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The analysis of Functional Connectivity (FC) is a key technique of fMRI, having been used to distinguish brain states and conditions. While many approaches to calculating FC are available, there have been few assessments of their differences, making it difficult to choose approaches, and compare results. Here, we assess the impact of methodological choices on discriminability, using a fully controlled data set of continuous active states involving basic visual and motor tasks, providing robust localized FC changes. We tested a range of anatomical and functional parcellations, including the AAL atlas, parcellations derived from the Human Connectome Project and Independent Component Analysis (ICA) of many dimensionalities. We measure amplitude, covariance, correlation, and regularized partial correlation under different temporal filtering choices. We evaluate features derived from these methods for discriminating states using MVPA. We find that multidimensional parcellations derived from functional data performed similarly, outperforming an anatomical atlas, with correlation and partial correlation (p 

Original publication




Journal article


Hum Brain Mapp

Publication Date





407 - 419


correlation, covariance, fMRI, functional connectivity, partial correlation, rfMRI, Adult, Brain, Connectome, Data Interpretation, Statistical, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Motor Activity, Visual Perception