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

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

Brain MRI Segmentation with Multiphase Minimal Partitioning: A Comparative Study

This paper presents the implementation and quantitative evaluation of a multiphase three-dimensional deformable model in a level set framework for automated segmentation of brain MRIs. The segmentation algorithm performs an optimal partitioning of three-dimensional data based on homogeneity measures that naturally evolves to the extraction of different tissue types in the brain. Random seed initialization was used to minimize the sensitivity of the method to initial conditions while avoiding the need for a priori information. This random initialization ensures robustness of the method with respect to the initialization and the minimization set up. Postprocessing corrections with morphological operators were applied to refine the details of the global segmentation method. A clinical study was performed on a database of 10 adult brain MRI volumes to compare the level set segmentation to three other methods: “idealized” intensity thresholding, fuzzy connectedness, and an expectation maximization classification using hidden Markov random fields. Quantitative evaluation of segmentation accuracy was performed with comparison to manual segmentation computing true positive and false positive volume fractions. A statistical comparison of the segmentation methods was performed through a Wilcoxon analysis of these error rates and results showed very high quality and stability of the multiphase three-dimensional level set method

Rich probabilistic models for semantic labeling

Das Ziel dieser Monographie ist es die Methoden und Anwendungen des semantischen Labelings zu erforschen. Unsere Beiträge zu diesem sich rasch entwickelten Thema sind bestimmte Aspekte der Modellierung und der Inferenz in probabilistischen Modellen und ihre Anwendungen in den interdisziplinären Bereichen der Computer Vision sowie medizinischer Bildverarbeitung und Fernerkundung

Advanced neuroimaging techniques to study the development of the cerebral cortex, subplate and thalamus in preterm infants at 3 Tesla

Preterm infants are at increased risk of neurodevelopmental delay, cognitive dysfunction, and behavioural disturbances. Recent studies of older preterm children with cognitive impairments implicate morphological and functional cortical abnormalities. However elucidation of the preterm cortical abnormalities has been challenging due to specific neonatal features. Using 3 Tesla neonatal MR images and Expectation Maximisation/Markov Random Field segmentation with incorporation of a novel knowledge based technique for removal of mislabelled partial volume voxels, neonatal 3D cortical extraction was possible from 25 to 48 weeks gestation. This enabled the study of the true cortical scaling exponent, cortical thickness, regional volumes and curvature measurements. It showed a relative excess of the cortical surface area for its volume which corresponded with a change in the intrinsic curvature and fissuration up to 36 weeks gestation, after which, the relative growth of the surface area and volume were proportional leading to dominant changes in the extrinsic curvature and cortical folding. Thus the curvature measurements showed an important mechanistic property of convolution. By term equivalent age, the cortex was thicker and there were changes in cortical curvature although there were no differences in the cortical surface area of preterm infants compared to term born controls. There were specific frontal and parietal deficits in the cortical volume. Diffusion MR showed that although the early cortical anisotropy diminished to noise levels by 35 weeks, the mean diffusivity reduced during the entire third trimester due to changes in the radial diffusivity. Regional variations in the mean diffusivity occurred during development with frontal abnormalities persisting at term equivalent age. Subplate and thalamic quantification showed important development features during the third trimester, however in the absence of overt lesions no associations with cortical measures were found. Thus this thesis provides interesting and novel insights into the macroscopic and microscopic development of the cortex.Imperial Users onl

Machine Learning Based Autism Detection Using Brain Imaging

Autism Spectrum Disorder (ASD) is a group of heterogeneous developmental disabilities that manifest in early childhood. Currently, ASD is primarily diagnosed by assessing the behavioral and intellectual abilities of a child. This behavioral diagnosis can be subjective, time consuming, inconclusive, does not provide insight on the underlying etiology, and is not suitable for early detection. Diagnosis based on brain magnetic resonance imaging (MRI)—a widely used non- invasive tool—can be objective, can help understand the brain alterations in ASD, and can be suitable for early diagnosis. However, the brain morphological findings in ASD from MRI studies have been inconsistent. Moreover, there has been limited success in machine learning based ASD detection using MRI derived brain features. In this thesis, we begin by demonstrating that the low success in ASD detection and the inconsistent findings are likely attributable to the heterogeneity of brain alterations in ASD. We then show that ASD detection can be significantly improved by mitigating the heterogeneity with the help of behavioral and demographics information. Here we demonstrate that finding brain markers in well-defined sub-groups of ASD is easier and more insightful than identifying markers across the whole spectrum. Finally, our study focused on brain MRI of a pediatric cohort (3 to 4 years) and achieved a high classification success (AUC of 95%). Results of this study indicate three main alterations in early ASD brains: 1) abnormally large ventricles, 2) highly folded cortices, and 3) low image intensity in white matter regions suggesting myelination deficits indicative of decreased structural connectivity. Results of this thesis demonstrate that the meaningful brain markers of ASD can be extracted by applying machine learning techniques on brain MRI data. This data-driven technique can be a powerful tool for early detection and understanding brain anatomical underpinnings of ASD

PHE-SICH-CT-IDS: A Benchmark CT Image Dataset for Evaluation Semantic Segmentation, Object Detection and Radiomic Feature Extraction of Perihematomal Edema in Spontaneous Intracerebral Hemorrhage

Intracerebral hemorrhage is one of the diseases with the highest mortality and poorest prognosis worldwide. Spontaneous intracerebral hemorrhage (SICH) typically presents acutely, prompt and expedited radiological examination is crucial for diagnosis, localization, and quantification of the hemorrhage. Early detection and accurate segmentation of perihematomal edema (PHE) play a critical role in guiding appropriate clinical intervention and enhancing patient prognosis. However, the progress and assessment of computer-aided diagnostic methods for PHE segmentation and detection face challenges due to the scarcity of publicly accessible brain CT image datasets. This study establishes a publicly available CT dataset named PHE-SICH-CT-IDS for perihematomal edema in spontaneous intracerebral hemorrhage. The dataset comprises 120 brain CT scans and 7,022 CT images, along with corresponding medical information of the patients. To demonstrate its effectiveness, classical algorithms for semantic segmentation, object detection, and radiomic feature extraction are evaluated. The experimental results confirm the suitability of PHE-SICH-CT-IDS for assessing the performance of segmentation, detection and radiomic feature extraction methods. To the best of our knowledge, this is the first publicly available dataset for PHE in SICH, comprising various data formats suitable for applications across diverse medical scenarios. We believe that PHE-SICH-CT-IDS will allure researchers to explore novel algorithms, providing valuable support for clinicians and patients in the clinical setting. PHE-SICH-CT-IDS is freely published for non-commercial purpose at: https://figshare.com/articles/dataset/PHE-SICH-CT-IDS/23957937