Repetitive transcranial magnetic stimulation (rTMS) has been increasingly explored for many neurological and neuropsychiatric conditions. However, the response rate is variable depending on baseline conditions. Optimizing rTMS protocols to improve treatment effects and response rates will depend on reliably assessing brain state conditions. In this regard, neural activity guided optimization has shown potential in several neuroimaging studies. In this paper, we present our ongoing work on optimizing rTMS treatment of a balance disorder called Mal de Debarquement Syndrome (MdDS), a motion perception disorder caused by entrainment to background motion. Our previous work has revealed that a neuroimaging marker of resting state functional connectivity may help predict therapeutic effect. Motivated by our previous pilot study with fMRI, the present study aims to extend the investigation to EEG data that were simultaneously acquired with fMRI, with the aim of transferring the fMRI imaging marker to a more accessible neural recording technology. Our current findings demonstrate that integrating EEG with fMRI measures of neural synchrony and functional connectivity may hold promise in optimizing rTMS protocols.