Functional near-infrared spectroscopy (fNIRS) has been applied to study of brain oxygenation and metabolism. In this study, we aimed to investigate the partial correlation (PC) in fNIRS signals on functional connectivity in the prefrontal cortex (PFC) during a modified version of the color-word matching Stroop task. A continuous wave 16 channels near-infrared spectroscopy device (ARGES Cerebro, Hemosoft Inc., Turkey) was used to measure the changes in HbO2 and Hb concentrations from 12 healthy volunteers. Partial correlation (PC) values were computed for each stimulus condition. The results of ANOVA test (p < 0.05) in HbO2 and Hb signals indicate the bilateral connections between two brain hemispheres. The partial correlation analysis, by removing the common effect of channel interference, offers a suitable measure to evaluate the performance of the prefrontal cortex. Also, the results of partial correlation showed that compared to Hb signal, HbO2 signal is more sensitive to brain activities. This study suggests that fNIRS is a valuable tool for demonstrating the relationship between cortical function in complex cognitive activities. (C) 2016 Elsevier GmbH. All rights reserved.