An extended non‐local means algorithm: Application to brain MRI

Improved adaptive nonlocal means (IANLM) is a variant of classical nonlocal means (NLM) denoising method based on adaptation of its search window size. In this article, an extended nonlocal means (XNLM) algorithm is proposed by adapting IANLM to Rician noise in images obtained by magnetic resonance (MR) imaging modality. Moreover, for improved denoising, a wavelet coefficient mixing procedure is used in XNLM to mix wavelet sub‐bands of two IANLM‐filtered images, which are obtained using different parameters of IANLM. Finally, XNLM includes a novel parameter‐free pixel preselection procedure for improving computational efficiency of the algorithm. The proposed algorithm is validated on T1‐weighted, T2‐weighted and Proton Density (PD) weighted simulated brain MR images (MRI) at several noise levels. Optimal values of different parameters of XNLM are obtained for each type of MRI sequence, and different variants are investigated to reveal the benefits of different extensions presented in this work. The proposed XNLM algorithm outperforms several contemporary denoising algorithms on all the tested MRI sequences, and preserves important pathological information more effectively. Quantitative and visual results show that XNLM outperforms several existing denoising techniques, preserves important pathological information more effectively, and is computationallyefficient.     

Brain MRI denoizing and segmentation based on improved adaptive nonlocal means

Denoizing of magnetic resonance (MR) brain images has been focus of numerous studies in the past. The performance of subsequent stages of image processing, in automated image analysis, is substantially improved by explicit consideration of noise. Nonlocal means (NLM) is a popular denoizing method which exploits usual redundancy present in an image to restore noise free image. It computes restored value of a pixel as weighted average of candidate pixels in a search window. In this article, we propose an improved version of the NLM algorithm which is modified in two ways. First, a robust threshold criterion is introduced, which helps selecting suitable pixels for participation in the restoration process. Second, the search window size is made adaptive using a window adaptation test based on the proposed threshold criterion. The modified NLM algorithm is named as improved adaptive nonlocal means (IANLM). An alternate implementation of IANLM is also proposed which exploits the image smoothness property to yield better denoizing performance. The computational burden is reduced significantly due to proposed modifications. Experiments are performed on simulated and real brain MR images at various noise levels. Results indicate that the proposed algorithm produces not only better denoizing results (quantitatively and qualitatively), but is also computationally more efficient. Moreover, the proposed technique is incorporated in an already proposed segmentation framework to check its validity in the practical scenario of segmentation. Improved segmentation results (quantitative and qualitative) verify the practical usefulness of the proposed algorithm in real world medical applications. © 2013 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 23, 235–248, 2013     

Automatic segmentation of cerebral hemispheres in MR human head scans

Automatic segmentation of cerebral hemispheres in magnetic resonance (MR) brain images help to quantify the brain asymmetry and correct several MR brain deformities. The detection of mid‐sagittal plane (MSP) in human brain image is necessary to segment the hemispheres for both operator‐based and automated brain image asymmetric analysis. In this article, a computationally simple and accurate technique to detect MSP in MRI human head scans using curve fitting is developed. The left and right hemispheres are segmented based on the detected MSP. The accuracy of the MSP is evaluated by comparing the segmented left and right hemispheres against the manually segmented ones. Experimental results using 78 volumes of T1, T2 and PD‐weighted MRI brain images show that the proposed method has accurately segmented the cerebral hemispheres based on the detected MSP in axial and coronal orientations of normal and pathological brain images.     

A rapid automatic brain tumor detection method for MRI images using modified minimum error thresholding technique

This proposed work is aimed to develop a rapid automatic method to detect the brain tumor from T2‐weighted MRI brain images using the principle of modified minimum error thresholding (MET) method. Initially, modified MET method is applied to produce well segmented and sub‐structural clarity for MRI brain images. Further, using FCM clustering the appearance of tumor area is refined. The obtained results are compared with corresponding ground truth images. The quantitative measures of results were compared with the results of those conventional methods using the metrics predictive accuracy (PA), dice coefficient (DC), and processing time. The PA and DC values of the proposed method attained maximum value and processing time is minimum while compared to conventional FCM and k‐means clustering techniques. This proposed method is more efficient and faster than the existing segmentation methods in detecting the tumor region from T2‐weighted MRI brain images. © 2015 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 25, 77–85, 2015     

Improved fuzzy entropy clustering algorithm for MRI brain image segmentation

Magnetic resonance imaging (MRI) brain image segmentation is essential at preliminary stage in the neuroscience research and computer‐aided diagnosis. However, presence of noise and intensity inhomogeneity in MRI brain images leads to improper segmentation. The fuzzy entropy clustering (FEC) is often used to deal with noisy data. One major disadvantage of the FEC algorithm is that it does not consider the local spatial information. In this article, we have proposed an improved fuzzy entropy clustering (IFEC) algorithm by introducing a new fuzzy factor, which incorporates both local spatial and gray‐level information. The IFEC algorithm is insensitive to noise, preserves the image detail during clustering, and is free of parameter selection. The efficacy of IFEC algorithm is demonstrated by comparing it quantitatively with the state‐of‐the‐art segmentation approaches in terms of similarity index on publically available real and simulated MRI brain images.     

A deep learning model integrating convolution neural network and multiple kernel K means clustering for segmenting brain tumor in magnetic resonance images

In medical imaging, segmenting brain tumor becomes a vital task, and it provides a way for early diagnosis and treatment. Manual segmentation of brain tumor in magnetic resonance (MR) images is a time‐consuming and challenging task. Hence, there is a need for a computer‐aided brain tumor segmentation approach. Using deep learning algorithms, a robust brain tumor segmentation approach is implemented by integrating convolution neural network (CNN) and multiple kernel K means clustering (MKKMC). In this proposed CNN‐MKKMC approach, classification of MR images into normal and abnormal is performed by CNN algorithm. At next, MKKMC algorithm is employed to segment the brain tumor from the abnormal brain image. The proposed CNN‐MKKMC algorithm is evaluated both visually and objectively in terms of accuracy, sensitivity, and specificity with the existing segmentation methods. The experimental results demonstrate that the proposed CNN‐MKKMC approach yields better accuracy in segmenting brain tumor with less time cost.     

Unsupervised tissue classification of brain MR images for voxel‐based morphometry analysis

In this article, a fully unsupervised method for brain tissue segmentation of T1‐weighted MRI 3D volumes is proposed. The method uses the Fuzzy C‐Means (FCM) clustering algorithm and a Fully Connected Cascade Neural Network (FCCNN) classifier. Traditional manual segmentation methods require neuro‐radiological expertise and significant time while semiautomatic methods depend on parameter's setup and trial‐and‐error methodologies that may lead to high intraoperator/interoperator variability. The proposed method selects the most useful MRI data according to FCM fuzziness values and trains the FCCNN to learn to classify brain’ tissues into White Matter, Gray Matter, and Cerebro‐Spinal Fluid in an unsupervised way. The method has been tested on the IBSR dataset, on the BrainWeb Phantom, on the BrainWeb SBD dataset, and on the real dataset “University of Palermo Policlinico Hospital” (UPPH), Italy. Sensitivity, Specificity, Dice and F‐Factor scores have been calculated on the IBSR and BrainWeb datasets segmented using the proposed method, the FCM algorithm, and two state‐of‐the‐art brain segmentation software packages (FSL and SPM) to prove the effectiveness of the proposed approach. A qualitative evaluation involving a group of five expert radiologists has been performed segmenting the real dataset using the proposed approach and the comparison algorithms. Finally, a usability analysis on the proposed method and reference methods has been carried out from the same group of expert radiologists. The achieved results show that the segmentations of the proposed method are comparable or better than the reference methods with a better usability and degree of acceptance.     

Analysis of denoising filters on MRI brain images

The magnetic resonance imaging (MRI) modality is an effective tool in the diagnosis of the brain. These MR images are introduced with noise during acquisition which reduces the image quality and limits the accuracy in diagnosis. Elimination of noise in medical images is an important task in preprocessing and there exist different methods to eliminate noise in medical images. In this article, different denoising algorithms such as nonlocal means, principal component analysis, bilateral, and spatially adaptive nonlocal means (SANLM) filters are studied to eliminate noise in MR. Comparative analysis of these techniques have been with help of various metrics such as signal‐to‐noise ratio, peak signal‐to‐noise ratio (PSNR), mean squared error, root mean squared error, and structure similarity (SSIM). This comparative study shows that the SANLM denoising filter gives the best performance in terms of better PSNR and SSIM in visual interpretation. It also helps in clinical diagnosis of the brain.     

Fuzzy C means integrated with spatial information and contrast enhancement for segmentation of MR brain images

This paper proposes a fully automated method for MR brain image segmentation into Gray Matter, White Matter and Cerebro‐spinal Fluid. It is an extension of Fuzzy C Means Clustering Algorithm which overcomes its drawbacks, of sensitivity to noise and inhomogeneity. In the conventional FCM, the membership function is computed based on the Euclidean distance between the pixel and the cluster center. It does not take into consideration the spatial correlation among the neighboring pixels. This means that the membership values of adjacent pixels belonging to the same cluster may not have the same range of membership value due to the contamination of noise and hence misclassified. Hence, in the proposed method, the membership function is convolved with mean filter and thus the local spatial information is incorporated in the clustering process. The method further includes pixel re‐labeling and contrast enhancement using non‐linear mapping to improve the segmentation accuracy. The proposed method is applied to both simulated and real T1‐weighted MR brain images from BrainWeb and IBSR database. Experiments show that there is an increase in segmentation accuracy of around 30% over the conventional methods and 6% over the state of the art methods.     

Tumor detection in T1, T2, FLAIR and MPR brain images using a combination of optimization and fuzzy clustering improved by seed‐based region growing algorithm

Tumor and Edema region present in Magnetic Resonance (MR) brain image can be segmented using Optimization and Clustering merged with seed‐based region growing algorithm. The proposed algorithm shows effectiveness in tumor detection in T1 ‐ w, T2 – w, Fluid Attenuated Inversion Recovery and Multiplanar Reconstruction type MR brain images. After an initial level segmentation exhibited by Modified Particle Swarm Optimization (MPSO) and Fuzzy C – Means (FCM) algorithm, the seed points are initialized using the region growing algorithm and based on these seed points; tumor detection in MR brain images is done. The parameters taken for comparison with the conventional techniques are Mean Square Error, Peak Signal to Noise Ratio, Jaccard (Tanimoto) index, Dice Overlap indices and Computational Time. These parameters prove the efficacy of the proposed algorithm. Heterogeneous type tumor regions present in the input MR brain images are segmented using the proposed algorithm. Furthermore, the algorithm shows augmentation in the process of brain tumor identification. Availability of gold standard images has led to the comparison of the suggested algorithm with MPSO‐based FCM and conventional Region Growing algorithm. Also, the algorithm recommended through this research is capable of producing Similarity Index value of 0.96, Overlap Fraction value of 0.97 and Extra Fraction value of 0.05, which are far better than the values articulated by MPSO‐based FCM and Region Growing algorithm. The proposed algorithm favors the segmentation of contrast enhanced images. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 33–45, 2017     

MRI brain image classification—a hybrid approach

The present article proposes a novel computer‐aided diagnosis (CAD) technique for the classification of the magnetic resonance brain images. The current method adopt color converted hybrid clustering segmentation algorithm with hybrid feature selection approach based on IGSFFS (Information gain and Sequential Forward Floating Search) and Multi‐Class Support Vector Machine (MC‐SVM) classifier technique to segregate the magnetic resonance brain images into three categories namely normal, benign and malignant. The proposed hybrid evolutionary segmentation algorithm which is the combination of WFF(weighted firefly) and K‐means algorithm called WFF‐K‐means and modified cuckoo search (MCS) and K‐means algorithm called MCS‐K‐means, which can find better cluster partition in brain tumor datasets and also overcome local optima problems in K‐means clustering algorithm. The experimental results show that the performance of the proposed algorithm is better than other algorithms such as PSO‐K‐means, color converted K‐means, FCM and other traditional approaches. The multiple feature set comprises color, texture and shape features derived from the segmented image. These features are then fed into a MC‐SVM classifier with hybrid feature selection algorithm, trained with data labeled by experts, enabling the detection of brain images at high accuracy levels. The performance of the method is evaluated using classification accuracy, sensitivity, specificity, and receiver operating characteristic (ROC) curves. The proposed method provides highest classification accuracy of greater than 98% with high sensitivity and specificity rates of greater than 95% for the proposed diagnostic model and this shows the promise of the approach. © 2015 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 25, 226–244, 2015     

Segmentation for brain magnetic resonance images using dual‐tree complex wavelet transform and spatial constrained self‐organizing tree map

In brain MR images, the noise and low‐contrast significantly deteriorate the segmentation results. In this paper, we introduce a novel application of dual‐tree complex wavelet transform (DT‐CWT), and propose an automatic unsupervised segmentation method integrating DT‐CWT with self‐organizing map for brain MR images. First, a multidimensional feature vector is constructed based on the intensity, low‐frequency subband of DT‐CWT, and spatial position information. Then, a spatial constrained self‐organizing tree map (SCSOTM) is presented as the segmentation system. It adaptively captures the complicated spatial layout of the individual tissues, and overcomes the problem of overlapping gray‐scale intensities for different tissues. SCSOTM applies a dual‐thresholding method for automatic growing of the tree map, which uses the information from the high‐frequency subbands of DT‐CWT. The proposed method is validated by extensive experiments using both simulated and real T1‐weighted MR images, and compared with the state‐of‐the‐art algorithms. © 2014 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 24, 208–214, 2014     

A fast and efficient computer aided diagnostic system to detect tumor from brain magnetic resonance imaging

In this work, a simple and efficient CAD (computer‐aided diagnostic) system is proposed for tumor detection from brain magnetic resonance imaging (MRI). Poor contrast MR images are preprocessed by using morphological operations and DSR (dynamic stochastic resonance) technique. The appropriate segmentation of MR images plays an important role in yielding the correct detection of tumor. On examination of three views of brain MRI, it was visible that the region of interest (ROI) lies in the middle and its size ranges from 240 × 240 mm² to 280 × 280 mm². The proposed system makes effective use of this information and identifies four blocks from the desired ROI through block‐based segmentation. Texture and shape features are extracted for each block of all MRIs in the training set. The range of these feature values defines the threshold to distinguish tumorous and nontumorous MRIs. Features of each block of an MRI view are checked against the threshold. For a particular feature, if a block is found tumorous in a view, then the other views are also checked for the presence of tumor. If corresponding blocks in all the views are found to be tumorous, then the MRI is classified as tumorous. This selective block processing technique improves computational efficiency of the system. The proposed technique is well adaptive and fast, and it is compared with well‐known existing techniques, like k‐means, fuzzy c‐means, etc. The performance analysis based on accuracy and precision parameters emphasizes the effectiveness and efficiency of the proposed work.     

NeXt for neuro‐radiosurgery: A fully automatic approach for necrosis extraction in brain tumor MRI using an unsupervised machine learning technique

Stereotactic neuro‐radiosurgery is a well‐established therapy for intracranial diseases, especially brain metastases and highly invasive cancers that are difficult to treat with conventional surgery or radiotherapy. Nowadays, magnetic resonance imaging (MRI) is the most used modality in radiation therapy for soft‐tissue anatomical districts, allowing for an accurate gross tumor volume (GTV) segmentation. Investigating also necrotic material within the whole tumor has significant clinical value in treatment planning and cancer progression assessment. These pathological necrotic regions are generally characterized by hypoxia, which is implicated in several aspects of tumor development and growth. Therefore, particular attention must be deserved to these hypoxic areas that could lead to recurrent cancers and resistance to therapeutic damage. This article proposes a novel fully automatic method for necrosis extraction (NeXt), using the Fuzzy C‐Means algorithm, after the GTV segmentation. This unsupervised Machine Learning technique detects and delineates the necrotic regions also in heterogeneous cancers. The overall processing pipeline is an integrated two‐stage segmentation approach useful to support neuro‐radiosurgery. NeXt can be exploited for dose escalation, allowing for a more selective strategy to increase radiation dose in hypoxic radioresistant areas. Moreover, NeXt analyzes contrast‐enhanced T1‐weighted MR images alone and does not require multispectral MRI data, representing a clinically feasible solution. This study considers an MRI dataset composed of 32 brain metastatic cancers, wherein 20 tumors present necroses. The segmentation accuracy of NeXt was evaluated using both spatial overlap‐based and distance‐based metrics, achieving these average values: Dice similarity coefficient 95.93% ± 4.23% and mean absolute distance 0.225 ± 0.229 (pixels).     

Rician noise removal in magnitude MRI images using efficient anisotropic diffusion filtering

In this article, a new methodology for denoising of Rician noise in Magnetic Resonance Images (MRI) is presented. MRI imaging creates a distinctive view into the interior of a human body and has become an essential tool of clinical diagnosis. However, Rician noise is a type of artifact inherent to the acquisition process of the magnitude MRI image, making diagnosis difficult. We proposed a moment‐based Rician noise reduction technique in anisotropic diffusion filtering. We extend the work of the classical anisotropic diffusion filter and have customized it to remove Rician noise in the magnitude MRI image in 3D domain space. Our proposed scheme shows better results against various quality measures in terms of noise removal and edge preservation while retaining fine textures.     

Denoising and segmentation of MR images using fourth order non-linear adaptive PDE and new convergent clustering

At present, digital image processing plays a vital role in medical imaging areas and specifically in magnetic resonance imaging (MRI) of brain images such as axial and coronal sections. This article mainly focused on the MRI brain images. The existing methods such as total variation (MC), parallel MRI, modified pyramidal dual-tree direction filter, adaptive dictionary selection algorithm, classifier methods, and fuzzy clustering techniques are poor in image eminence and precision. Thus, this article presents a novel approach consisting of denoising followed by segmentation. The objective of these proposed methods was visual eminence improvement of medical images to examine tumor extent using an adaptive partial differential equation (APDE)-based analysis with soft threshold function in denoising. The fourth order, nonlinear APDE was used to denoise the image depending on gradient and Laplacian operators associated with the new adaptive Haar-type wavelet transform. A second approach was the new convergent K-means clustering for segmentation. The convergent K-means procedure diminishes the summation of the squared deviations of structures in a cluster from the center. The significance of these proposed methods was to compute their performances in terms of mean squared error, peak signal-to-noise ratio, structure similarity, segmentation accuracy, false hit, missed-term, and elapsed time. The results were analyzed with the MATLAB software.     

A complete automated algorithm for segmentation of tissues and identification of tumor region in T1, T2, and FLAIR brain images using optimization and clustering techniques

Tissues in brain are the most complicated parts of our body, a clear examination and study are therefore required by a radiologist to identify the pathologies. Normal magnetic resonance (MR) scanner is capable of producing brain images with bounded tissues, where unique and segregated views of the tissues are required. A distinguished view upon the images is manually impossible and can be subjected to operator errors. With the assistance of a soft computing technique, an automated unique segmentation upon the brain tissues along with the identification of the tumor region can be effectively done. These functionalities assist the radiologist extensively. Several soft computing techniques have been proposed and one such technique which is being proposed is PSO‐based FCM algorithm. The results of the proposed algorithm is compared with fuzzy C‐means (FCM) and particle swarm optimization (PSO) algorithms using comparison factors such as mean square error (MSE), peak signal to noise ratio (PSNR), entropy (energy function), Jaccard (Tanimoto Coefficient) index, dice overlap index and memory requirement for processing the algorithm. The efficiency of the PSO‐FCM algorithm is verified using the comparison factors.     

Hierarchical fuzzy segmentation of brain MR images

In brain magnetic resonance (MR) images, image segmentation and 3D visualization are very useful tools for the diagnosis of abnormalities. Segmentation of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is the basic process for 3D visualization of brain MR images. Of the many algorithms, the fuzzy c‐means (FCM) technique has been widely used for segmentation of brain MR images. However, the FCM technique does not yield sufficient results under radio frequency (RF) nonuniformity. We propose a hierarchical FCM (HFCM), which provides good segmentation results under RF nonuniformity and does not require any parameter setting. We also generate Talairach templates of the brain that are deformed to 3D brain MR images. Using the deformed templates, only the cerebrum region is extracted from the 3D brain MR images. Then, the proposed HFCM partitions the cerebrum region into WM, GM, and CSF. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 13, 115–125, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.10035     

An Improved Jellyfish Algorithm for Multilevel Thresholding of Magnetic Resonance Brain Image Segmentations

Image segmentation is vital when analyzing medical images, especially magnetic resonance (MR) images of the brain. Recently, several image segmentation techniques based on multilevel thresholding have been proposed for medical image segmentation; however, the algorithms become trapped in local minima and have low convergence speeds, particularly as the number of threshold levels increases. Consequently, in this paper, we develop a new multilevel thresholding image segmentation technique based on the jellyfish search algorithm (JSA) (an optimizer). We modify the JSA to prevent descents into local minima, and we accelerate convergence toward optimal solutions. The improvement is achieved by applying two novel strategies: Ranking-based updating and an adaptive method. Ranking-based updating is used to replace undesirable solutions with other solutions generated by a novel updating scheme that improves the qualities of the removed solutions. We develop a new adaptive strategy to exploit the ability of the JSA to find a best-so-far solution; we allow a small amount of exploration to avoid descents into local minima. The two strategies are integrated with the JSA to produce an improved JSA (IJSA) that optimally thresholds brain MR images. To compare the performances of the IJSA and JSA, seven brain MR images were segmented at threshold levels of 3, 4, 5, 6, 7, 8, 10, 15, 20, 25, and 30. IJSA was compared with several other recent image segmentation algorithms, including the improved and standard marine predator algorithms, the modified salp and standard salp swarm algorithms, the equilibrium optimizer, and the standard JSA in terms of fitness, the Structured Similarity Index Metric (SSIM), the peak signal-to-noise ratio (PSNR), the standard deviation (SD), and the Features Similarity Index Metric (FSIM). The experimental outcomes and the Wilcoxon rank-sum test demonstrate the superiority of the proposed algorithm in terms of the FSIM, the PSNR, the objective values, and the SD; in terms of the SSIM, IJSA was competitive with the others.     

A novel Markov random field model based on region adjacency graph for T1 magnetic resonance imaging brain segmentation

Tissue segmentation in magnetic resonance brain scans is the most critical task in different aspects of brain analysis. Because manual segmentation of brain magnetic resonance imaging (MRI) images is a time‐consuming and labor‐intensive procedure, automatic image segmentation is widely used for this purpose. As Markov Random Field (MRF) model provides a powerful tool for segmentation of images with a high level of artifacts, it has been considered as a superior method. But because of the high computational cost of MRF, it is not appropriate for online processing. This article has proposed a novel method based on a proper combination of MRF model and watershed algorithm in order to alleviate the MRF's drawbacks. Results illustrate that the proposed method has a good ability in MRI image segmentation, and also decreases the computational time effectively, which is a valuable improvement in the online applications. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 78–88, 2017