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Transcranial magnetic stimulation (TMS) is a noninvasive method to stimulate the cortex. In TMS with a figure-of-eight coil, the induced electric field elicited by the pulsed magnetic fields is gathered beneath the center of the figure-of-eight coil, so the point on the cortex beneath the center of the figure-of-eight coil has been regarded as a stimulating site conventionally. However, the stimulating point determined in this way is not supposed to be plausible because electric field induced in TMS is dispersed over the brain vectorially. The present study proposed the novel method for the accurate estimation of stimulating points of the cortex in TMS. In our proposed method, the cortical structure and property of neural excitation in magnetic nerve stimulation were taken into account. The basic unit of the cerebral cortex is the cylindrical column containing pyramidal neurons perpendicular to the cortical surface, and neural excitation in the magnetic nerve stimulation is determined by the spatial derivative of the electric field parallel to the cablelike neuron such as a pyramidal neuron. According to these understandings, the relative intensity of nerve stimulation in TMS corresponds to the strength of the component of the induced electrical field perpendicular to the cortical surface. We realized the method for the estimation of stimulating sites of the cortex in TMS by using this principle. The component of the electric field perpendicular to the cortical surface at each pixel of magnetic resonance imaging was obtained with computation of the dot product of the electric field and the unit vector perpendicular to the cortex surface. The strength of the component of the electric field perpendicular to the cortical surface was regarded as the stimulating strength at each pixel of the cortical surface in TMS. We conducted the experiments of TMS to confirm the validity of this method. The cortex sites, which innervate muscles of the upper limb, were successfully de- lineated in primary motor area by the proposed method.