Quantitative magnetic susceptibility offers a non-invasive measure of important brain tissue molecules, such as iron complexes and myelin, potentially providing significant information about normal and pathological conditions during aging. We developed an automated process to quantify tissue susceptibility in a biologically meaningful set of structures, thereby generating universal and sharable quantitative susceptibility measures. Our susceptibility-based multi-atlas outperformed the single atlas and the T1-weighted multi-atlases. Our tool and normalization algorithm offered consistent measures of magnetic susceptibility over different image protocols and platforms. Automatic and reliable quantitative susceptibility mapping measures will facilitate individual analyses and studies on aging and neurodegeneration.