1. A method of generating adjusted image data to compensate for modality-induced distortion in a computing device having a processor interconnected with a memory and a display, comprising, at the processor: receiving a three-dimensional image captured with a first imaging modality and including (i) distorted surface image data depicting a surface of an object and (ii) distorted volume image data depicting a volume of the object; extracting the distorted surface image data from the three-dimensional image; receiving reference surface image data captured with a second imaging modality and depicting the surface of the object; determining a surface transformation for registering the distorted surface image data with the reference surface image data; determining a volume transformation informed by the surface transformation, by: applying the surface transformation to the distorted volume image data; for each of a plurality of slices in the distorted volume image data; retrieving control parameters of the first imaging modality from the three-dimensional image; selecting a planar transformation based on the control parameters; projecting the reference surface image data onto a plane corresponding to the slice; and optimizing the planar transformation to minimize an error level between the slice and the projected reference surface image data; generating an adjusted three-dimensional image by applying the volume transformation to the three-dimensional image; and storing the adjusted three-dimensional image in the memory.