This tutorial by André M. Bastos and Jan-Mathijs Schoffelen reviews and summarizes current methods used in electrophysiology to study functional connectivity, both in invasive and non-invasive settings. The authors provide an intuitive understanding of various metrics for functional connectivity, including coherence, phase synchronization, phase-slope index, and Granger causality. They highlight common interpretational pitfalls such as the common reference problem, signal-to-noise ratio issues, volume conduction problems, common input problems, and sample size bias. These pitfalls are illustrated through MATLAB scripts that simulate potential issues, providing practical steps to address them. The tutorial also discusses the limitations of current methods and suggests future directions for improvement. The review covers a taxonomy of functional connectivity metrics, their mathematical foundations, and their applications in different contexts, emphasizing the importance of choosing appropriate methods based on the underlying hypothesis.This tutorial by André M. Bastos and Jan-Mathijs Schoffelen reviews and summarizes current methods used in electrophysiology to study functional connectivity, both in invasive and non-invasive settings. The authors provide an intuitive understanding of various metrics for functional connectivity, including coherence, phase synchronization, phase-slope index, and Granger causality. They highlight common interpretational pitfalls such as the common reference problem, signal-to-noise ratio issues, volume conduction problems, common input problems, and sample size bias. These pitfalls are illustrated through MATLAB scripts that simulate potential issues, providing practical steps to address them. The tutorial also discusses the limitations of current methods and suggests future directions for improvement. The review covers a taxonomy of functional connectivity metrics, their mathematical foundations, and their applications in different contexts, emphasizing the importance of choosing appropriate methods based on the underlying hypothesis.