Combining spatial priors and anatomical information for fMRI detection

In this paper, we analyze Markov Random Field (MRF) as a spatial regularizer in fMRI detection. The low signal-to-noise ratio (SNR) in fMRI images presents a serious challenge for detection algorithms, making regularization necessary to achieve good detection accuracy. Gaussian smoothing, traditionally employed to boost SNR, often produces over-smoothed activation maps. Recently, the use of MRF priors has been suggested as an alternative regularization approach. However, solving for an optimal configuration of the MRF is NP-hard in general. In this work, we investigate fast inference algorithms based on the Mean Field approximation in application to MRF priors for fMRI detection. Furthermore, we propose a novel way to incorporate anatomical information into the MRF-based detection framework and into the traditional smoothing methods. Intuitively speaking, the anatomical evidence increases the likelihood of activation in the gray matter and improves spatial coherency of the resulting activation maps within each tissue type. Validation using the receiver operating characteristic (ROC) analysis and the confusion matrix analysis on simulated data illustrates substantial improvement in detection accuracy using the anatomically guided MRF spatial regularizer. We further demonstrate the potential benefits of the proposed method in real fMRI signals of reduced length. The anatomically guided MRF regularizer enables significant reduction of the scan length while maintaining the quality of the resulting activation maps.National Institutes of Health (U.S.) (National Institute for Biomedical Imaging and Bioengineering (U.S.)/National Alliance for Medical Image Computing (U.S.) Grant U54-EB005149)National Science Foundation (U.S.) (Grant IIS 9610249)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Biomedical Informatics Research Network Grant U24-RR021382)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Neuroimaging Analysis Center (U.S.) Grant P41-RR13218)National Institutes of Health (U.S.) (National Institute of Neurological Disorders and Stroke (U.S.) Grant R01-NS051826)National Science Foundation (U.S.) (CAREER Grant 0642971)National Science Foundation (U.S.). Graduate Research FellowshipNational Center for Research Resources (U.S.) (FIRST-BIRN Grant)Neuroimaging Analysis Center (U.S.

Model based three dimensional medical image segmentation

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.Includes bibliographical references (leaves 115-123).by Tina Kapur.Ph.D

Prior information for brain parcellation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 171-184).To better understand brain disease, many neuroscientists study anatomical differences between normal and diseased subjects. Frequently, they analyze medical images to locate brain structures influenced by disease. Many of these structures have weakly visible boundaries so that standard image analysis algorithms perform poorly. Instead, neuroscientists rely on manual procedures, which are time consuming and increase risks related to inter- and intra-observer reliability [53]. In order to automate this task, we develop an algorithm that robustly segments brain structures. We model the segmentation problem in a Bayesian framework, which is applicable to a variety of problems. This framework employs anatomical prior information in order to simplify the detection process. In this thesis, we experiment with different types of prior information such as spatial priors, shape models, and trees describing hierarchical anatomical relationships. We pose a maximum a posteriori probability estimation problem to find the optimal solution within our framework. From the estimation problem we derive an instance of the Expectation Maximization algorithm, which uses an initial imperfect estimate to converge to a good approximation.(cont.) The resulting implementation is tested on a variety of studies, ranging from the segmentation of the brain into the three major brain tissue classes, to the parcellation of anatomical structures with weakly visible boundaries such as the thalamus or superior temporal gyrus. In general, our new method performs significantly better than other :standard automatic segmentation techniques. The improvement is due primarily to the seamless integration of medical image artifact correction, alignment of the prior information to the subject, detection of the shape of anatomical structures, and representation of the anatomical relationships in a hierarchical tree.by Kilian Maria Pohl.Ph.D

Probabilistic Atlas and Geometric Variability Estimation to Drive Tissue Segmentation

International audienceComputerized anatomical atlases play an important role in medical image analysis. While an atlas usually refers to a standard or mean image also called template, that presumably represents well a given population, it is not enough to characterize the observed population in detail. A template image should be learned jointly with the geometric variability of the shapes represented in the observations. These two quantities will in the sequel form the atlas of the corresponding population. The geometric variability is modelled as deformations of the template image so that it fits the observations. In this paper, we provide a detailed analysis of a new generative statistical model based on dense deformable templates that represents several tissue types observed in medical images. Our atlas contains both an estimation of probability maps of each tissue (called class) and the deformation metric. We use a stochastic algorithm for the estimation of the probabilistic atlas given a dataset. This atlas is then used for atlas-based segmentation method to segment the new images. Experiments are shown on brain T1 MRI datasets

An MRI Segmentation Framework for Brains with Anatomical Deviations

The segmentation of brain Magnetic Resonance (MR) images, where the brain is partitioned into anatomical regions of interest, is a notoriously difficult problem when the underlying brain structures are influenced by pathology or are undergoing rapid development. This dissertation proposes a new automatic segmentation method for brain MRI that makes use of a model of a homogeneous population to detect anatomical deviations. The chosen population model is a brain atlas created by averaging a set of MR images and the corresponding segmentations. The segmentation method is an integration of robust parameter estimation techniques and the Expectation-Maximization algorithm. In clinical applications, the segmentation of brains with anatomical deviations from those commonly observed within a homogeneous population is of particular interest. One example is provided by brain tumors, since delineation of the tumor and of any surrounding edema is often critical for treatment planning. A second example is provided by the dynamic brain changes that occur in newborns, since study of these changes may generate insights into regional growth trajectories and maturation patterns. Brain tumor and edema can be considered as anatomical deviations from a healthy adult population, whereas the rapid growth of newborn brains can be considered as an anatomical deviation from a population of fully developed infant brains. A fundamental task associated with image segmentation is the validation of segmentation accuracy. In cases in which the brain deviates from standard anatomy, validation is often an ill-defined task since there is no knowledge of the ground truth (information about the actual structures observed through MRI). This dissertation presents a new method of simulating ground truth with pathology that facilitates objective validation of brain tumor segmentations. The simulation method generates realistic-appearing tumors within the MRI of a healthy subject. Since the location, shape, and volume of the synthetic tumors are known with certainty, the simulated MRI can be used to objectively evaluate the accuracy of any brain tumor segmentation method

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

Fast and robust hybrid framework for infant brain classification from structural MRI : a case study for early diagnosis of autism.

The ultimate goal of this work is to develop a computer-aided diagnosis (CAD) system for early autism diagnosis from infant structural magnetic resonance imaging (MRI). The vital step to achieve this goal is to get accurate segmentation of the different brain structures: whitematter, graymatter, and cerebrospinal fluid, which will be the main focus of this thesis. The proposed brain classification approach consists of two major steps. First, the brain is extracted based on the integration of a stochastic model that serves to learn the visual appearance of the brain texture, and a geometric model that preserves the brain geometry during the extraction process. Secondly, the brain tissues are segmented based on shape priors, built using a subset of co-aligned training images, that is adapted during the segmentation process using first- and second-order visual appearance features of infant MRIs. The accuracy of the presented segmentation approach has been tested on 300 infant subjects and evaluated blindly on 15 adult subjects. The experimental results have been evaluated by the MICCAI MR Brain Image Segmentation (MRBrainS13) challenge organizers using three metrics: Dice coefficient, 95-percentile Hausdorff distance, and absolute volume difference. The proposed method has been ranked the first in terms of performance and speed

Recognizing deviations from normalcy for brain tumor segmentation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.Includes bibliographical references (p. 180-189).A framework is proposed for the segmentation of brain tumors from MRI. Instead of training on pathology, the proposed method trains exclusively on healthy tissue. The algorithm attempts to recognize deviations from normalcy in order to compute a fitness map over the image associated with the presence of pathology. The resulting fitness map may then be used by conventional image segmentation techniques for honing in on boundary delineation. Such an approach is applicable to structures that are too irregular, in both shape and texture, to permit construction of comprehensive training sets. We develop the method of diagonalized nearest neighbor pattern recognition, and we use it to demonstrate that recognizing deviations from normalcy requires a rich understanding of context. Therefore, we propose a framework for a Contextual Dependency Network (CDN) that incorporates context at multiple levels: voxel intensities, neighborhood coherence, intra-structure properties, inter-structure relationships, and user input. Information flows bi-directionally between the layers via multi-level Markov random fields or iterated Bayesian classification. A simple instantiation of the framework has been implemented to perform preliminary experiments on synthetic and MRI data.by David Thomas Gering.Ph.D

Clique Identification and Propagation for Multimodal Brain Tumor Image Segmentation

Brain tumors vary considerably in size, morphology, and location across patients, thus pose great challenge in automated brain tumor segmentation methods. Inspired by the concept of clique in graph theory, we present a clique-based method for multimodal brain tumor segmentation that considers a brain tumor image as a graph and automatically segment it into different sub-structures based on the clique homogeneity. Our proposed method has three steps, neighborhood construction, clique identification, and clique propagation. We constructed the neighborhood of each pixel based on its similarities to the surrounding pixels, and then extracted all cliques with a certain size k to evaluate the correlations among different pixels. The connections among all cliques were represented as a transition matrix, and a clique propagation method was developed to group the cliques into different regions. This method is also designed to accommodate multimodal features, as multimodal neuroimaging data is widely used in mapping the tumor-induced changes in the brain. To evaluate this method, we conduct the segmentation experiments on the publicly available Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) dataset. The qualitative and quantitative results demonstrate that our proposed clique-based method achieved better performance compared to the conventional pixel-based methods

Extending Bayesian network models for mining and classification of glaucoma

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Glaucoma is a degenerative disease that damages the nerve fiber layer in the retina of the eye. Its mechanisms are not fully known and there is no fully-effective strategy to prevent visual impairment and blindness. However, if treatment is carried out at an early stage, it is possible to slow glaucomatous progression and improve the quality of life of sufferers. Despite the great amount of heterogeneous data that has become available for monitoring glaucoma, the performance of tests for early diagnosis are still insufficient, due to the complexity of disease progression and the diffculties in obtaining sufficient measurements. This research aims to assess and extend Bayesian Network (BN) models to investigate the nature of the disease and its progression, as well as improve early diagnosis performance. The exibility of BNs and their ability to integrate with clinician expertise make them a suitable tool to effectively exploit the available data. After presenting the problem, a series of BN models for cross-sectional data classification and integration are assessed; novel techniques are then proposed for classification and modelling of glaucoma progression. The results are validated against literature, direct expert knowledge and other Artificial Intelligence techniques, indicating that BNs and their proposed extensions improve glaucoma diagnosis performance and enable new insights into the disease process