The combined use of transcranial magnetic stimulation (TMS), electroencephalogram (EEG), and behavioral performance allows investigation of causal relationships between neural markers and their functional relevance across a number of perceptual and cognitive processes. Here, we present a protocol for combining and applying these techniques on human subjects. We describe correlation approach and causal approach to disentangle the role of different oscillatory parameters, namely alpha frequency and amplitude that control for accuracy and metacognitive abilities, respectively, in a visual detection task. For complete details on the use and execution of this protocol, please refer to Di Gregorio et al. (2022).