We give recommendations regarding the combined EEG+MEG source estimation in our 2019 article about group analysis, but indeed this is missing from the online tutorials:
Magnetoencephalography and EEG sensor data can be processed jointly to produce combined source estimates. Joint processing presents unique challenges because EEG and MEG use head models that exhibit differing sensitivities to modeling errors, which can in turn lead to inconsistencies between EEG and MEG with respect to the (common) source model. In practice joint processing is relatively rare (Baillet et al., 1999). However, these data are complementary, which means that joint processing can potentially yield insights that cannot be seen with either modality alone. For example, in the evoked responses in the data set used here, the first peak over the occipital areas is observed in MEG (90 ms) slightly before EEG (110 ms). This delay is too large to be caused by acquisition imprecisions. This indicates that we are not capturing the same brain processes with the two modalities, possibly because the orientation and type of activity in the underlying cortical sources is different. MEG and EEG have different sensitivities to source orientation and depth. Given the challenges of joint processing, our advice is to first look at the source reconstructions for the two modalities separately before trying to use any type of fusion technique. In the following, since our goal is to illustrate an end-to-end processing pipeline rather than comprehensively demonstrate all of Brainstorm’s features, we restrict our inverse results to MEG-only processing and do not present results either for EEG alone or joint MEG/EEG processing.