3D image registration is one of the most complex algorithms employed in medical imaging applications. Software solution struggles to reach high accuracy in a reasonable time, therefore this work presents ATHENA, a framework for rigid 3D Image Registration, exploiting heterogeneous architecture for acceleration, and also providing support for memory-constrained devices. Moreover, ATHENA presents a tool for automatically generating misalignent between volumes, to perform a robustness analysis on different kinds of distortions. We compared ATHENA with SimpleITK, a well-known software library, and with a software version of the proposed algorithm, achieving a top speedup of 18.1× and 53.7× respectively.