Quantification of cortical folding using MR image data

The cerebral cortex is a thin layer of tissue lining the brain where neural circuits perform important high level functions including sensory perception, motor control and language processing. In the third trimester the fetal cortex folds rapidly from a smooth sheet into a highly convoluted arrangement of gyri and sulci. Premature birth is a high risk factor for poor neurodevelopmental outcome and has been associated with abnormal cortical development, however the nature of the disruption to developmental processes is not fully understood. Recent developments in magnetic resonance imaging have allowed the acquisition of high quality brain images of preterms and also fetuses in-utero. The aim of this thesis is to develop techniques which quantify folding from these images in order to better understand cortical development in these two populations. A framework is presented that quantifies global and regional folding using curvature-based measures. This methodology was applied to fetuses over a wide gestational age range (21.7 to 38.9 weeks) for a large number of subjects (N = 80) extending our understanding of how the cortex folds through this critical developmental period. The changing relationship between the folding measures and gestational age was modelled with a Gompertz function which allowed an accurate prediction of physiological age. A spectral-based method is outlined for constructing a spatio-temporal surface atlas (a sequence of mean cortical surface meshes for weekly intervals). A key advantage of this method is the ability to do group-wise atlasing without bias to the anatomy of an initial reference subject. Mean surface templates were constructed for both fetuses and preterms allowing a preliminary comparison of mean cortical shape over the postmenstrual age range 28-36 weeks. Displacement patterns were revealed which intensified with increasing prematurity, however more work is needed to evaluate the reliability of these findings.Open Acces

Template based shape processing

As computers can only represent and process discrete data, information gathered from the real world always has to be sampled. While it is nowadays possible to sample many signals accurately and thus generate high-quality reconstructions (for example of images and audio data), accurately and densely sampling 3D geometry is still a challenge. The signal samples may be corrupted by noise and outliers, and contain large holes due to occlusions. These issues become even more pronounced when also considering the temporal domain. Because of this, developing methods for accurate reconstruction of shapes from a sparse set of discrete data is an important aspect of the computer graphics processing pipeline. In this thesis we propose novel approaches to including semantic knowledge into reconstruction processes using template based shape processing. We formulate shape reconstruction as a deformable template fitting process, where we try to fit a given template model to the sampled data. This approach allows us to present novel solutions to several fundamental problems in the area of shape reconstruction. We address static problems like constrained texture mapping and semantically meaningful hole-filling in surface reconstruction from 3D scans, temporal problems such as mesh based performance capture, and finally dynamic problems like the estimation of physically based material parameters of animated templates.Analoge Signale müssen digitalisiert werden um sie auf modernen Computern speichern und verarbeiten zu können. Für viele Signale, wie zum Beispiel Bilder oder Tondaten, existieren heutzutage effektive und effiziente Digitalisierungstechniken. Aus den so gewonnenen Daten können die ursprünglichen Signale hinreichend akkurat wiederhergestellt werden. Im Gegensatz dazu stellt das präzise und effiziente Digitalisieren und Rekonstruieren von 3D- oder gar 4D-Geometrie immer noch eine Herausforderung dar. So führen Verdeckungen und Fehler während der Digitalisierung zu Löchern und verrauschten Meßdaten. Die Erforschung von akkuraten Rekonstruktionsmethoden für diese groben digitalen Daten ist daher ein entscheidender Schritt in der Entwicklung moderner Verarbeitungsmethoden in der Computergrafik. In dieser Dissertation wird veranschaulicht, wie deformierbare geometrische Modelle als Vorlage genutzt werden können, um semantische Informationen in die robuste Rekonstruktion von 3D- und 4D Geometrie einfließen zu lassen. Dadurch wird es möglich, neue Lösungsansätze für mehrere grundlegenden Probleme der Computergrafik zu entwickeln. So können mit dieser Technik Löcher in digitalisierten 3D Modellen semantisch sinnvoll aufgefüllt, oder detailgetreue virtuelle Kopien von Darstellern und ihrer dynamischen Kleidung zu erzeugt werden

A scalable, efficient, and accurate solution to non-rigid structure from motion

© . This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Most Non-Rigid Structure from Motion (NRSfM) solutions are based on factorization approaches that allow reconstructing objects parameterized by a sparse set of 3D points. These solutions, however, are low resolution and generally, they do not scale well to more than a few tens of points. While there have been recent attempts at bringing NRSfM to a dense domain, using for instance variational formulations, these are computationally demanding alternatives which require certain spatial continuity of the data, preventing their use for articulated shapes with large deformations or situations with multiple discontinuous objects. In this paper, we propose incorporating existing point trajectory low-rank models into a probabilistic framework for matrix normal distributions. With this formalism, we can then simultaneously learn shape and pose parameters using expectation maximization, and easily exploit additional priors such as known point correlations. While similar frameworks have been used before to model distributions over shapes, here we show that formulating the problem in terms of distributions over trajectories brings remarkable improvements, especially in generality and efficiency. We evaluate the proposed approach in a variety of scenarios including one or multiple objects, sparse or dense reconstructions, missing observations, mild or sharp deformations, and in all cases, with minimal prior knowledge and low computational cost.Peer ReviewedPostprint (author's final draft

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