A Tutorial Review of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls

Abstract

Oscillatory neuronal activity may provide a mechanism for dynamic network coordination. Rhythmic neuronal interactions can be quantified using multiple metrics, each with their own advantages and disadvantages. This tutorial will review and summarize current analysis methods used in the field of invasive and non-invasive electrophysiology to study the dynamic connections between neuronal populations. First, we review metrics for functional connectivity, including coherence, phase synchronization, phase-slope index, and Granger causality, with the specific aim to provide an intuition for how these metrics work, as well as their quantitative definition. Next, we highlight a number of interpretational caveats and common pitfalls that can arise when performing functional connectivity analysis, including the common reference problem, the signal to noise ratio problem, the volume conduction problem, the common input problem, and the sample size bias problem. These pitfalls will be illustrated by presenting a set of MATLAB-scripts, which can be executed by the reader to simulate each of these potential problems. We discuss how these issues can be addressed using current methods.

Analysis of Functional Connectivity During an Auditory Oddball Task in Schizophrenia

“…The main advantage of ICOH is that it is able to remove instantaneous interactions, which may be spurious due to volume conduction, as it discards interactions at a phase difference of 0° or 180° [3]. It is, however, generally a small measure, which increases the risk of missing meaningful interactions [6].…”

“…Magnitude squared coherence (MSC) and the imaginary part of coherency (ICOH) are two non-directed measures that seek to capture independence and evaluate phase synchrony between signals [3]. MSC is a classical method that has been widely used in the literature.…”

“…MSC is a classical method that has been widely used in the literature. In contrast, ICOH is a novel measure that has gained some momentum over the past years in electroencephalographic (EEG) connectivity studies [3]. The aim of this study was to compute these two measures for SCH patients and healthy controls, in order to analyze abnormal coupling patterns in SCH.…”

Brain oscillations in language comprehension

“…Furthermore, oscillations may provide a mechanism for communication between spatially separated regions that can be reflected in functional and effective connectivity (Bastos & Schoffelen, 2015;Valdes-Sosa, Roebroeck, Daunizeau, & Friston, 2011) as well as graph theoretical measures (Bullmore & Sporns, 2009;Stam & Reijneveld, 2007).…”

Mechanisms underlying memory enhancement in humans

“…We calculated for each patient, condition and contact the absolute value of the iCoh and PLV at the theta frequency determined by the sliding method. Given that coherence and phase locking value measures suffer from bias when comparing conditions with different number of trials (Bastos & Schoffelen, 2015), we randomly selected the number of trials for the expected condition to match the unexpected and averaging across 500 randomizations for each subject. For each subject we ended up with iCoh and PLV measures both for within and between subregion contacts pairs (Table 12) …”