OBJECTIVE: Transcranial magnetic stimulation (TMS) activates brain structures non-invasively. Computational models can be used to elucidate the activation site; however, the exact activation site is controversial. The aim is to present an imaging technique of the TMS activation cortical site estimation using individualized multi-scale realistic head models based on experimentally-derived TMS fields. APPROACH: The induced electric field (EF) was computed using subject-specific head models and experimental-specific TMS coil configuration during suprathreshold stimulation for relaxed muscles. The experimentally-derived EFs were used to calculate the activation of pyramidal tract model embedded in the head models to derive the activation site on the cortical surface at the macroscopic level. MAIN RESULTS: The TMS activation site was located at the anterior wall of the central sulcus, which agreed with a concurrent TMS/fMRI study. In contrast, the EF strength was not entirely consistent with TMS/fMRI studies. Multiscale physical modelling is a feasible imaging technique to investigate the activation site for TMS. SIGNIFICANCE: By combining subject-specific multiscale modelling with experimental TMS measurements, we showed that this method could serve as a TMS imaging technique at suprathreshold condition.