Psychiatry established itself as an academic discipline in the last quarter of the nineteenth century. Emil Kraepelin strongly advocated the clinical method, which prioritised clinical phenotype, course of illness and outcome for psychiatric nosology. He rejected brain-based models of mental illness but imagined that emerging neuroscience methods will reveal disease mechanisms. The introduction of in-vivo neuroimaging methods, including computed tomography (CT) and magnetic resonance imaging (MRI), greatly accelerated the biological revolution of psychiatry in the last quarter of the twentieth century. But brain images devolved into pictorial icons and the broken brain became metaphor, not mechanism. An interactive form of pluralism is needed to fully realise the potential of neuroimaging methods in our efforts to understand mental illness by studying the brain.