Image-Based Registration in Canonical Atlas Space

Benjamin Hou, Bishesh Khanal, Amir Alansary, Steven McDonagh, Alice Davidson, Mary Rutherford, Jo V. Hajnal, Daniel Rueckert, Ben Glocker, Bernhard Kainz

Abstract: Limited capture range, and the requirement to provide high quality initialization for optimization-based 2D/3D image registration methods, can significantly degrade the performance of 3D image reconstruction and motion compensation pipelines. Challenging clinical imaging scenarios, which contain significant subject motion such as fetal in-utero imaging, complicate the 3D image and volume reconstruction process. In this paper we present a learning based image registration method using Convolutional Neural Networks (CNNs) to predicting 3D rigid transformations of arbitrarily oriented 2D image slices, with respect to a learned canonical atlas co-ordinate system. Only image slice intensity information is used to perform registration and canonical alignment. We extensively evaluate the effectiveness of our approach quantitatively on simulated Magnetic Resonance Imaging (MRI), fetal brain imagery with synthetic motion and further demonstrate qualitative results on real fetal MRI data where our method is integrated into a full reconstruction and motion compensation pipeline. Furthermore, we utilise Monte Carlo Dropout for the purpose of establishing a prediction confidence metric.

Author Affiliation: Imperial College London, Kings College London