Taken together, our findings show that, in Alzheimer’s disease, Aβ load correlates with a slightly increased cortical thickness relatively to the atrophic Alzheimer’s disease cortex, while p-tau load is the strongest contributor to regional cortical atrophy in frontal and temporal regions, and reactive microglia load is the strongest correlate of cortical atrophy in the parietal region. The gene discussed is MAPT; the disease is Cerebral cortical atrophy.