A Quantum-Inspired Self-Supervised Network model for automatic segmentation of brain MR images

Manual segmentation of Magnetic Resonance Images (MRI) is a time-consuming process, thus automatic segmentation of brain MR images has attracted more attention in recent years. In this paper, we introduce Dynamic Classifier Selection Markov Random Field (DCSMRF) algorithm for supervised segmentation of brain MR images into three main tissues such as White Matter (WM), Gray Matter (GM) and Cerebrospinal Fluid (CSF). DCSMRF combines a novel ensemble method with the Markov Random Field (MRF) algorithm and tries to obtain the advantages of both algorithms. For the ensemble part of DCSMRF, we propose an ensemble method called Dynamic Classifier System-Weighted Local Accuracy (DCS-WLA) which is a type of Combination of Multiple Classifier (CMC) algorithm. Later, the MRF algorithm is utilized for incorporating spatial, contextual and textural information in this paper. For the MRF section, an energy function based on the output of the DCS-WLA algorithm is proposed, then maximum value for Maximum A Posterior (MAP) criterion is searched to obtain optimal segmentation. The MRF algorithm applies similar to a post processing step in which only a subset of pixels is selected for optimization step. Hence, a vast amount of search space is pruned. Consequently, the computational burden of the proposed algorithm is more tolerable than the conventional MRF-based methods. Moreover, by employing ensemble algorithms, the accuracy and reliability of final results are enhanced compared to the individual methods.

Artificial intelligence algorithms have been used in a wide range of applications in clinical aided diagnosis, such as automatic MR image segmentation and seizure EEG signal analyses. In recent years, many machine learning-based automatic MR brain image segmentation methods have been proposed as auxiliary methods of medical image analysis in clinical treatment. Nevertheless, many problems regarding precise medical images, which cannot be effectively utilized to improve partition performance, remain to be solved. Due to the poor contrast in grayscale images, the ambiguity and complexity of MR images, and individual variability, the performance of classic algorithms in medical image segmentation still needs improvement. In this paper, we introduce a distributed multitask fuzzy c-means (MT-FCM) clustering algorithm for MR brain image segmentation that can extract knowledge common among different clustering tasks. The proposed distributed MT-FCM algorithm can effectively exploit information common among different but related MR brain image segmentation tasks and can avoid the negative effects caused by noisy data that exist in some MR images. Experimental results on clinical MR brain images demonstrate that the distributed MT-FCM method demonstrates more desirable performance than the classic signal task method.

Accurate brain tissue segmentation in Magnetic Resonance Imaging (MRI) has attracted the attention of medical doctors and researchers since variations in tissue volume help in diagnosing and monitoring neurological diseases. Several proposals have been designed throughout the years comprising conventional machine learning strategies as well as convolutional neural networks (CNN) approaches. In particular, in this paper, we analyse a sub-group of deep learning methods producing dense predictions. This branch, referred in the literature as Fully CNN (FCNN), is of interest as these architectures can process an input volume in less time than CNNs and local spatial dependencies may be encoded since several voxels are classified at once. Our study focuses on understanding architectural strengths and weaknesses of literature-like approaches. Hence, we implement eight FCNN architectures inspired by robust state-of-the-art methods on brain segmentation related tasks. We evaluate them using the IBSR18, MICCAI2012 and iSeg2017 datasets as they contain infant and adult data and exhibit varied voxel spacing, image quality, number of scans and available imaging modalities. The discussion is driven in three directions: comparison between 2D and 3D approaches, the importance of multiple modalities and overlapping as a sampling strategy for training and testing models. To encourage other researchers to explore the evaluation framework, a public version is accessible to download from our research website.

The Fuzzy C Means (FCM) and Expectation Maximization (EM) algorithms are the most prevalent methods for automatic segmentation of MR brain images into three classes Gray Matter (GM), White Matter (WM) and Cerebrospinal Fluid (CSF). The major difficulties associated with these conventional methods for MR brain image segmentation are the Intensity Non-uniformity (INU) and noise. In this paper, EM and FCM with spatial information and bias correction are proposed to overcome these effects. The spatial information is incorporated by convolving the posterior probability during E-Step of the EM algorithm with mean filter. Also, a method of pixel re-labeling is included to improve the segmentation accuracy. The proposed method is validated by extensive experiments on both simulated and real brain images from standard database. Quantitative and qualitative results depict that the method is superior to the conventional methods by around 25% and over the state-of-the art method by 8%.

We present an automatic segmentation method using the Maximum a posterior (MAP)-Markov random field (MRF) framework that possesses regional adaptive capability for the segmentation of MR brain images with the presence of noise and the intensity inhomogeneity. A spatial-varying Gaussian mixture (SVGM) is used to model the conditional probability distribution of each of the three brain tissues (WM, GM and CSF), and the MRF is used to represent prior probabilities. A three-component random vector consisting of spatial and intensity information is used in SVGM such that the model can represent more complex image characteristics, such as intensity inhomogeneity. The regional adaptive capability is achieved by imposing a similarity criterion that minimizes the intensity variation of the segmented tissues in local regions. Initial parameters of SVGM are estimated from a brain atlas using either the expectation maximization (EM) algorithm or modified k-mean (MKM) algorithm, and the iterated conditional modes (ICM) algorithm is used to perform the segmentation. The parameters estimation and the ICM algorithm are alternatively operated until a stopping criterion is reached. The implement of the method is validated by quantitatively comparing with other published classification methods on fifteen simulated and twenty in vivo brain volumes using the same evaluation criteria. Our algorithm demonstrates superior performance in all cases other than two, and is especially suitable for the volumes with higher noise and inhomogeneity. The complete experiments illustrate that the incorporations of the spatial information and the regional adaptive processing into MAP-MRF framework provide better solution to the segmentation of MR brain images.

As magnetic resonance imaging (MRI) is an important technology of radiological evaluation and computer- aided diagnosis, the accuracy of the MR image segmentation directly influences the validity of following processing. The paper concerns medical image segmentation based on t-mixture model because of merits of the model. By analyzing the features of MR images, the main procedure of white matter segmentation of brain MR Images based on t-mixture model is outlined follows. The parameters of t-mixture model for the image are firstly estimated. Then the posterior probabilities of the pixels of the image are computed. At last, the image is segmented according to the Bayes decision rule for minimum error. Experimental results show that t-mixture model fits for medical image segmentation.

Abdominal image segmentation is a challenging, yet important clinical problem. Variations in body size, position, and relative organ positions greatly complicate the segmentation process. Historically, multi-atlas methods have achieved leading results across imaging modalities and anatomical targets. However, deep learning is rapidly overtaking classical approaches for image segmentation. Recently, Zhou et al. showed that fully convolutional networks produce excellent results in abdominal organ segmentation of computed tomography (CT) scans. Yet, deep learning approaches have not been applied to whole abdomen magnetic resonance imaging (MRI) segmentation. Herein, we evaluate the applicability of an existing fully convolutional neural network (FCNN) designed for CT imaging to segment abdominal organs on T2 weighted (T2w) MRI's with two examples. In the primary example, we compare a classical multi-atlas approach with FCNN on forty-five T2w MRI's acquired from splenomegaly patients with five organs labeled (liver, spleen, left kidney, right kidney, and stomach). Thirty-six images were used for training while nine were used for testing. The FCNN resulted in a Dice similarity coefficient (DSC) of 0.930 in spleens, 0.730 in left kidneys, 0.780 in right kidneys, 0.913 in livers, and 0.556 in stomachs. The performance measures for livers, spleens, right kidneys, and stomachs were significantly better than multi-atlas (p < 0.05, Wilcoxon rank-sum test). In a secondary example, we compare the multi-atlas approach with FCNN on 138 distinct T2w MRI's with manually labeled pancreases (one label). On the pancreas dataset, the FCNN resulted in a median DSC of 0.691 in pancreases versus 0.287 for multi-atlas. The results are highly promising given relatively limited training data and without specific training of the FCNN model and illustrate the potential of deep learning approaches to transcend imaging modalities.

The segmentation and identification of neoplasm from brain MR images have gotten enormous consideration in the zone of biomedical research analysis. Segmentation is the way toward parting an image into various sections called segments. The precise segmentation of brain MR images into different units assumes a significant job in the early analysis and treatment of carcinoma. In this chapter, an active contour Chan-Vese segmentation algorithm is used. This algorithm comprises two energies, of which one power diminishes the form and the other expansion of the shape. These two energies get adjusted when the chapter arrives at the furthest point of our ideal item, which brings about total segmentation. The proposed design comprises five fundamental steps: preprocessing, creation of an introductory mask, giving the most extreme number of cycles(iterations), application of Chan-Vese active contour approach for the finding of the tumor, and extraction of its region. The competence of the proposed design has been tested on various brain MR images. We have found that the proposed methodology can detect and extract the tumor and its area.

The study deals with the challenging task of automatic segmentation of MR brain images with multiple sclerosis lesions (MSL). Multi-Channel data is used, including "fast fluid attenuated inversion recovery" (fast FLAIR or FF), and statistical modeling tools are developed, in order to improve cerebrospinal fluid (CSF) classification and to detect MSL. Two new concepts are proposed for use within an EM framework. The first concept is the integration of prior knowledge as it relates to tissue behavior in different MRI modalities, with special attention given to the FF modality. The second concept deals with running the algorithm on a subset of the input that is most likely to be noise- and artifact-free data. This enables a more reliable learning of the Gaussian mixture model (GMM) parameters for brain tissue statistics. The proposed method focuses on the problematic CSF intensity distribution, which is a key to improved overall segmentation and lesion detection. A level-set based active contour stage is performed for lesion delineation, using gradient and shape properties combined with previously learned region intensity statistics. In the proposed scheme there is no need for preregistration of an atlas, a common characteristic in brain segmentation schemes. Experimental results on real data are presented.

One of the fundamental and significant distinctiveness of an image is that, adjacent pixels are extremely correlated. The spatial information in the image improves the quality of clustering which is not utilized in the standard Fuzzy C-Means (FCM). FCM algorithm is not robust against noise. In this paper, we proposed an enhanced version of Fuzzy C-Means algorithm that incorporates spatial information into the membership function for clustering of brain MR images. The modified Fuzzy C-Means finds optimal clusters in an automatic way with the help of some cluster validity criteria. Additionally, spatial weighted information is incorporated in the spatial FCM. The spatial function is the weighted summation of the membership function in the neighborhood of each pixel under consideration. The advantages of this new method are: (a) it yields regions more homogeneous than those of other methods and (b) it removes noisy spots. It is less sensitive to noise as compared to other techniques. We tested our method on various brain MR images, and the technique has proved as a powerful method in the segmentation of noisy images.

In this paper, the automatic segmentation of multispectral magnetic resonance image of the brain is posed as a clustering problem in the intensity space. Thereafter an automatic clustering technique is proposed to solve this problem. The proposed real-coded variable string length genetic clustering technique (MCVGAPS clustering) is able to evolve the number of clusters present in the data set automatically. Each cluster is divided into several small hyperspherical subclusters and the centers of all these small sub-clusters are encoded in a string to represent the whole clustering. For assigning points to different clusters, these local sub-clusters are considered individually. For the purpose of objective function evaluation, these sub-clusters are merged appropriately to form a variable number of global clusters. A recently developed point symmetry distance based cluster validity index, Sym-index, is optimized to automatically evolve the appropriate number of clusters present in an MR brain image. The proposed method is applied on several simulated T1-weighted, T2- weighted and proton density normal and MS lesion magnetic resonance brain images. Superiority of the proposed method over Fuzzy C-means, Expectation Maximization clustering algorithms are demonstrated quantitatively. The automatic segmentation obtained by multiseed based multiobjective clustering technique (MCVGAPS) is also compared with the available ground truth information.

Idiopathic generalized epilepsy (IGE) and symptomatic generalized epilepsy (SGE) are two kinds of generalized epilepsy. In this study, we discussed the methods of automatically segmentation of MR images for patients with these two kinds of epilepsy. K-Means clustering, expectation-maximization, and fuzzy c-means algorithms were employed to perform segmentation on brain images for patients with IGE. For patients with SGE, a trimmed likelihood estimator combined with Gaussian mixture model, which we improved based on other's existing work, was employed to detect obvious brain lesions on fluid-attenuated inversion recovery images. Gray matter, white matter, and cerebrospinal fluid were then segmented from the remaining normal brain part. Similarity metrics were used to evaluate the performance of the different segmentation methods. The Dice similarity coefficient of the segmentation results exceeded 70% and satisfied the basic clinical requirement. Actually, the segmentation results were acceptable to clinicians and can provide clinicians more disease information to diagnose and treat epilepsy.

In this work, we propose a novel learning-based segmentation technique for delineating liver volumes in magnetic resonance images. The method utilizes the shape prior of the liver for improved accuracy. Instead of labeling the tissue via binary classification, our method completes the segmentation by deforming a label template of the liver average shape based on the learned image features. The average shape of the liver we used is estimated from a large set of expert-labeled computed tomography images. A fully convolutional neural network (FCN) is trained to maximize the overlap between the deformed liver label template and the ground truth segmentation. The proposed method is validated with 51 T2-weighted liver image volumes and achieves an average Dice coefficient of 95.2% with a mean Hausdorff distance of 20.0 mm. Compared to the results obtained with a standard FCN-based method, a three-fold improvement of the Hausdorff distance is observed, indicating the substantial gains achieved by incorporating the shape prior.

With the success of convolutional neural network (CNN) in the field of image processing and image recognition, an improved fully convolutional neural network (FCNN) based on CNN is proposed. Although FCNN has better performance than CNN, the number of parameters of FCNN has also increased significantly compared to CNN. Consequently, this paper proposes a multi‐feature fusion decision convolutional neural network (MFFD‐CNN), which use two kinds down‐sample methods in the pooling layer, and chooses the concatenate or add operation as the way that consolidates the feature of the convolutional layer with a stride of 2 and the max‐pooling layer to execute fusion operations. Meanwhile replaces the traditional softmax loss with an additive margin Softmax (AM‐Softmax) loss. The structure, which is based on the multi‐target classification experiment results of the MSTAR data set, shows can not only obtain an average correct recognition rate 1.2% higher than FCNN, but also better stability without augmenting the training samples of MSTAR data.

The study presents the results of the development and testing of deep learning neural network architectures, which demonstrate high accuracy rates in classifying neurophysiological data, in particular hemodynamic brain activation patterns obtained by functional near-infrared spectroscopy, during solving mathematical problems on spatial-numerical associations. The analyzed signal represents a multidimensional time series of oxyhemoglobin and deoxyhemoglobin dynamics. Taking the specificity of the fNIRS signal into account, a comparative analysis of 2 types of neural network architectures was carried out: (1) architectures based on recurrent neural networks: recurrent neural network with long short-term memory, recurrent neural network with long short-term memory with fully connected layers, bidirectional recurrent neural network with long short-term memory, convolutional recurrent neural network with long short-term memory; (2) architectures based on convolutional neural networks with 1D convolutions: convolutional neural network, fully convolutional neural network, residual neural network. Trained long short-term memory recurrent neural network architectures showed worse results in accuracy in comparison with 1D convolutional neural network architectures. Residual neural network (model_Resnet) demonstrated the highest accuracy rates in three experimental conditions more than 88% in detecting age-related differences in brain activation during spatial-numerical association tasks considering the individual characteristics of the respondents’ signal.