Alzheimer’s disease (AD), the most common type of dementia in elderly individuals, slowly and progressively diminishes the cognitive function. Mild cognitive impairment (MCI) is also a significant risk factor for the onset of AD. Magnetic resonance imaging (MRI) is widely used for the detection and understanding of the natural progression of AD and other neurodegenerative disorders. For proper assessment of these diseases, a reliable database of images from cognitively healthy participants is important. However, differences in magnetic field strength or the sex and age of participants between a normal database and an evaluation data set can affect the accuracy of the detection and evaluation of neurodegenerative disorders. We developed a brain segmentation procedure, based on 30 Japanese brain atlases, and suggest a harmonized Z-score to correct the differences in field strength and sex and age from a large data set (1235 cognitively healthy participants), including 1.5 T and 3 T T1-weighted brain images. We evaluated our harmonized Z-score for AD discriminative power and classification accuracy between stable MCI and progressive MCI. Our procedure can perform brain segmentation in approximately 30 min. The harmonized Z-score of the hippocampus achieved high accuracy (AUC = 0.96) for AD detection and moderate accuracy (AUC = 0.70) to classify stable or progressive MCI. These results show that our method can detect AD with high accuracy and high generalization capability. Moreover, it may discriminate between stable and progressive MCI. Our study has some limitations: the age groups in the 1.5 T data set and 3 T data set are significantly different. In this study, we focused on AD, which is primarily a disease of elderly patients. For other diseases in different age groups, the harmonized Z-score needs to be recalculated using different data sets.