Functional neuro-imaging studies of Parkinson's disease (PD) patients and animal models show inconsistent cortical responses to sensory stimulation: some present increased sensorimotor cortex activation contradicting classical basal ganglia–cortex circuitry models, whereas others show decreased activation. As functional neuro-imaging activation is defined as the signal difference between stimulation ON and stimulation OFF, reduced ‘activation’ can point to either increased neuronal activity during stimulation ON or to decreased basal neuronal activity during stimulation OFF. A unique non-invasive method that uses the temporal and the spatial variances of functional magnetic resonance imaging signal is employed here to compare basal neuronal activity levels and ‘functional homogeneity’ between groups. Based on the assumption that the temporal variance reflects average neuronal activity, the variance of activity within a predefined region is defined as the region's ‘functional homogeneity’, which is assumed to estimate neuronal synchronization. Comparison of temporal and spatial variances of the sensorimotor cortex and the striatum in the 6-hydroxydopamine (6-OHDA) PD rat model and a control rat group show bilaterally decreased temporal and spatial variances in the 6-OHDA rat group, suggesting bilateral reduction of basal neuronal activity levels together with an increase in local neuronal synchronization in line with classical basal ganglia–cortex circuit models.