Applications of Deep Learning Techniques for Automated Multiple Sclerosis Detection Using Magnetic Resonance Imaging: A Review

Multiple Sclerosis (MS) is a type of brain disease which causes visual, sensory, and motor problems for people with a detrimental effect on the functioning of the nervous system. In order to diagnose MS, multiple screening methods have been proposed so far; among them, magnetic resonance imaging (MRI) has received considerable attention among physicians. MRI modalities provide physicians with fundamental information about the structure and function of the brain, which is crucial for the rapid diagnosis of MS lesions. Diagnosing MS using MRI is time-consuming, tedious, and prone to manual errors. Research on the implementation of computer aided diagnosis system (CADS) based on artificial intelligence (AI) to diagnose MS involves conventional machine learning and deep learning (DL) methods. In conventional machine learning, feature extraction, feature selection, and classification steps are carried out by using trial and error; on the contrary, these steps in DL are based on deep layers whose values are automatically learn. In this paper, a complete review of automated MS diagnosis methods performed using DL techniques with MRI neuroimaging modalities is provided. Initially, the steps involved in various CADS proposed using MRI modalities and DL techniques for MS diagnosis are investigated. The important preprocessing techniques employed in various works are analyzed. Most of the published papers on MS diagnosis using MRI modalities and DL are presented. The most significant challenges facing and future direction of automated diagnosis of MS using MRI modalities and DL techniques are also provided

Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni- / multi- modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software.Comment: Add new discussion

TISS-net: Brain tumor image synthesis and segmentation using cascaded dual-task networks and error-prediction consistency

Accurate segmentation of brain tumors from medical images is important for diagnosis and treatment planning, and it often requires multi-modal or contrast-enhanced images. However, in practice some modalities of a patient may be absent. Synthesizing the missing modality has a potential for filling this gap and achieving high segmentation performance. Existing methods often treat the synthesis and segmentation tasks separately or consider them jointly but without effective regularization of the complex joint model, leading to limited performance. We propose a novel brain Tumor Image Synthesis and Segmentation network (TISS-Net) that obtains the synthesized target modality and segmentation of brain tumors end-to-end with high performance. First, we propose a dual-task-regularized generator that simultaneously obtains a synthesized target modality and a coarse segmentation, which leverages a tumor-aware synthesis loss with perceptibility regularization to minimize the high-level semantic domain gap between synthesized and real target modalities. Based on the synthesized image and the coarse segmentation, we further propose a dual-task segmentor that predicts a refined segmentation and error in the coarse segmentation simultaneously, where a consistency between these two predictions is introduced for regularization. Our TISS-Net was validated with two applications: synthesizing FLAIR images for whole glioma segmentation, and synthesizing contrast-enhanced T1 images for Vestibular Schwannoma segmentation. Experimental results showed that our TISS-Net largely improved the segmentation accuracy compared with direct segmentation from the available modalities, and it outperformed state-of-the-art image synthesis-based segmentation methods

Topology-Aware Focal Loss for 3D Image Segmentation

The efficacy of segmentation algorithms is frequently compromised by topological errors like overlapping regions, disrupted connections, and voids. To tackle this problem, we introduce a novel loss function, namely Topology-Aware Focal Loss (TAFL), that incorporates the conventional Focal Loss with a topological constraint term based on the Wasserstein distance between the ground truth and predicted segmentation masks' persistence diagrams. By enforcing identical topology as the ground truth, the topological constraint can effectively resolve topological errors, while Focal Loss tackles class imbalance. We begin by constructing persistence diagrams from filtered cubical complexes of the ground truth and predicted segmentation masks. We subsequently utilize the Sinkhorn-Knopp algorithm to determine the optimal transport plan between the two persistence diagrams. The resultant transport plan minimizes the cost of transporting mass from one distribution to the other and provides a mapping between the points in the two persistence diagrams. We then compute the Wasserstein distance based on this travel plan to measure the topological dissimilarity between the ground truth and predicted masks. We evaluate our approach by training a 3D U-Net with the MICCAI Brain Tumor Segmentation (BraTS) challenge validation dataset, which requires accurate segmentation of 3D MRI scans that integrate various modalities for the precise identification and tracking of malignant brain tumors. Then, we demonstrate that the quality of segmentation performance is enhanced by regularizing the focal loss through the addition of a topological constraint as a penalty term

Deep Learning Methods for Classification of Gliomas and Their Molecular Subtypes, From Central Learning to Federated Learning

The most common type of brain cancer in adults are gliomas. Under the updated 2016 World Health Organization (WHO) tumor classification in central nervous system (CNS), identification of molecular subtypes of gliomas is important. For low grade gliomas (LGGs), prediction of molecular subtypes by observing magnetic resonance imaging (MRI) scans might be difficult without taking biopsy. With the development of machine learning (ML) methods such as deep learning (DL), molecular based classification methods have shown promising results from MRI scans that may assist clinicians for prognosis and deciding on a treatment strategy. However, DL requires large amount of training datasets with tumor class labels and tumor boundary annotations. Manual annotation of tumor boundary is a time consuming and expensive process.The thesis is based on the work developed in five papers on gliomas and their molecular subtypes. We propose novel methods that provide improved performance. \ua0The proposed methods consist of a multi-stream convolutional autoencoder (CAE)-based classifier, a deep convolutional generative adversarial network (DCGAN) to enlarge the training dataset, a CycleGAN to handle domain shift, a novel federated learning (FL) scheme to allow local client-based training with dataset protection, and employing bounding boxes to MRIs when tumor boundary annotations are not available.Experimental results showed that DCGAN generated MRIs have enlarged the original training dataset size and have improved the classification performance on test sets. CycleGAN showed good domain adaptation on multiple source datasets and improved the classification performance. The proposed FL scheme showed a slightly degraded performance as compare to that of central learning (CL) approach while protecting dataset privacy. Using tumor bounding boxes showed to be an alternative approach to tumor boundary annotation for tumor classification and segmentation, with a trade-off between a slight decrease in performance and saving time in manual marking by clinicians. The proposed methods may benefit the future research in bringing DL tools into clinical practice for assisting tumor diagnosis and help the decision making process

3D Convolution Neural Networks for Medical Imaging; Classification and Segmentation : A Doctor’s Third Eye

Master's thesis in Information- and communication technology (IKT591)In this thesis, we studied and developed 3D classification and segmentation models for medical imaging. The classification is done for Alzheimer’s Disease and segmentation is for brain tumor sub-regions. For the medical imaging classification task we worked towards developing a novel deep architecture which can accomplish the complex task of classifying Alzheimer’s Disease volumetrically from the MRI scans without the need of any transfer learning. The experiments were performed for both binary classification of Alzheimer’s Disease (AD) from Normal Cognitive (NC), as well as multi class classification between the three stages of Alzheimer’s called NC, AD and Mild cognitive impairment (MCI). We tested our model on the ADNI dataset and achieved mean accuracy of 94.17% and 89.14% for binary classification and multiclass classification respectively. In the second part of this thesis which is segmentation of tumors sub-regions in brain MRI images we studied some popular architecture for segmentation of medical imaging and inspired from them, proposed our architecture of end-to-end trainable fully convolutional neural net-work which uses attention block to learn the localization of different features of the multiple sub-regions of tumor. Also experiments were done to see the effect of weighted cross-entropy loss function and dice loss function on the performance of the model and the quality of the output segmented labels. The results of evaluation of our model are received through BraTS’19 dataset challenge. The model is able to achieve a dice score of 0.80 for the segmentation of whole tumor, and a dice scores of 0.639 and 0.536 for other two sub-regions within the tumor on validation data. In this thesis we successfully applied computer vision techniques for medical imaging analysis. We show the huge potential and numerous benefits of deep learning to combat and detect diseases opens up more avenues for research and application for automating medical imaging analysis