Quantitative Susceptibility Mapping (QSM) and volumetry are used to study the deep gray-matter nuclei of patients with Alzheimer’s Disease (AD) and healthy control subjects. QSM is performed using “Joint background-field removal and segmentation-Enhanced Dipole Inversion” (JEDI), which leverages the information from automated model-based segmentation and allows the compact single-step formulation of the ill-posed inversion problem of QSM. For comparison QSM is also performed using L1-MEDI from the MEDI-Toolbox. The tissue magnetic susceptibility shows no significant difference between the Alzheimer group compared to the healthy control group. In contrast, the normalized volume of segmented gray-matter regions is significantly reduced in AD patients.