The effects of TMS have been largely studied in the motor system, using motor evoked potentials (MEP) as the output. There is a large between-pulse variability in MEP’s, requiring multiple pulses and averaging. One potential source of the MEP variability might be the EEG phase cycle of the motor cortex relative to the TMS pulse. We have succeeded in performing TMS in the fMRI scanner with high fidelity EEG. As the first step in understanding whether the phase of a brain region matters with respect to the effect of a TMS pulse, we have started in motor system, using local and secondary BOLD response, and assessing whether the local alpha phase influences the TMS pulse impact.