Ahmed Elazab

Segmentation of Brain Tissues from Magnetic Resonance Images Using Adaptively Regularized Kernel-Based Fuzzy C-Means Clustering.

An adaptively regularized kernel-based fuzzy C-means clustering framework is proposed for segmentation of brain magnetic resonance images. The framework can be in the form of three algorithms for the local average grayscale being replaced by the grayscale of the average filter, median filter, and devised weighted images, respectively. The algorithms employ the heterogeneity of grayscales in the neighborhood and exploit this measure for local contextual information and replace the standard Euclidean distance with Gaussian radial basis kernel functions. The main advantages are adaptiveness to local context, enhanced robustness to preserve image details, independence of clustering parameters, and decreased computational costs. The algorithms have been validated against both synthetic and clinical magnetic resonance images with different types and levels of noises and compared with 6 recent soft clustering algorithms. Experimental results show that the proposed algorithms are superior in preserving image details and segmentation accuracy while maintaining a low computational complexity.

Robust kernelized local information fuzzy C-means clustering for brain magnetic resonance image segmentation

Brain tissue segmentation from magnetic resonance (MR) images is an importance task for clinical use. The segmentation process becomes more challenging in the presence of noise, grayscale inhomogeneity, and other image artifacts. In this paper, we propose a robust kernelized local information fuzzy C-means clustering algorithm (RKLIFCM). It incorporates local information into the segmentation process (both grayscale and spatial) for more homogeneous segmentation. In addition, the Gaussian radial basis kernel function is adopted as a distance metric to replace the standard Euclidean distance. The main advantages of the new algorithm are: efficient utilization of local grayscale and spatial information, robustness to noise, ability to preserve image details, free from any parameter initialization, and with high speed as it runs on image histogram. We compared the proposed algorithm with 7 soft clustering algorithms that run on both image histogram and image pixels to segment brain MR images. Experimental results demonstrate that the proposed RKLIFCM algorithm is able to overcome the influence of noise and achieve higher segmentation accuracy with low computational complexity.

Simultaneous reconstruction of the time-dependent Robin coefficient and heat flux in heat conduction problems

Abstract This paper aims to solve an inverse heat conduction problem in two-dimensional space under transient regime, which consists of the estimation of multiple time-dependent heat sources placed at the boundaries. Robin boundary condition (third type boundary condition) is considered at the working domain boundary. The simultaneous identification problem is formulated as a constrained minimization problem using the output least squares method with Tikhonov regularization. The properties of the continuous and discrete optimization problem are studied. Differentiability results and the adjoint problems are established. The numerical estimation is investigated using a modified conjugate gradient method. Furthermore, to verify the performance of the proposed algorithm, obtained results are compared with results obtained from the well-known finite-element software COMSOL Multiphysics under the same conditions. The numerical results show that the proposed algorithm is accurate, robust and capable of simultaneously representing the time effects on reconstructing the time-dependent Robin coefficient and heat flux.

Content based modified reaction-diffusion equation for modeling tumor growth of low grade glioma

This paper presents a content based modified reaction diffusion (RD) equation for modeling glioma growth. The reaction diffusion equation is modified by a weighted parameter that measures the white matter proportion in a small window. Given two MRI time-points scans of the same patient, the manually segmented tumor of the first scan is used as an initial seed to the proposed method while the second scan is used as the ground truth to measure the accuracy of the simulated results. For healthy tissues segmentation around the initial seed, spatial fuzzy C-means algorithm that accounts for neighborhood information of the image is used. As a proof of concept, the proposed method is tested on one low grade glioma case with 7 month difference between the two scans. The preliminary results of the modified RD equation show higher accuracy as compared with the standard RD equation.

Low grade glioma growth modeling considering chemotherapy and radiotherapy effects from magnetic resonance images

Studying tumor growth using mathematical models from magnetic resonance (MR) images is an important application that is believed to play a major role in cancer treatment by predicting tumor evolution, quantifying the response to therapy, and treatment planning. Reaction diffusion is the most popular model because of its simplicity and consistency with the biological growth process. However, most of the current growth models focus on presurgical images and likely without treatment. In this paper, we propose a new reaction diffusion model to consider the chemotherapy and radiotherapy effects on the tumor growth modelling for patients with low grade glioma. The proposed model does not consider the tensor information from diffusion tensor imaging. Instead it uses a weighted parameter to promote higher diffusivity in white matter. The radiotherapy and chemotherapy effects are considered as a loss terms in the proposed model. The preliminary results of the proposed model on synthetic and 2 real MR images show that, our model can effectively simulate tumor growth with high accuracies when treatments are administrated to low grade glioma patients.

Segmentation of hyper-acute cerebral infarct based on random forest and sparse coding from diffusion weighted imaging

Irreversible infarcts are critical for the assessment of potential risk and benefit pertaining to thrombolysis in hyper-acute ischemic stroke. It is a challenging work to segment infarct at hyper-acute stage due to the substantial variability. A general abnormal tissue segmentation method is proposed and applied to segment hyper-acute ischemic infarct in this paper. Multiple features are designed to train a random forest classifier for voxel classification. Sparse coding based bag-of-features is adopted to train a region classifier for infarct region recognition. The proposed method has been validated on 98 consecutive patients recruited within 6 hours from onset and achieved a higher Dice coefficient 0.774±0.117 than the other two existing methods (0.755±0.118; 0.597±0.204). It could provide a potential tool to quantify infarcts from diffusion weighted imaging at hyper-acute stage with accuracy to assist the decision making especially for thrombolytic therapy.

Post-Surgery Glioma Growth Modeling from Magnetic Resonance Images for Patients with Treatment

Reaction diffusion is the most common growth modelling methodology due to its simplicity and consistency with the biological tumor growth process. However, current extensions of the reaction diffusion model lack one or more of the following: efficient inclusion of treatments’ effects, taking into account the viscoelasticity of brain tissues, and guaranteed stability of the numerical solution. We propose a new model to overcome the aforementioned drawbacks. Guided by directional information derived from diffusion tensor imaging, our model relates tissue heterogeneity with the absorption of the chemotherapy, adopts the linear-quadratic term to simulate the radiotherapy effect, employs Maxwell-Weichert model to incorporate brain viscoelasticity, and ensures the stability of the numerical solution. The performance is verified through experiments on synthetic and real MR images. Experiments on 9 MR datasets of patients with low grade gliomas undergoing surgery with different treatment regimens are carried out and validated using Jaccard score and Dice coefficient. The growth simulation accuracies of the proposed model are in ranges of [0.673 0.822] and [0.805 0.902] for Jaccard scores and Dice coefficients, respectively. The accuracies decrease up to 4% and 2.4% when ignoring treatment effects and the tensor information, while brain viscoelasticity has no significant impact on the accuracies.

Cortical and Subcortical Structural Plasticity Associated with the Glioma Volumes in Patients with Cerebral Gliomas Revealed by Surface-Based Morphometry

Postlesional plasticity has been identified in patients with cerebral gliomas by inducing a large functional reshaping of brain networks. Although numerous non-invasive functional neuroimaging methods have extensively investigated the mechanisms of this functional redistribution in patients with cerebral gliomas, little effort has been made to investigate the structural plasticity of cortical and subcortical structures associated with the glioma volume. In this study, we aimed to investigate whether the contralateral cortical and subcortical structures are able to actively reorganize by themselves in these patients. The compensation mechanism following contralateral cortical and subcortical structural plasticity is considered. We adopted the surface-based morphometry to investigate the difference of cortical and subcortical gray matter (GM) volumes in a cohort of 14 healthy controls and 13 patients with left-hemisphere cerebral gliomas [including 1 patients with World Health Organization (WHO I), 8 WHO II, and 4 WHO III]. The glioma volume ranges from 5.1633 to 208.165 cm2. Compared to healthy controls, we found significantly increased GM volume of the right cuneus and the left thalamus, as well as a trend toward enlargement in the right globus pallidus in patients with cerebral gliomas. Moreover, the GM volumes of these regions were positively correlated with the glioma volumes of the patients. These results provide evidence of cortical and subcortical enlargement, suggesting the usefulness of surface-based morphometry to investigate the structural plasticity. Moreover, the structural plasticity might be acted as the compensation mechanism to better fulfill its functions in patients with cerebral gliomas as the gliomas get larger.