Echo-planar imaging is a common technique used in functional magnetic resonance imaging (fMRI); however, it suffers from image distortion and signal loss because of large susceptibility effects that are related to the phase-encoding direction of the scan. Despite this relation, the majority of neuroimaging studies has not considered the influence of phase-encoding direction. Here, we aimed to clarify how phase-encoding direction can affect the outcome of an fMRI connectivity study of schizophrenia (SCZ).