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

An Information Theoretic Approach For Feature Selection And Segmentation In Posterior Fossa Tumors

Posterior Fossa (PF) is a type of brain tumor located in or near brain stem and cerebellum. About 55% - 70 % pediatric brain tumors arise in the posterior fossa, compared with only 15% - 20% of adult tumors. For segmenting PF tumors we should have features to study the characteristics of tumors. In literature, different types of texture features such as Fractal Dimension (FD) and Multifractional Brownian Motion (mBm) have been exploited for measuring randomness associated with brain and tumor tissues structures, and the varying appearance of tissues in magnetic resonance images (MRI). For selecting best features techniques such as neural network and boosting methods have been exploited. However, neural network cannot descirbe about the properties of texture features. We explore methods such as information theroetic methods which can perform feature selection based on properties of texture features. The primary contribution of this dissertation is investigating efficacy of different image features such as intensity, fractal texture, and level - set shape in segmentation of PF tumor for pediatric patients. We explore effectiveness of using four different feature selection and three different segmentation techniques respectively to discriminate tumor regions from normal tissue in multimodal brain MRI. Our research suggest that Kullback - Leibler Divergence (KLD) measure for feature ranking and selection and Expectation Maximization (EM) algorithm for feature fusion and tumor segmentation offer the best performance for the patient data in this study. To improve segmentation accuracy, we need to consider abnormalities such as cyst, edema and necrosis which surround tumors. In this work, we exploit features which describe properties of cyst and technique which can be used to segment it. To achieve this goal, we extend the two class KLD techniques to multiclass feature selection techniques, so that we can effectively select features for tumor, cyst and non tumor tissues. We compute segemntation accuracy by computing number of pixels segemented to total number of pixels for the best features. For automated process we integrate the inhomoheneity correction, feature selection using KLD and segmentation in an integrated EM framework. To validate results we have used similarity coefficients for computing the robustness of segmented tumor and cyst

Segmentation of brain MRI during early childhood

The objective of this thesis is the development of automatic methods to measure the changes in volume and growth of brain structures in prematurely born infants. Automatic tools for accurate tissue quantification from magnetic resonance images can provide means for understanding how the neurodevelopmental effects of the premature birth, such as cognitive, neurological or behavioural impairment, are related to underlying changes in brain anatomy. Understanding these changes forms a basis for development of suitable treatments to improve the outcomes of premature birth. In this thesis we focus on the segmentation of brain structures from magnetic resonance images during early childhood. Most of the current brain segmentation techniques have been focused on the segmentation of adult or neonatal brains. As a result of rapid development, the brain anatomy during early childhood differs from anatomy of both adult and neonatal brains and therefore requires adaptations of available techniques to produce good results. To address the issue of anatomical differences of the brain during early childhood compared to other age-groups, population-specific deformable and probabilistic atlases are introduced. A method for generation of population-specific prior information in form of a probabilistic atlas is proposed and used to enhance existing segmentation algorithms. The evaluation of registration-based and intensity-based approaches shows the techniques to be complementary in the quality of automatic segmentation in different parts of the brain. We propose a novel robust segmentation method combining the advantages of both approaches. The method is based on multiple label propagation using B-spline non-rigid registration followed by EM segmentation. Intensity inhomogeneity is a shading artefact resulting from the acquisition process, which significantly affects modern high resolution MR data acquired at higher magnetic field strengths. A novel template based method focused on correcting the intensity inhomogeneity in data acquired at higher magnetic field strengths is therefore proposed. The proposed segmentation method combined with proposed intensity inhomogeneity correction method offers a robust tool for quantification of volumes and growth of brain structures during early childhood. The tool have been applied to 67 T1-weigted images of subject at one and two years of age

Level set segmentation using non-negative matrix factorization with application to brain MRI

We address the problem of image segmentation using a new deformable model based on the level set method (LSM) and non-negative matrix factorization (NMF). We describe the use of NMF to reduce the dimension of large images from thousands of pixels to a handful of metapixels or regions. In addition, the exact number of regions is discovered using the nuclear norm of the NMF factors. The proposed NMF-LSM characterizes the histogram of the image, calculated over the image blocks, as nonnegative combinations of basic histograms computed using NMF (V ~ W H). The matrix W represents the histograms of the image regions, whereas the matrix H provides the spatial clustering of the regions. NMF-LSM takes into account the bias field present particularly in medical images. We define two local clustering criteria in terms of the NMF factors. The first criterion defines a local intensity clustering property based on the matrix W by computing the average intensity and standard deviation of every region. The second criterion defines a local spatial clustering using the matrix H. The local clustering is then summed over all regions to give a global criterion of image segmentation. In LSM, these criteria define an energy minimized w.r.t. LSFs and the bias field to achieve the segmentation. The proposed method is validated on synthetic binary and gray-scale images, and then applied to real brain MRI images. NMF-LSM provides a general approach for robust region discovery and segmentation in heterogeneous images

Automatic pharynx and larynx cancer segmentation framework (PLCSF) on contrast enhanced MR images

A novel and effective pharynx and larynx cancer segmentation framework (PLCSF) is presented for automatic base of tongue and larynx cancer segmentation from gadolinium-enhanced T1-weighted magnetic resonance images (MRI). The aim of the proposed PLCSF is to assist clinicians in radiotherapy treatment planning. The initial processing of MRI data in PLCSF includes cropping of region of interest; reduction of artefacts and detection of the throat region for the location prior. Further, modified fuzzy c-means clustering is developed to robustly separate candidate cancer pixels from other tissue types. In addition, region-based level set method is evolved to ensure spatial smoothness for the final segmentation boundary after noise removal using non-linear and morphological filtering. Validation study of PLCSF on 102 axial MRI slices demonstrate mean dice similarity coefficient of 0.79 and mean modified Hausdorff distance of 2.2 mm when compared with manual segmentations. Comparison of PLCSF with other algorithms validates the robustness of the PLCSF. Inter- and intra-variability calculations from manual segmentations suggest that PLCSF can help to reduce the human subjectivity

A review of algorithms for medical image segmentation and their applications to the female pelvic cavity

This paper aims to make a review on the current segmentation algorithms used for medical images. Algorithms are classified according to their principal methodologies, namely the ones based on thresholds, the ones based on clustering techniques and the ones based on deformable models. The last type is focused on due to the intensive investigations into the deformable models that have been done in the last few decades. Typical algorithms of each type are discussed and the main ideas, application fields, advantages and disadvantages of each type are summarised. Experiments that apply these algorithms to segment the organs and tissues of the female pelvic cavity are presented to further illustrate their distinct characteristics. In the end, the main guidelines that should be considered for designing the segmentation algorithms of the pelvic cavity are proposed

A comparative evaluation for liver segmentation from spir images and a novel level set method using signed pressure force function

Thesis (Doctoral)--Izmir Institute of Technology, Electronics and Communication Engineering, Izmir, 2013Includes bibliographical references (leaves: 118-135)Text in English; Abstract: Turkish and Englishxv, 145 leavesDeveloping a robust method for liver segmentation from magnetic resonance images is a challenging task due to similar intensity values between adjacent organs, geometrically complex liver structure and injection of contrast media, which causes all tissues to have different gray level values. Several artifacts of pulsation and motion, and partial volume effects also increase difficulties for automatic liver segmentation from magnetic resonance images. In this thesis, we present an overview about liver segmentation methods in magnetic resonance images and show comparative results of seven different liver segmentation approaches chosen from deterministic (K-means based), probabilistic (Gaussian model based), supervised neural network (multilayer perceptron based) and deformable model based (level set) segmentation methods. The results of qualitative and quantitative analysis using sensitivity, specificity and accuracy metrics show that the multilayer perceptron based approach and a level set based approach which uses a distance regularization term and signed pressure force function are reasonable methods for liver segmentation from spectral pre-saturation inversion recovery images. However, the multilayer perceptron based segmentation method requires a higher computational cost. The distance regularization term based automatic level set method is very sensitive to chosen variance of Gaussian function. Our proposed level set based method that uses a novel signed pressure force function, which can control the direction and velocity of the evolving active contour, is faster and solves several problems of other applied methods such as sensitivity to initial contour or variance parameter of the Gaussian kernel in edge stopping functions without using any regularization term