The complex neural architecture and brain connectivity of mouse models of human disease can be studied ex vivo by diffusion tensor imaging; however, acquisition times are long and make cohort studies prohibitively time-consuming. Throughput can be increased by the simultaneous use of multiple coils placed in proximity to the magnet isocenter. We quantify the impact of the multiple-coil configuration on throughput, on diffusion metrics used in tractography, and on mouse brain connectivity matrices. We show that fractional anisotropy is underestimated off-isocenter, while the main eigenvector direction is minimally affected. The effect on brain connectivity networks is currently being quantified.