The validity of functional magnetic resonance imaging (FMRI) brain maps with respect to the sites of neuronal activation is still unknown. One source of localization error may be pixels with large signal amplitudes, since such pixels may be expected to overlie large vessels, running remote from the centre of neuronal activation. In this study, magnetoencephalography was used to determine the centre of neuronal activation in a simple finger tapping task. The localization accuracy of conventional FMRI depending on FMRI signal enhancement was investigated relative to the magnetoencephalography reference. The results show a deterioration of FMRI localization with increasing signal amplitude related to increased contributions from large vessels. We conclude that FMRI data analysis should exclude large signal amplitudes and that magnetoencephalography may help to improve FMRI brain mapping results in a multimethod approach.