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

3D freeform surfaces from planar sketches using neural networks

A novel intelligent approach into 3D freeform surface reconstruction from planar sketches is proposed. A multilayer perceptron (MLP) neural network is employed to induce 3D freeform surfaces from planar freehand curves. Planar curves were used to represent the boundaries of a freeform surface patch. The curves were varied iteratively and sampled to produce training data to train and test the neural network. The obtained results demonstrate that the network successfully learned the inverse-projection map and correctly inferred the respective surfaces from fresh curves

Sampling and Reconstruction of Shapes with Algebraic Boundaries

We present a sampling theory for a class of binary images with finite rate of innovation (FRI). Every image in our model is the restriction of \mathds{1}_{\{p\leq0\}} to the image plane, where \mathds{1} denotes the indicator function and $p$ is some real bivariate polynomial. This particularly means that the boundaries in the image form a subset of an algebraic curve with the implicit polynomial $p$. We show that the image parameters --i.e., the polynomial coefficients-- satisfy a set of linear annihilation equations with the coefficients being the image moments. The inherent sensitivity of the moments to noise makes the reconstruction process numerically unstable and narrows the choice of the sampling kernels to polynomial reproducing kernels. As a remedy to these problems, we replace conventional moments with more stable \emph{generalized moments} that are adjusted to the given sampling kernel. The benefits are threefold: (1) it relaxes the requirements on the sampling kernels, (2) produces annihilation equations that are robust at numerical precision, and (3) extends the results to images with unbounded boundaries. We further reduce the sensitivity of the reconstruction process to noise by taking into account the sign of the polynomial at certain points, and sequentially enforcing measurement consistency. We consider various numerical experiments to demonstrate the performance of our algorithm in reconstructing binary images, including low to moderate noise levels and a range of realistic sampling kernels.Comment: 12 pages, 14 figure