A unified framework for dissecting the effects of common signals on functional and effective connectivity analyses: power, coherence, and Granger causality

When analyzing neural data it is important to consider the limitations of the particular experimental setup. An enduring issue in the context of electrophysiology is the presence of common signals. For example a non-silent reference electrode adds a common signal across all recorded data and this adversely affects functional and effective connectivity analysis. To address the common signals problem, a number of methods have been proposed, but relatively few detailed investigations have been carried out. We address this gap by analyzing local field potentials recorded from the small brains of fruit flies. We conduct our analysis following a solid mathematical framework that allows us to make precise predictions regarding the nature of the common signals. We demonstrate how a framework that jointly analyzes power, coherence and quantities from the Granger causality framework allows us to detect and assess the nature of the common signals. Our analysis revealed substantial common signals in our data, in part due to a non-silent reference electrode. We further show that subtracting spatially adjacent signals (bipolar rereferencing) largely removes the effects of the common signals. However, in some special cases this operation itself introduces a common signal. The mathematical framework and analysis pipeline we present can readily be used by others to detect and assess the nature of the common signals in their data, thereby reducing the chance of misinterpreting the results of functional and effective connectivity analysis.