Owing to the nature of TMS-EEG, many of the initial challenges of combining these two powerful techniques were methodological: related to the non-neural consequences of applying TMS pulses whilst EEG is taking place simultaneously⁹. Significant process has since been made in dealing with these non-neural consequences — artefacts — produced by TMS pulses during EEG by carrying out data collection carefully, or by dealing with the TMS-induced artefact with offline processing techniques.

There are now a number of widely-known and used countermeasures to successfully avoid artefacts that are produced by applying TMS during EEG. Perhaps surprisingly, the biggest complication in conducting TMS-EEG studies is not related to the large electric field induced during TMS, but, rather, a result of the current induced within the scalp, which can be removed using independent components analysis (ICA), or minimised by carefully placing the TMS coil above a scalp location near the midline¹⁰.

Another unavoidable consequence of applying TMS during EEG recording is that the clicking sound produced by transcranial magnetic stimulation is measured by the EEG¹¹. This clicking sound can be masked, but careful attention must be paid to the acoustic waveform that is used to mask it: recent debates emphasise the critical important and ensuring that the sound is properly masked in TMS-EEG datasets^12,13 — something that can be achieved by mixing the time-varying frequency content of the clicking sound with white noise, for instance.

One final consideration when combining TMS and EEG is that some stimulators — particularly those delivering monophasic pulses — can produce a period of decay after a high-amplitude voltage measurement caused by a TMS pulse: some EEG caps contain rotatable TMS-EEG electrode leads that can minimise the duration of this decay.