This abstract introduces an analysis pipeline of voxel-based magnetic susceptibility and morphometry (VBMSM) on single MR scan. To validate the proposed pipeline, we conducted VBMSM in control and Alzheimer’s disease (AD) groups. VBM was performed using the magnitude image. The susceptibility map was estimated by new dipole inversion utilized segmentation result. For whole brain susceptibility comparison, the susceptibility map was spatially normalized by the same transformation parameter for VBM. Significant susceptibility increases could be detected in regions associated withβ-amyloid deposition in AD. Brain atrophy also could be detected in AD. VBMSM is adaptable to neurodegenerative diseases including AD.