Digital brain atlases can be used in conjunction with magnetic resonance imaging (MRI) and computed tomography (CT) for planning and guidance during neurosurgery. Digital atlases are advantageous, since they can be warped nonlinearly to fit each patient's unique anatomy. Two atlas-to-patient warping techniques are compared in this paper. The first technique uses an MRI template as an intermediary to estimate a nonlinear atlas-to-patient transformation. The second, is novel, and uses a pseudo-MRI volume, derived from the voxel-label-atlas, to estimate the atlas-to-patient transformation directly. Manual segmentations and functional data are used to validate the two methods.