A template-to-slice block matching approach for automatic localization of brain in fetal MRI

To enhance post-acquisition processing of fetal brain MRI we have developed a template-to-slice block matching technique that matches a spatiotemporal (4D) atlas of the fetal brain to the corresponding section of the brain in each 2D fetal MRI scan. As compared to the recent studies which used feature based approaches for fetal brain localization, we propose a template matching approach that registers the template to each slice of the brain in 3D. In addition to brain localization, this novel technique registers the template to each fetal MRI scan thus is useful for slice-level motion correction, brain segmentation, and reconstruction. In this paper we describe the details of our algorithm and report statistical analysis of the accuracy of localization and registration. We examined the algorithm on 366 scans obtained from fetal MRI of 30 subjects and used a 4D MRI atlas of the fetal brain as template. Our results show 94% success rate in brain localization, and 73% successful matching, with a median localization error of 6.45 mm for all scans, and median target registration error of 4.2 mm for successfully localized scans. This algorithm can be used for automatic localization of fetal brain as the first step of fetal MRI analysis pipeline.