Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Dynamic Body VSLAM with Semantic Constraints

Image based reconstruction of urban environments is a challenging problem that deals with optimization of large number of variables, and has several sources of errors like the presence of dynamic objects. Since most large scale approaches make the assumption of observing static scenes, dynamic objects are relegated to the noise modeling section of such systems. This is an approach of convenience since the RANSAC based framework used to compute most multiview geometric quantities for static scenes naturally confine dynamic objects to the class of outlier measurements. However, reconstructing dynamic objects along with the static environment helps us get a complete picture of an urban environment. Such understanding can then be used for important robotic tasks like path planning for autonomous navigation, obstacle tracking and avoidance, and other areas. In this paper, we propose a system for robust SLAM that works in both static and dynamic environments. To overcome the challenge of dynamic objects in the scene, we propose a new model to incorporate semantic constraints into the reconstruction algorithm. While some of these constraints are based on multi-layered dense CRFs trained over appearance as well as motion cues, other proposed constraints can be expressed as additional terms in the bundle adjustment optimization process that does iterative refinement of 3D structure and camera / object motion trajectories. We show results on the challenging KITTI urban dataset for accuracy of motion segmentation and reconstruction of the trajectory and shape of moving objects relative to ground truth. We are able to show average relative error reduction by a significant amount for moving object trajectory reconstruction relative to state-of-the-art methods like VISO 2, as well as standard bundle adjustment algorithms