Supervised learning-based multimodal MRI brain image analysis

Medical imaging plays an important role in clinical procedures related to cancer, such as diagnosis, treatment selection, and therapy response evaluation. Magnetic resonance imaging (MRI) is one of the most popular acquisition modalities which is widely used in brain tumour analysis and can be acquired with different acquisition protocols, e.g. conventional and advanced. Automated segmentation of brain tumours in MR images is a difficult task due to their high variation in size, shape and appearance. Although many studies have been conducted, it still remains a challenging task and improving accuracy of tumour segmentation is an ongoing field. The aim of this thesis is to develop a fully automated method for detection and segmentation of the abnormal tissue associated with brain tumour (tumour core and oedema) from multimodal MRI images. In this thesis, firstly, the whole brain tumour is segmented from fluid attenuated inversion recovery (FLAIR) MRI, which is commonly acquired in clinics. The segmentation is achieved using region-wise classification, in which regions are derived from superpixels. Several image features including intensity-based, Gabor textons, fractal analysis and curvatures are calculated from each superpixel within the entire brain area in FLAIR MRI to ensure a robust classification. Extremely randomised trees (ERT) classifies each superpixel into tumour and non-tumour. Secondly, the method is extended to 3D supervoxel based learning for segmentation and classification of tumour tissue subtypes in multimodal MRI brain images. Supervoxels are generated using the information across the multimodal MRI data set. This is then followed by a random forests (RF) classifier to classify each supervoxel into tumour core, oedema or healthy brain tissue. The information from the advanced protocols of diffusion tensor imaging (DTI), i.e. isotropic (p) and anisotropic (q) components is also incorporated to the conventional MRI to improve segmentation accuracy. Thirdly, to further improve the segmentation of tumour tissue subtypes, the machine-learned features from fully convolutional neural network (FCN) are investigated and combined with hand-designed texton features to encode global information and local dependencies into feature representation. The score map with pixel-wise predictions is used as a feature map which is learned from multimodal MRI training dataset using the FCN. The machine-learned features, along with hand-designed texton features are then applied to random forests to classify each MRI image voxel into normal brain tissues and different parts of tumour. The methods are evaluated on two datasets: 1) clinical dataset, and 2) publicly available Multimodal Brain Tumour Image Segmentation Benchmark (BRATS) 2013 and 2017 dataset. The experimental results demonstrate the high detection and segmentation performance of the III single modal (FLAIR) method. The average detection sensitivity, balanced error rate (BER) and the Dice overlap measure for the segmented tumour against the ground truth for the clinical data are 89.48%, 6% and 0.91, respectively; whilst, for the BRATS dataset, the corresponding evaluation results are 88.09%, 6% and 0.88, respectively. The corresponding results for the tumour (including tumour core and oedema) in the case of multimodal MRI method are 86%, 7%, 0.84, for the clinical dataset and 96%, 2% and 0.89 for the BRATS 2013 dataset. The results of the FCN based method show that the application of the RF classifier to multimodal MRI images using machine-learned features based on FCN and hand-designed features based on textons provides promising segmentations. The Dice overlap measure for automatic brain tumor segmentation against ground truth for the BRATS 2013 dataset is 0.88, 0.80 and 0.73 for complete tumor, core and enhancing tumor, respectively, which is competitive to the state-of-the-art methods. The corresponding results for BRATS 2017 dataset are 0.86, 0.78 and 0.66 respectively. The methods demonstrate promising results in the segmentation of brain tumours. This provides a close match to expert delineation across all grades of glioma, leading to a faster and more reproducible method of brain tumour detection and delineation to aid patient management. In the experiments, texton has demonstrated its advantages of providing significant information to distinguish various patterns in both 2D and 3D spaces. The segmentation accuracy has also been largely increased by fusing information from multimodal MRI images. Moreover, a unified framework is present which complementarily integrates hand-designed features with machine-learned features to produce more accurate segmentation. The hand-designed features from shallow network (with designable filters) encode the prior-knowledge and context while the machine-learned features from a deep network (with trainable filters) learn the intrinsic features. Both global and local information are combined using these two types of networks that improve the segmentation accuracy

Pieces-of-parts for supervoxel segmentation with global context: Application to DCE-MRI tumour delineation

Rectal tumour segmentation in dynamic contrast-enhanced MRI (DCE-MRI) is a challenging task, and an automated and consistent method would be highly desirable to improve the modelling and prediction of patient outcomes from tissue contrast enhancement characteristics – particularly in routine clinical practice. A framework is developed to automate DCE-MRI tumour segmentation, by introducing: perfusion-supervoxels to over-segment and classify DCE-MRI volumes using the dynamic contrast enhancement characteristics; and the pieces-of-parts graphical model, which adds global (anatomic) constraints that further refine the supervoxel components that comprise the tumour. The framework was evaluated on 23 DCE-MRI scans of patients with rectal adenocarcinomas, and achieved a voxelwise area-under the receiver operating characteristic curve (AUC) of 0.97 compared to expert delineations. Creating a binary tumour segmentation, 21 of the 23 cases were segmented correctly with a median Dice similarity coefficient (DSC) of 0.63, which is close to the inter-rater variability of this challenging task. A second study is also included to demonstrate the method’s generalisability and achieved a DSC of 0.71. The framework achieves promising results for the underexplored area of rectal tumour segmentation in DCE-MRI, and the methods have potential to be applied to other DCE-MRI and supervoxel segmentation problems

Enhancing the Potential of the Conventional Gaussian Mixture Model for Segmentation: from Images to Videos

Segmentation in images and videos has continuously played an important role in image processing, pattern recognition and machine vision. Despite having been studied for over three decades, the problem of segmentation remains challenging yet appealing due to its ill-posed nature. Maintaining spatial coherence, particularly at object boundaries, remains difficult for image segmentation. Extending to videos, maintaining spatial and temporal coherence, even partially, proves computationally burdensome for recent methods. Finally, connecting these two, foreground segmentation, also known as background suppression, suffers from noisy or dynamic backgrounds, slow foregrounds and illumination variations, to name a few. This dissertation focuses more on probabilistic model based segmentation, primarily due to its applicability in images as well as videos, its past success and mainly because it can be enhanced by incorporating spatial and temporal cues. The first part of the dissertation focuses on enhancing conventional GMM for image segmentation using Bilateral filter due to its power of spatial smoothing while preserving object boundaries. Quantitative and qualitative evaluations are done to show the improvements over a number of recent approaches. The later part of the dissertation concentrates on enhancing GMM towards foreground segmentation as a connection between image and video segmentation. First, we propose an efficient way to include multiresolution features in GMM. This novel procedure implicitly incorporates spatial information to improve foreground segmentation by suppressing noisy backgrounds. The procedure is shown with Wavelets, and gradually extended to propose a generic framework to include other multiresolution decompositions. Second, we propose a more accurate foreground segmentation method by enhancing GMM with the use of Adaptive Support Weights and Histogram of Gradients. Extensive analyses, quantitative and qualitative experiments are presented to demonstrate their performances as comparable to other state-of-the-art methods. The final part of the dissertation proposes the novel application of GMM towards spatio-temporal video segmentation connecting spatial segmentation for images and temporal segmentation to extract foreground. The proposed approach has a simple architecture and requires a low amount of memory for processing. The analysis section demonstrates the architectural efficiency over other methods while quantitative and qualitative experiments are carried out to show the competitive performance of the proposed method

Medical Image Segmentation with Deep Learning

Medical imaging is the technique and process of creating visual representations of the body of a patient for clinical analysis and medical intervention. Healthcare professionals rely heavily on medical images and image documentation for proper diagnosis and treatment. However, manual interpretation and analysis of medical images is time-consuming, and inaccurate when the interpreter is not well-trained. Fully automatic segmentation of the region of interest from medical images have been researched for years to enhance the efficiency and accuracy of understanding such images. With the advance of deep learning, various neural network models have gained great success in semantic segmentation and spark research interests in medical image segmentation using deep learning. We propose two convolutional frameworks to segment tissues from different types of medical images. Comprehensive experiments and analyses are conducted on various segmentation neural networks to demonstrate the effectiveness of our methods. Furthermore, datasets built for training our networks and full implementations are published

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries

This two-volume set LNCS 12962 and 12963 constitutes the thoroughly refereed proceedings of the 7th International MICCAI Brainlesion Workshop, BrainLes 2021, as well as the RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge, the Federated Tumor Segmentation (FeTS) Challenge, the Cross-Modality Domain Adaptation (CrossMoDA) Challenge, and the challenge on Quantification of Uncertainties in Biomedical Image Quantification (QUBIQ). These were held jointly at the 23rd Medical Image Computing for Computer Assisted Intervention Conference, MICCAI 2020, in September 2021. The 91 revised papers presented in these volumes were selected form 151 submissions. Due to COVID-19 pandemic the conference was held virtually. This is an open access book

Liver segmentation using 3D CT scans.

Master of Science in Computer Science. University of KwaZulu-Natal, Durban, 2018.Abstract available in PDF file

Medical Image Modality Synthesis and Resolution Enhancement Based on Machine Learning Techniques

To achieve satisfactory performance from automatic medical image analysis algorithms such as registration or segmentation, medical imaging data with the desired modality/contrast and high isotropic resolution are preferred, yet they are not always available. We addressed this problem in this thesis using 1) image modality synthesis and 2) resolution enhancement. The first contribution of this thesis is computed tomography (CT)-tomagnetic resonance imaging (MRI) image synthesis method, which was developed to provide MRI when CT is the only modality that is acquired. The main challenges are that CT has poor contrast as well as high noise in soft tissues and that the CT-to-MR mapping is highly nonlinear. To overcome these challenges, we developed a convolutional neural network (CNN) which is a modified U-net. With this deep network for synthesis, we developed the first segmentation method that provides detailed grey matter anatomical labels on CT neuroimages using synthetic MRI. The second contribution is a method for resolution enhancement for a common type of acquisition in clinical and research practice, one in which there is high resolution (HR) in the in-plane directions and low resolution (LR) in the through-plane direction. The challenge of improving the through-plane resolution for such acquisitions is that the state-of-art convolutional neural network (CNN)-based super-resolution methods are sometimes not applicable due to lack of external LR/HR paired training data. To address this challenge, we developed a self super-resolution algorithm called SMORE and its iterative version called iSMORE, which are CNN-based yet do not require LR/HR paired training data other than the subject image itself. SMORE/iSMORE create training data from the HR in-plane slices of the subject image itself, then train and apply CNNs to through-plane slices to improve spatial resolution and remove aliasing. In this thesis, we perform SMORE/iSMORE on multiple simulated and real datasets to demonstrate their accuracy and generalizability. Also, SMORE as a preprocessing step is shown to improve segmentation accuracy. In summary, CT-to-MR synthesis, SMORE, and iSMORE were demonstrated in this thesis to be effective preprocessing algorithms for visual quality and other automatic medical image analysis such as registration or segmentation

Medical Image Segmentation with Deep Convolutional Neural Networks

Medical imaging is the technique and process of creating visual representations of the body of a patient for clinical analysis and medical intervention. Healthcare professionals rely heavily on medical images and image documentation for proper diagnosis and treatment. However, manual interpretation and analysis of medical images are time-consuming, and inaccurate when the interpreter is not well-trained. Fully automatic segmentation of the region of interest from medical images has been researched for years to enhance the efficiency and accuracy of understanding such images. With the advance of deep learning, various neural network models have gained great success in semantic segmentation and sparked research interests in medical image segmentation using deep learning. We propose three convolutional frameworks to segment tissues from different types of medical images. Comprehensive experiments and analyses are conducted on various segmentation neural networks to demonstrate the effectiveness of our methods. Furthermore, datasets built for training our networks and full implementations are published