Abstract

A major challenge in systems neuroscience is understanding how external perturbations interact with ongoing brain activity. Transcranial magnetic stimulation (TMS), increasingly used in both basic and clinical neuroscience and often combined with electroencephalography (EEG), provides a unique opportunity to probe this interaction. However, how intrinsic dynamics constrain the propagation of TMS-evoked activity remains poorly understood. In particular, effective connectivity (EC)--capturing directed, state-dependent interactions between brain regions--is thought to critically shape perturbational spread, yet remains difficult to estimate at the whole-brain EEG level. Here we introduce an analytically tractable, generative whole-brain model that links spontaneous EEG activity to cortical responses under perturbation. By deriving a closed-form expression for the model's cross-spectral density, we directly fit empirical resting-state EEG spectra and infer biophysically interpretable local dynamical parameters without time-domain simulations. We then estimate stimulation-site-specific EC using only a small fraction of the TMS-EEG trials. The resulting model accurately predicts the spatiotemporal structure of TMS-evoked potentials (TEPs) in unseen trials. Moreover, even without subject-specific refitting, group-level EC templates capture canonical site-specific propagation motifs underlying single-subject early TMS responses. Together, our results establish an analytical framework for individualized whole-brain modeling of TMS-EEG with potential applicability to model-based neuromodulation.