Low-resolution, whole-head volumes can be acquired rapidly with EPI-based volumetric navigators (vNavs). vNavs interspersed in a longer scan are widely used for prospective motion correction in a variety of sequences. To further improve the accuracy and flexibility of vNavs, we present a novel registration algorithm, tailored specifically for the vNavs application. Accuracy of the algorithm is tested on navigator volumes acquired with human volunteers at three isotropic resolutions, 6.4mm, 8mm, and 10mm, using a series of field of view (FOV) rotations and translations to provide ground truth rigid "motion".