Magnetic Resonance Imaging (MRI) including structural and functional neuroimaging has been applied extensively to examine response to antipsychotic treatment, however, questions remain regarding the interaction between these measurements and their unique role. Our study provided a comprehensive examination of interaction and contribution for voxel-wise measurements related with treatment response. We found that brain functional measurements in certain brain regions have advantages in predicting treatment response. Furthermore, the functional activities were different between short- and long-term treatment of antipsychotic drugs. These findings revealed that functional changes were more sensitive to the antipsychotic treatment and could be promising biomarkers in treatment prediction.