The aim of this study was to evaluate changes in measured volumes using Statistical Parametric Mapping (SPM) 12 caused by contrast changes in magnetic resonance (MR) image. Twenty-one healthy subjects participated in the study. From all subjects, 3D T1-weighted images (T1WIs) were obtained using a 3T scanner. In the first step of creating reference volume data, we used SPM12 to binarize all the segmented data. In the second step, we assigned simulated 3D-T1WI signal intensities to each tissue image and used the following values. The last step was integration of each tissue image to generate 3D-T1WI simulated reference volume data for each participant. To create the reference 3D-T1WIs with various contrasts from the reference volume data, we varied the signal intensity of gray matter from 900 to 600, 700, 1100, 1300, and 1400. The reference 3D-T2WI was acquired using the method used for 3D-T1WIs. Then, six 3D-T1WIs were processed using intrasubject bias-correction processing with SPM12, resulting in six new 3D-T1WIs of nonuniform signal intensities. Thirteen volume data sets were segmented into native-space tissue probability data using SPM12. Examination of the 3D data without nonuniform signal intensity showed that significant differences in measured volumes were not observed on repeated analysis of variance, but examination of the 3D data with nonuniform signal intensity did show significant differences in measured volumes in gray matter and CSF but not in white matter. Measured volumes using segmented tissue probability data obtained using SPM12 were not influenced by the contrasts of analyzed images.