Purpose: Radiation dose to the heart and cardiac substructures has been linked to cardiotoxicities. As cardiac substructures are poorly visualized on treatment planning computed tomography (CT), we employed the superior soft tissue contrast of magnetic resonance (MR) imaging to optimize a hybrid MR/CT atlas for substructure dose assessment using CT.Methods: Thirty-one left breast cancer patients underwent a T2-weighted MR and non-contrast simulation CTs. A radiation oncologist delineated 13 substructures (chambers, great vessels, coronary arteries etc.) using MR/CT information via cardiac-confined rigid registration. Ground truth contours for 20 patients were input into an intensity-based deformable registration atlas and applied to 11 validation patients. Automatic segmentations involved employing majority vote and Simultaneous Truth and Performance Level Estimation (STAPLE) strategies with 1-15 atlas matches. Performance was evaluated via Dice similarity coefficient (DSC), mean distance to agreement (MDA), and centroid displacement. Three physicians evaluated segmentation performance via consensus scoring using a 5-point scale. Dosimetric assessment included measurements of mean heart dose (MHD), left ventricular volume receiving 5Gy (LV-V5), and left anterior descending artery mean and maximum doses (LADAmean, LADAmax).Results: Atlas approaches performed similarly well with 7/13 substructures (heart, chambers, ascending aorta, and pulmonary artery) having DSC>0.75, when averaged over 11 validation