated with decision-making capacity must be addressed. Although it is not currently possible to assess decision-making capacity through neuroimaging methods, it may be in the future, provided that certain conceptual and empirical steps are taken to demonstrate that brain–computer interfaces satisfy requisite criteria of capacity assessment. In this article we lay out the conceptual foundations for a mechanistic explanation of capacity that would allow the necessary empirical steps for incorporating neuroimaging techniques into the standard capacity assessment battery utilized in clinical practice.