AUTOMATIC 3D DEFORMED MIDSAGITTAL SURFACE LOCALIZATION BY CONSTRAINED MONTE CARLO OPTIMIZATION

AUTOMATIC 3D DEFORMED MIDSAGITTAL SURFACE LOCALIZATION BY CONSTRAINED MONTE CARLO OPTIMIZATIO

Feature extraction of the brain tumours with the help of MRI, based on symmetry and partitioning

Computer-aided diagnostic (CAD) studies are used for scientific observations for explanation since very long time, but they are extraordinarily powerful to perform completely machine-driven algorithmic analyses for brain magnetic resonance imaging lesions. Structural and purposeful imbalance within the human brain could be reviewed. This imbalance analysis of the brain has terrific importance in an image analysis. In the present work, the imbalance between the two hemispheres is considered as the base for the detection of the tumour. We have segmented the brain into the two halves using thresholding technique, followed by statistical feature extraction for the double authentication of the existence of tumour which proves to be the better approach. The approach also takes into consideration corrections needed for the tilt observed while capturing the MRI

Segmentation of corpus callosum using diffusion tensor imaging: validation in patients with glioblastoma

Abstract Background This paper presents a three-dimensional (3D) method for segmenting corpus callosum in normal subjects and brain cancer patients with glioblastoma. Methods Nineteen patients with histologically confirmed treatment naïve glioblastoma and eleven normal control subjects underwent DTI on a 3T scanner. Based on the information inherent in diffusion tensors, a similarity measure was proposed and used in the proposed algorithm. In this algorithm, diffusion pattern of corpus callosum was used as prior information. Subsequently, corpus callosum was automatically divided into Witelson subdivisions. We simulated the potential rotation of corpus callosum under tumor pressure and studied the reproducibility of the proposed segmentation method in such cases. Results Dice coefficients, estimated to compare automatic and manual segmentation results for Witelson subdivisions, ranged from 94% to 98% for control subjects and from 81% to 95% for tumor patients, illustrating closeness of automatic and manual segmentations. Studying the effect of corpus callosum rotation by different Euler angles showed that although segmentation results were more sensitive to azimuth and elevation than skew, rotations caused by brain tumors do not have major effects on the segmentation results. Conclusions The proposed method and similarity measure segment corpus callosum by propagating a hyper-surface inside the structure (resulting in high sensitivity), without penetrating into neighboring fiber bundles (resulting in high specificity)

Cortical encoding and decoding models of speech production

To speak is to dynamically orchestrate the movements of the articulators (jaw, tongue, lips, and larynx), which in turn generate speech sounds. It is an amazing mental and motor feat that is controlled by the brain and is fundamental for communication. Technology that could translate brain signals into speech would be transformative for people who are unable to communicate as a result of neurological impairments. This work first investigates how articulator movements that underlie natural speech production are represented in the brain. Building upon this, this work also presents a neural decoder that can synthesize audible speech from brain signals. Data to support these results were from direct cortical recordings of the human sensorimotor cortex while participants spoke natural sentences. Neural activity at individual electrodes encoded a diversity of articulatory kinematic trajectories (AKTs), each revealing coordinated articulator movements towards specific vocal tract shapes. The neural decoder was designed to leverage the kinematic trajectories encoded in the sensorimotor cortex which enhanced performance even with limited data. In closed vocabulary tests, listeners could readily identify and transcribe speech synthesized from cortical activity. These findings advance the clinical viability of using speech neuroprosthetic technology to restore spoken communication

Brain connectivity mapping with diffusion MRI across individuals and species

The human brain is a highly complex organ that integrates functionally specialised subunits. Underpinning this complexity and functional specialisation is a network of structural connections, which may be probed using diffusion tractography, a unique, powerful and non-invasive MRI technique. Estimates of brain connectivity derived through diffusion tractography allow for explorations of how the brain’s functional subunits are inter-linked to subsequently produce experiences and behaviour. This thesis develops new diffusion tractography methodology for mapping brain connectivity, both across individuals and also across species; and explores frameworks for discovering associations of such brain connectivity features with behavioural traits. We build upon the hypothesis that connectional patterns can probe regions of functional equivalence across brains. To test this hypothesis we develop standardised and automated frameworks for mapping these patterns in very diverse brains, such as from human and non-human primates. We develop protocols to extract homologous fibre bundles across two species (human and macaque monkeys). We demonstrate robustness and generalisability of these protocols, but also their ability to capture individual variability. We also present investigations into how structural connectivity profiles may be used to inform us of how functionally-related features can be linked across different brains. Further, we explore how fully data-driven tractography techniques may be utilised for similar purposes, opening the door for future work on data-driven connectivity mapping. Subsequently, we explore how such individual variability in features that probe brain organisation are associated with differences in human behaviour. One approach to performing such explorations is the use of powerful multivariate statisitical techniques, such as canonical correlation analysis (CCA). After identifying issues in out-of-sample replication using multi-modal connectivity information, we perform comprehensive explorations into the robustness of such techniques and devise a generative model for forward predictions, demonstrating significant challlenges and limitations in their current applications. Specifically, we predict that the stability and generalisability of these techniques requires an order of magnitude more subjects than typically used to avoid overfitting and mis-interpretation of results. Using population-level data from the UK Biobank and confirmations from independent imaging modalities from the Human Connectome Project, we validate this prediction and demonstrate the direct link of CCA stability and generalisability with the number of subjects used per considered feature

Brain connectivity mapping with diffusion MRI across individuals and species

The human brain is a highly complex organ that integrates functionally specialised subunits. Underpinning this complexity and functional specialisation is a network of structural connections, which may be probed using diffusion tractography, a unique, powerful and non-invasive MRI technique. Estimates of brain connectivity derived through diffusion tractography allow for explorations of how the brain’s functional subunits are inter-linked to subsequently produce experiences and behaviour. This thesis develops new diffusion tractography methodology for mapping brain connectivity, both across individuals and also across species; and explores frameworks for discovering associations of such brain connectivity features with behavioural traits. We build upon the hypothesis that connectional patterns can probe regions of functional equivalence across brains. To test this hypothesis we develop standardised and automated frameworks for mapping these patterns in very diverse brains, such as from human and non-human primates. We develop protocols to extract homologous fibre bundles across two species (human and macaque monkeys). We demonstrate robustness and generalisability of these protocols, but also their ability to capture individual variability. We also present investigations into how structural connectivity profiles may be used to inform us of how functionally-related features can be linked across different brains. Further, we explore how fully data-driven tractography techniques may be utilised for similar purposes, opening the door for future work on data-driven connectivity mapping. Subsequently, we explore how such individual variability in features that probe brain organisation are associated with differences in human behaviour. One approach to performing such explorations is the use of powerful multivariate statisitical techniques, such as canonical correlation analysis (CCA). After identifying issues in out-of-sample replication using multi-modal connectivity information, we perform comprehensive explorations into the robustness of such techniques and devise a generative model for forward predictions, demonstrating significant challlenges and limitations in their current applications. Specifically, we predict that the stability and generalisability of these techniques requires an order of magnitude more subjects than typically used to avoid overfitting and mis-interpretation of results. Using population-level data from the UK Biobank and confirmations from independent imaging modalities from the Human Connectome Project, we validate this prediction and demonstrate the direct link of CCA stability and generalisability with the number of subjects used per considered feature

Object detection and segmentation using discriminative learning

Object detection and segmentation algorithms need to use prior knowledge of objects' shape and appearance to guide solutions to correct ones. A promising way of obtaining prior knowledge is to learn it directly from expert annotations by using machine learning techniques. Previous approaches commonly use generative learning approaches to achieve this goal. In this dissertation, I propose a series of discriminative learning algorithms based on boosting principles to learn prior knowledge from image databases with expert annotations. The learned knowledge improves the performance of detection and segmentation, leading to fast and accurate solutions. For object detection, I present a learning procedure called a Probabilistic Boosting Network (PBN) suitable for real-time object detection and pose estimation. Based on the law of total probability, PBN integrates evidence from two building blocks, namely a multiclass classifier for pose estimation and a detection cascade for object detection. Both the classifier and detection cascade employ boosting. By inferring the pose parameter, I avoid the exhaustive scan over pose parameters, which hampers real-time detection. I implement PBN using a graph-structured network that alternates the two tasks of object detection and pose estimation in an effort to reject negative cases as quickly as possible. Compared with previous approaches, PBN has higher accuracy in object localization and pose estimation with noticeable reduced computation. For object segmentation, I cast deformable object segmentation as optimizing the conditional probability density function p(C|I), where I is an image and C is a vector of model parameters describing the object shape. I propose a regression approach to learn the density p(C|I) discriminatively based on boosting principles. The learned density p(C|I) possesses a desired unimodal, smooth shape, which can be used by optimization algorithms to efficiently estimate a solution. To handle the high-dimensional learning challenges, I propose a multi-level approach and a gradient-based sampling strategy to learn regression functions efficiently. I show that the regression approach consistently outperforms state-of-the-art methods on a variety of testing datasets. Finally, I present a comparative study on how to apply three discriminative learning approaches - classification, regression, and ranking - to deformable shape segmentation. I discuss how to extend the idea of the regression approach to build discriminative models using classification and ranking. I propose sampling strategies to collect training examples from a high-dimensional model space for the classification and the ranking approach. I also propose a ranking algorithm based on Rankboost to learn a discriminative model for segmentation. Experimental results on left ventricle and left atrium segmentation from ultrasound images and facial feature localization demonstrate that the discriminative models outperform generative models and energy minimization methods by a large margin

Observations on the dynamic control of an articulatory synthesizer using speech production data

This dissertation explores the automatic generation of gestural score based control structures for a three-dimensional articulatory speech synthesizer. The gestural scores are optimized in an articulatory resynthesis paradigm using a dynamic programming algorithm and a cost function which measures the deviation from a gold standard in the form of natural speech production data. This data had been recorded using electromagnetic articulography, from the same speaker to which the synthesizer\u27s vocal tract model had previously been adapted. Future work to create an English voice for the synthesizer and integrate it into a text-to-speech platform is outlined.Die vorliegende Dissertation untersucht die automatische Erzeugung von gesturalpartiturbasierten Steuerdaten für ein dreidimensionales artikulatorisches Sprachsynthesesystem. Die gesturalen Partituren werden in einem artikulatorischen Resynthese-Paradigma mittels dynamischer Programmierung optimiert, unter Zuhilfenahme einer Kostenfunktion, die den Abstand zu einem "Gold Standard" in Form natürlicher Sprachproduktionsdaten mißt. Diese Daten waren mit elektromagnetischer Artikulographie am selben Sprecher aufgenommen worden, an den zuvor das Vokaltraktmodell des Synthesesystems angepaßt worden war. Weiterführende Forschung, eine englische Stimme für das Synthesesystem zu erzeugen und sie in eine Text-to-Speech-Plattform einzubetten, wird umrissen

An automated system for the classification and segmentation of brain tumours in MRI images based on the modified grey level co-occurrence matrix

The development of an automated system for the classification and segmentation of brain tumours in MRI scans remains challenging due to high variability and complexity of the brain tumours. Visual examination of MRI scans to diagnose brain tumours is the accepted standard. However due to the large number of MRI slices that are produced for each patient this is becoming a time consuming and slow process that is also prone to errors. This study explores an automated system for the classification and segmentation of brain tumours in MRI scans based on texture feature extraction. The research investigates an appropriate technique for feature extraction and development of a three-dimensional segmentation method. This was achieved by the investigation and integration of several image processing methods that are related to texture features and segmentation of MRI brain scans. First, the MRI brain scans were pre-processed by image enhancement, intensity normalization, background segmentation and correcting the mid-sagittal plane (MSP) of the brain for any possible skewness in the patient’s head. Second, the texture features were extracted using modified grey level co-occurrence matrix (MGLCM) from T2-weighted (T2-w) MRI slices and classified into normal and abnormal using multi-layer perceptron neural network (MLP). The texture feature extraction method starts from the standpoint that the human brain structure is approximately symmetric around the MSP of the brain. The extracted features measure the degree of symmetry between the left and right hemispheres of the brain, which are used to detect the abnormalities in the brain. This will enable clinicians to reject the MRI brain scans of the patients who have normal brain quickly and focusing on those who have pathological brain features. Finally, the bounding 3D-boxes based genetic algorithm (BBBGA) was used to identify the location of the brain tumour and segments it automatically by using three-dimensional active contour without edge (3DACWE) method. The research was validated using two datasets; a real dataset that was collected from the MRI Unit in Al-Kadhimiya Teaching Hospital in Iraq in 2014 and the standard benchmark multimodal brain tumour segmentation (BRATS 2013) dataset. The experimental results on both datasets proved that the efficacy of the proposed system in the successful classification and segmentation of the brain tumours in MRI scans. The achieved classification accuracies were 97.8% for the collected dataset and 98.6% for the standard dataset. While the segmentation’s Dice scores were 89% for the collected dataset and 89.3% for the standard dataset