Indiana University-Purdue University Indianapolis (IUPUI) / Adaptive Optics Optical Coherence Tomography (AO-OCT) is a high-speed, high-resolution ophthalmic imaging technique offering detailed 3D analysis of retina structure in vivo. However, AO-OCT volume images are sensitive to involuntary eye movements that occur even during steady fixation and include tremor, drifts, and micro-saccades. To correct eye motion artifacts within a volume and to stabilize a sequence of volumes acquired of the same retina area, we propose a stripe-wise 3D image registration algorithm with phase correlation. In addition, using several ideas such as coarse-to-fine approach, spike noise filtering, pre-computation caching, and parallel processing on a GPU, our approach can register a volume of size 512 x 512 x 512 in less than 6 seconds, which is a 33x speedup as compared to an equivalent CPU version in MATLAB. Moreover, our 3D registration approach is reliable even in the presence of large motions (micro-saccades) that distort the volumes. Such motion was an obstacle for a previous en face approach based on 2D projected images. The thesis also investigates GPU implementations for 3D phase correlation and 2D normalized cross-correlation, which could be useful for other image processing algorithms.