A functional connectivity (FC) analysis from resting-state functional MRI (rsfMRI) is gaining its popularity toward the clinical application such as diagnosis of neuropsychiatric disease. To delineate the brain networks from rsfMRI data, non-neuronal components including head motions and physiological artifacts mainly observed in cerebrospinal fluid (CSF), white matter (WM) along with a global brain signal have been regarded as nuisance variables in calculating the FC level. However, it is still unclear how the non-neuronal components can affect the performance toward diagnosis of neuropsychiatric disease. In this study, a systematic comparison of classification performance of schizophrenia patients was provided employing the partial correlation coefficients (CCs) as feature elements. Pair-wise partial CCs were calculated between brain regions, in which six combinatorial sets of nuisance variables were considered. The partial CCs were used as candidate feature elements followed by feature selection based on the statistical significance test between two groups in the training set. Once a linear support vector machine was trained using the selected features from the training set, the classification performance was evaluated using the features from the test set (i.e. leaveone- out cross validation scheme). From the results, the error rate using all non-neuronal components as nuisance variables (12.4%) was significantly lower than those using remaining combination of non-neuronal components as nuisance variables (13.8 ~ 20.0%). In conclusion, the non-neuronal components substantially degraded the automated diagnosis performance, which supports our hypothesis that the non-neuronal components are crucial in controlling the automated diagnosis performance of the neuropsychiatric disease using an fMRI modality.