Neurobiological investigations of empathy often support an embodied simulation account. Using functional magnetic resonance imaging (fMRI), we monitored statistical associations between brain activations indicating self-focused threat to those indicating threats to a familiar friend or an unfamiliar stranger. Results in regions such as the anterior insula, putamen and supramarginal gyrus indicate that self-focused threat activations are robustly correlated with friend-focused threat activations but not stranger-focused threat activations. These results suggest that one of the defining features of human social bonding may be increasing levels of overlap between neural representations of self and other. This article presents a novel and important methodological approach to fMRI empathy studies, which informs how differences in brain activation can be detected in such studies and how covariate approaches can provide novel and important information regarding the brain and empathy.