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

Real-Time Segmentation of 4D Ultrasound by Active Geometric Functions

Four-dimensional ultrasound based on matrix phased array transducers can capture the complex 4D cardiac motion in a complete and real-time fashion. However, the large amount of information residing in 4D ultrasound scans and novel applications under interventional settings pose a big challenge in efficiency for workflow and computer-aided diagnostic algorithms such as segmentation. In this context, a novel formulation framework of the minimal surface problem, called active geometric functions (AGF), is proposed to reach truly real-time performance in segmenting 4D ultrasound data. A specific instance of AGF based on finite element modeling and Hermite surface descriptors was implemented and evaluated on 35 4D ultrasound data sets with a total of 425 time frames. Quantitative comparison to manual tracing showed that the proposed method provides LV contours close to manual segmentation and that the discrepancy was comparable to inter-observer tracing variability. The ability of such realtime segmentation will not only facilitate the diagnoses and workflow, but also enables novel applications such as interventional guidance and interactive image acquisition with online segmentation

Interactive energy minimizing segmentation frameworks

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