Statistical model-based approaches for functional connectivity analysis of neuroimaging data

•Frames the literature on functional connectivity in terms of statistical models.•Differentiates between directed versus undirected and static versus dynamic.•Broad coverage of methods applicable to fMRI, EEG, and MEG neuroimaging modalities.•Reviews statistical models of neural signals in the time and frequency domains.•Discusses challenges of model selection, testing, and cross-frequency analyses.