Brain MR Image Segmentation: From Multi-Atlas Method To Deep Learning Models

Quantitative analysis of the brain structures on magnetic resonance (MR) images plays a crucial role in examining brain development and abnormality, as well as in aiding the treatment planning. Although manual delineation is commonly considered as the gold standard, it suffers from the shortcomings in terms of low efficiency and inter-rater variability. Therefore, developing automatic anatomical segmentation of human brain is of importance in providing a tool for quantitative analysis (e.g., volume measurement, shape analysis, cortical surface mapping). Despite a large number of existing techniques, the automatic segmentation of brain MR images remains a challenging task due to the complexity of the brain anatomical structures and the great inter- and intra-individual variability among these anatomical structures. To address the existing challenges, four methods are proposed in this thesis. The first work proposes a novel label fusion scheme for the multi-atlas segmentation. A two-stage majority voting scheme is developed to address the over-segmentation problem in the hippocampus segmentation of brain MR images. The second work of the thesis develops a supervoxel graphical model for the whole brain segmentation, in order to relieve the dependencies on complicated pairwise registration for the multi-atlas segmentation methods. Based on the assumption that pixels within a supervoxel are supposed to have the same label, the proposed method converts the voxel labeling problem to a supervoxel labeling problem which is solved by a maximum-a-posteriori (MAP) inference in Markov random field (MRF) defined on supervoxels. The third work incorporates attention mechanism into convolutional neural networks (CNN), aiming at learning the spatial dependencies between the shallow layers and the deep layers in CNN and producing an aggregation of the attended local feature and high-level features to obtain more precise segmentation results. The fourth method takes advantage of the success of CNN in computer vision, combines the strength of the graphical model with CNN, and integrates them into an end-to-end training network. The proposed methods are evaluated on public MR image datasets, such as MICCAI2012, LPBA40, and IBSR. Extensive experiments demonstrate the effectiveness and superior performance of the three proposed methods compared with the other state-of-the-art methods

Characterizing and comparing acoustic representations in convolutional neural networks and the human auditory system

Le traitement auditif dans le cerveau humain et dans les systèmes informatiques consiste en une cascade de transformations représentationnelles qui extraient et réorganisent les informations pertinentes pour permettre l'exécution des tâches. Cette thèse s'intéresse à la nature des représentations acoustiques et aux principes de conception et d'apprentissage qui soutiennent leur développement. Les objectifs scientifiques sont de caractériser et de comparer les représentations auditives dans les réseaux de neurones convolutionnels profonds (CNN) et la voie auditive humaine. Ce travail soulève plusieurs questions méta-scientifiques sur la nature du progrès scientifique, qui sont également considérées. L'introduction passe en revue les connaissances actuelles sur la voie auditive des mammifères et présente les concepts pertinents de l'apprentissage profond. Le premier article soutient que les questions philosophiques les plus pressantes à l'intersection de l'intelligence artificielle et biologique concernent finalement la définition des phénomènes à expliquer et ce qui constitue des explications valables de tels phénomènes. Je surligne les théories pertinentes de l'explication scientifique que j’espére fourniront un échafaudage pour de futures discussions. L'article 2 teste un modèle populaire de cortex auditif basé sur des modulations spectro-temporelles. Nous constatons qu'un modèle linéaire entraîné uniquement sur les réponses BOLD aux ondulations dynamiques simples (contenant seulement une fréquence fondamentale, un taux de modulation temporelle et une échelle spectrale) peut se généraliser pour prédire les réponses aux mélanges de deux ondulations dynamiques. Le troisième article caractérise la spécificité linguistique des couches CNN et explore l'effet de l'entraînement figé et des poids aléatoires. Nous avons observé trois régions distinctes de transférabilité: (1) les deux premières couches étaient entièrement transférables, (2) les couches 2 à 8 étaient également hautement transférables, mais nous avons trouvé évidence de spécificité de la langue, (3) les couches suivantes entièrement connectées étaient plus spécifiques à la langue mais pouvaient être adaptées sur la langue cible. Dans l'article 4, nous utilisons l'analyse de similarité pour constater que la performance supérieure de l'entraînement figé obtenues à l'article 3 peuvent être attribuées aux différences de représentation dans l'avant-dernière couche: la deuxième couche entièrement connectée. Nous analysons également les réseaux aléatoires de l'article 3, dont nous concluons que la forme représentationnelle est doublement contrainte par l'architecture et la forme de l'entrée et de la cible. Pour tester si les CNN acoustiques apprennent une hiérarchie de représentation similaire à celle du système auditif humain, le cinquième article compare l'activité des réseaux «freeze trained» de l'article 3 à l'activité IRMf 7T dans l'ensemble du système auditif humain. Nous ne trouvons aucune évidence d'une hiérarchie de représentation partagée et constatons plutôt que tous nos régions auditifs étaient les plus similaires à la première couche entièrement connectée. Enfin, le chapitre de discussion passe en revue les mérites et les limites d'une approche d'apprentissage profond aux neurosciences dans un cadre de comparaison de modèles. Ensemble, ces travaux contribuent à l'entreprise naissante de modélisation du système auditif avec des réseaux de neurones et constituent un petit pas vers une science unifiée de l'intelligence qui étudie les phénomènes qui se manifestent dans l'intelligence biologique et artificielle.Auditory processing in the human brain and in contemporary machine hearing systems consists of a cascade of representational transformations that extract and reorganize relevant information to enable task performance. This thesis is concerned with the nature of acoustic representations and the network design and learning principles that support their development. The primary scientific goals are to characterize and compare auditory representations in deep convolutional neural networks (CNNs) and the human auditory pathway. This work prompts several meta-scientific questions about the nature of scientific progress, which are also considered. The introduction reviews what is currently known about the mammalian auditory pathway and introduces the relevant concepts in deep learning.The first article argues that the most pressing philosophical questions at the intersection of artificial and biological intelligence are ultimately concerned with defining the phenomena to be explained and with what constitute valid explanations of such phenomena. I highlight relevant theories of scientific explanation which we hope will provide scaffolding for future discussion. Article 2 tests a popular model of auditory cortex based on frequency-specific spectrotemporal modulations. We find that a linear model trained only on BOLD responses to simple dynamic ripples (containing only one fundamental frequency, temporal modulation rate, and spectral scale) can generalize to predict responses to mixtures of two dynamic ripples. Both the third and fourth article investigate how CNN representations are affected by various aspects of training. The third article characterizes the language specificity of CNN layers and explores the effect of freeze training and random weights. We observed three distinct regions of transferability: (1) the first two layers were entirely transferable between languages, (2) layers 2--8 were also highly transferable but we found some evidence of language specificity, (3) the subsequent fully connected layers were more language specific but could be successfully finetuned to the target language. In Article 4, we use similarity analysis to find that the superior performance of freeze training achieved in Article 3 can be largely attributed to representational differences in the penultimate layer: the second fully connected layer. We also analyze the random networks from Article 3, from which we conclude that representational form is doubly constrained by architecture and the form of the input and target. To test whether acoustic CNNs learn a similar representational hierarchy as that of the human auditory system, the fifth article presents a similarity analysis to compare the activity of the freeze trained networks from Article 3 to 7T fMRI activity throughout the human auditory system. We find no evidence of a shared representational hierarchy and instead find that all of our auditory regions were most similar to the first fully connected layer. Finally, the discussion chapter reviews the merits and limitations of a deep learning approach to neuroscience in a model comparison framework. Together, these works contribute to the nascent enterprise of modeling the auditory system with neural networks and constitute a small step towards a unified science of intelligence that studies the phenomena that are exhibited in both biological and artificial intelligence

Brain-Inspired Computing

This open access book constitutes revised selected papers from the 4th International Workshop on Brain-Inspired Computing, BrainComp 2019, held in Cetraro, Italy, in July 2019. The 11 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They deal with research on brain atlasing, multi-scale models and simulation, HPC and data infra-structures for neuroscience as well as artificial and natural neural architectures

Evaluation of deep learning transformers models for brain stroke lesions automatic segmentation

Brain stroke represents a leading cause in long-term disability worldwide, stroke rehabilitation research is focused on the understating of the relationship between brain, behavior, and recovery, using as a basis brain changes generated after a stroke, this allows for precise diagnostic and possible predictions in terms of functional outcomes. Neuroimaging represents the main resource for brain stroke research and therapies, it is of particular interest high-resolution T1- weighted (T1w) anatomical MRIs, which are used to evaluate/examine structural brain changes after stroke episodes. Several techniques have been developed in order to accurately calculate or approximate the percentage between lesions and critical brain structures, this step constitutes a paramount step for precise lesion annotation. Despite the technological progress or advance, to date, manual lesion tracing by a team of experts in neuroimaging remains as the gold standard to draw valid clinical inferences for lesion segmentation. The following work proposes a review of the machine and deep learning models that have been developed focusing in the transformers algorithm which is a state of the art method based on the self attention mechanism that has outperformed recurrent neural networks in terms of evaluation metrics such as the dice value, being able to capture long distant dependencies which is a fundamental step when processing 3D volumes, formed by a stacked 2D MRI images. The models were tested using the ATLAS dataset (Anatomical tracing of lesions after stroke) which is an open source data set of T1-weighted MRIs with manual segmented brain lesions.Brain stroke represents a leading cause in long-term disability worldwide, stroke rehabilitation research is focused on the understating of the relationship between brain, behavior, and recovery, using as a basis brain changes generated after a stroke, this allows for precise diagnostic and possible predictions in terms of functional outcomes. Neuroimaging represents the main resource for brain stroke research and therapies, it is of particular interest high-resolution T1- weighted (T1w) anatomical MRIs, which are used to evaluate/examine structural brain changes after stroke episodes. Several techniques have been developed in order to accurately calculate or approximate the percentage between lesions and critical brain structures, this step constitutes a paramount step for precise lesion annotation. Despite the technological progress or advance, to date, manual lesion tracing by a team of experts in neuroimaging remains as the gold standard to draw valid clinical inferences for lesion segmentation. The following work proposes a review of the machine and deep learning models that have been developed focusing in the transformers algorithm which is a state of the art method based on the self attention mechanism that has outperformed recurrent neural networks in terms of evaluation metrics such as the dice value, being able to capture long distant dependencies which is a fundamental step when processing 3D volumes, formed by a stacked 2D MRI images. The models were tested using the ATLAS dataset (Anatomical tracing of lesions after stroke) which is an open source data set of T1-weighted MRIs with manual segmented brain lesions

Neuron-level dynamics of oscillatory network structure and markerless tracking of kinematics during grasping

Oscillatory synchrony is proposed to play an important role in flexible sensory-motor transformations. Thereby, it is assumed that changes in the oscillatory network structure at the level of single neurons lead to flexible information processing. Yet, how the oscillatory network structure at the neuron-level changes with different behavior remains elusive. To address this gap, we examined changes in the fronto-parietal oscillatory network structure at the neuron-level, while monkeys performed a flexible sensory-motor grasping task. We found that neurons formed separate subnetworks in the low frequency and beta bands. The beta subnetwork was active during steady states and the low frequency network during active states of the task, suggesting that both frequencies are mutually exclusive at the neuron-level. Furthermore, both frequency subnetworks reconfigured at the neuron-level for different grip and context conditions, which was mostly lost at any scale larger than neurons in the network. Our results, therefore, suggest that the oscillatory network structure at the neuron-level meets the necessary requirements for the coordination of flexible sensory-motor transformations. Supplementarily, tracking hand kinematics is a crucial experimental requirement to analyze neuronal control of grasp movements. To this end, a 3D markerless, gloveless hand tracking system was developed using computer vision and deep learning techniques. 2021-11-3

Brain Tumor Detection and Classification from MRI Images

A brain tumor is detected and classified by biopsy that is conducted after the brain surgery. Advancement in technology and machine learning techniques could help radiologists in the diagnosis of tumors without any invasive measures. We utilized a deep learning-based approach to detect and classify the tumor into Meningioma, Glioma, Pituitary tumors. We used registration and segmentation-based skull stripping mechanism to remove the skull from the MRI images and the grab cut method to verify whether the skull stripped MRI masks retained the features of the tumor for accurate classification. In this research, we proposed a transfer learning based approach in conjunction with discriminative learning rates to perform the classification of brain tumors. The data set used is a 3064 T MRI images dataset that contains T1 flair MRI images. We achieved a classification accuracy of 98.83%, 96.26%, and 95.18% for training, validation, and test sets and an F1 score of 0.96 on the T1 Flair MRI dataset

Deep Learning for Multiclass Classification, Predictive Modeling and Segmentation of Disease Prone Regions in Alzheimer’s Disease

One of the challenges facing accurate diagnosis and prognosis of Alzheimer’s Disease (AD) is identifying the subtle changes that define the early onset of the disease. This dissertation investigates three of the main challenges confronted when such subtle changes are to be identified in the most meaningful way. These are (1) the missing data challenge, (2) longitudinal modeling of disease progression, and (3) the segmentation and volumetric calculation of disease-prone brain areas in medical images. The scarcity of sufficient data compounded by the missing data challenge in many longitudinal samples exacerbates the problem as we seek statistical meaningfulness in multiclass classification and regression analysis. Although there are many participants in the AD Neuroimaging Initiative (ADNI) study, many of the observations have a lot of missing features which often lead to the exclusion of potentially valuable data points that could add significant meaning in many ongoing experiments. Motivated by the necessity of examining all participants, even those with missing tests or imaging modalities, multiple techniques of handling missing data in this domain have been explored. Specific attention was drawn to the Gradient Boosting (GB) algorithm which has an inherent capability of addressing missing values. Prior to applying state-of-the-art classifiers such as Support Vector Machine (SVM) and Random Forest (RF), the impact of imputing data in common datasets with numerical techniques has been also investigated and compared with the GB algorithm. Furthermore, to discriminate AD subjects from healthy control individuals, and Mild Cognitive Impairment (MCI), longitudinal multimodal heterogeneous data was modeled using recurring neural networks (RNNs). In the segmentation and volumetric calculation challenge, this dissertation places its focus on one of the most relevant disease-prone areas in many neurological and neurodegenerative diseases, the hippocampus region. Changes in hippocampus shape and volume are considered significant biomarkers for AD diagnosis and prognosis. Thus, a two-stage model based on integrating the Vision Transformer and Convolutional Neural Network (CNN) is developed to automatically locate, segment, and estimate the hippocampus volume from the brain 3D MRI. The proposed architecture was trained and tested on a dataset containing 195 brain MRIs from the 2019 Medical Segmentation Decathlon Challenge against the manually segmented regions provided therein and was deployed on 326 MRI from our own data collected through Mount Sinai Medical Center as part of the 1Florida Alzheimer Disease Research Center (ADRC)