Volumetric texture description and discriminant feature selection for MRI

This paper considers the problem of classification of Magnetic Resonance Images using 2D and 3D texture measures. Joint statistics such as co-occurrence matrices are common for analysing texture in 2D since they are simple and effective to implement. However, the computational complexity can be prohibitive especially in 3D. In this work, we develop a texture classification strategy by a sub-band filtering technique that can be extended to 3D. We further propose a feature selection technique based on the Bhattacharyya distance measure that reduces the number of features required for the classification by selecting a set of discriminant features conditioned on a set training texture samples. We describe and illustrate the methodology by quantitatively analysing a series of images: 2D synthetic phantom, 2D natural textures, and MRI of human knees

Texture Analysis Platform for Imaging Biomarker Research

abstract: The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope. Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers. This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Quantitative MRI Brain Studies in Mild Cognitive Impairment and Alzheimer's disease: A Methodological Review

Classifying and predicting Alzheimer's disease (AD) in individuals with memory disorders through clinical and psychometric assessment is challenging especially in Mild Cognitive Impairment (MCI) subjects. Quantitative structural Magnetic Resonance Imaging (MRI) acquisition methods in combination with Computer-Aided Diagnosis (CAD) are currently being used for the assessment AD. These acquisitions methods include: i) Voxel-based Morphometry (VBM), ii) volumetric measurements in specific Regions of Interest (ROIs), iii) cortical thickness measurements, iv) shape analysis and v) texture analysis. This review evaluates the aforementioned methods in the classification of cases into one of the following 3 groups: Normal Controls (NC), MCI and AD subjects. Furthermore, the performance of the methods is assessed on the prediction of conversion from MCI to AD. In parallel, it is also assessed which ROIs are preferred in both classification and prognosis through the different states of the disease. Structural changes in the early stages of the disease are more pronounced in the Medial Temporal Lobe (MTL) especially in the entorhinal cortex, whereas with disease progression both entorhinal cortex and hippocampus offer similar discriminative power. However, for the conversion from MCI subjects to AD, entorhinal cortex provides better predictive accuracies rather than other structures, such as the hippocampus

Tensor-Based Grading: A Novel Patch-Based Grading Approach for the Analysis of Deformation Fields in Huntington's Disease

The improvements in magnetic resonance imaging have led to the development of numerous techniques to better detect structural alterations caused by neurodegenerative diseases. Among these, the patch-based grading framework has been proposed to model local patterns of anatomical changes. This approach is attractive because of its low computational cost and its competitive performance. Other studies have proposed to analyze the deformations of brain structures using tensor-based morphometry, which is a highly interpretable approach. In this work, we propose to combine the advantages of these two approaches by extending the patch-based grading framework with a new tensor-based grading method that enables us to model patterns of local deformation using a log-Euclidean metric. We evaluate our new method in a study of the putamen for the classification of patients with pre-manifest Huntington's disease and healthy controls. Our experiments show a substantial increase in classification accuracy (87.5 $\pm$ 0.5 vs. 81.3 $\pm$ 0.6) compared to the existing patch-based grading methods, and a good complement to putamen volume, which is a primary imaging-based marker for the study of Huntington's disease

Model-Based Approach for Diffuse Glioma Classification, Grading, and Patient Survival Prediction

The work in this dissertation proposes model-based approaches for molecular mutations classification of gliomas, grading based on radiomics features and genomics, and prediction of diffuse gliomas clinical outcome in overall patient survival. Diffuse gliomas are types of Central Nervous System (CNS) brain tumors that account for 25.5% of primary brain and CNS tumors and originate from the supportive glial cells. In the 2016 World Health Organization’s (WHO) criteria for CNS brain tumor, a major reclassification of the diffuse gliomas is presented based on gliomas molecular mutations and the growth behavior. Currently, the status of molecular mutations is determined by obtaining viable regions of tumor tissue samples. However, an increasing need to non-invasively analyze the clinical outcome of tumors requires careful modeling and co-analysis of radiomics (i.e., imaging features) and genomics (molecular and proteomics features). The variances in diffuse Lower-grade gliomas (LGG), which are demonstrated by their heterogeneity, can be exemplified by radiographic imaging features (i.e., radiomics). Therefore, radiomics may be suggested as a crucial non-invasive marker in the tumor diagnosis and prognosis. Consequently, we examine radiomics extracted from the multi-resolution fractal representations of the tumor in classifying the molecular mutations of diffuse LGG non-invasively. The proposed radiomics in the decision-tree-based ensemble machine learning molecular prediction model confirm the efficacy of these fractal features in glioma prediction. Furthermore, this dissertation proposes a novel non-invasive statistical model to classify and predict LGG molecular mutations based on radiomics and count-based genomics data. The performance results of the proposed statistical model indicate that fusing radiomics to count-based genomics improves the performance of mutations prediction. Furthermore, the radiomics-based glioblastoma survival prediction framework is proposed in this work. The survival prediction framework includes two survival prediction pipelines that combine different feature selection and regression approaches. The framework is evaluated using two recent widely used benchmark datasets from Brain Tumor Segmentation (BraTS) challenges in 2017 and 2018. The first survival prediction pipeline offered the best overall performance in the 2017 Challenge, and the second survival prediction pipeline offered the best performance using the validation dataset. In summary, in this work, we develop non-invasive computational and statistical models based on radiomics and genomics to investigate overall survival, tumor progression, and the molecular classification in diffuse gliomas. The methods discussed in our study are important steps towards a non-invasive approach to diffuse brain tumor classification, grading, and patient survival prediction that may be recommended prior to invasive tissue sampling in a clinical setting

Feature Extraction

Feature extraction is a procedure aimed at selecting and transforming a data set in order to increase the performance of a pattern recognition or machine learning system. Nowadays, since the amount of data available and its dimension is growing exponentially, it is a fundamental procedure to avoid overfitting and the curse of dimensionality, while, in some cases, allowing a interpretative analysis of the data. The topic itself is a thriving discipline of study, and it is difficult to address every single feature extraction algorithm. Therefore, we provide an overview of the topic, introducing widely used techniques, while at the same time presenting some domain-specific feature extraction algorithms. Finally, as a case, study, we will illustrate the vastness of the field by analysing the usage and impact of feature extraction in neuroimaging

Texture Segmentation: An Objective Comparison between Traditional and Deep-Learning Methodologies

This paper compares a series of traditional and deep learning methodologies for the segmentation of textures. Six well-known texture composites first published by Randen and Hus{\o}y were used to compare traditional segmentation techniques (co-occurrence, filtering, local binary patterns, watershed, multiresolution sub-band filtering) against a deep-learning approach based on the U-Net architecture. For the latter, the effects of depth of the network, number of epochs and different optimisation algorithms were investigated. Overall, the best results were provided by the deep-learning approach. However, the best results were distributed within the parameters, and many configurations provided results well below the traditional techniques