This work considers electrical impedance tomography imaging of the human head, with the ultimate goal of locating and classifying a stroke in emergency care. One of the main difficulties in the envisioned application is that the electrode locations and the shape of the head are not precisely known, leading to significant imaging artifacts due to impedance tomography being sensitive to modeling errors. In this study, the natural variations in the geometry of the head and skull are modeled based on a library of head anatomies. The effect of these variations, as well as that of misplaced electrodes, on (absolute) impedance tomography measurements is in turn modeled by the approximation error method. This enables reliably reconstructing the conductivity perturbation caused by the stroke in an average head model, instead of the actual head, relative to its average conductivity levels. The functionality of a certain edge-preferring reconstruction algorithm for locating the stroke is demonstrated via numerical experiments based on simulated three-dimensional data.