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).     

Fast and accurate fuzzy C‐means algorithm for MR brain image segmentation

Fuzzy theory based intelligent techniques are widely preferred for medical applications because of high accuracy. Among the fuzzy based techniques, Fuzzy C‐Means (FCM) algorithm is popular than the other approaches due to the availability of expert knowledge. But, one of the hidden facts is that the computational complexity of the FCM algorithm is significantly high. Since medical applications need to be time effective, suitable modifications must be made in this algorithm for practical feasibility. In this study, necessary changes are included in the FCM approach to make the approach time effective without compromising the segmentation efficiency. An additional data reduction approach is performed in the conventional FCM to minimize the computational complexity and the convergence rate. A comparative analysis with the conventional FCM algorithm and the proposed Fast and Accurate FCM (FAFCM) is also given to show the superior nature of the proposed approach. These techniques are analyzed in terms of segmentation efficiency and convergence rate. Experimental results show promising results for the proposed approach. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 188–195, 2016     

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.     

Multi‐modal brain tumor image segmentation based on SDAE

Accurate tumor segmentation has the ability to provide doctors with a basis for surgical planning. Moreover, brain tumor segmentation needs to extract different tumor tissues (Edema, tumor, tumor enhancement, and necrosis) from normal tissues which is a big challenge because tumor structures vary considerably across patients in terms of size, extension, and localization. In this article, we evaluate a fully automated method for segmenting brain tumor images from multi‐modal magnetic resonance imaging volumes based on stacked de‐noising auto‐encoders (SDAEs). Specially, we adopted multi‐modality information from T1, T1c, T2, and Flair images, respectively. We extracted gray level patches from different modalities as the input of the SDAE. After trained by the SDAE, the raw network parameters will be obtained, which are adopted as a parameter of the feed forward neural network for classification. A simple post‐processing is implemented by threshold segmentation method to generate a mask to get the final segmentation result. By evaluating the proposed method on the BRATS 2015, it can be proven that our method obtains the better performance than other state‐of‐the‐art counterpart methods. And a preliminary dice score of 0.86 for whole tumor segmentation has been achieved.     

Automatic brain tissue segmentation in MR images using hybrid atlas forest based on confidence-weighted probability matrix

The segmentation of specific tissues in an MR brain image for quantitative analysis can assist the disease diagnosis and medical research. Therefore, a robust and accurate method for automatic segmentation is necessary. Atlas-based-method is a common and effective method of automatic segmentation where an atlas refers to a pair of image consist of an intensity image and its corresponding label image. Apart from the general multi-atlas-based methods, which propagate labels through the single atlas then fuse them, we proposed a hybrid atlas forest based on confidence-weighted probability matrix to consider the atlases set as a whole and treat each voxel differently. In the framework, we first register the atlas to the image space of target and calculate the confidence of voxels in the registered atlas. Then, a confidence-weighted probability matrix is generated and it augments to the intensity image of the atlas or target for providing spatial information of the target tissue. Third, a hybrid atlas forest is trained to gather the features and correlation information among the atlases in the dataset. Finally, the segmentation of the target tissues is predicted by the trained hybrid atlas forest. The segment performance and the components efficiency of the proposed method are evaluated on the two public datasets. Based on the experiment results and quantitative comparisons, our method can gather spatial information and correlation among the atlases to obtain an accurate segmentation.     

A fully automated hybrid methodology using Cuckoo‐based fuzzy clustering technique for magnetic resonance brain image segmentation

This article aims at developing an automated hybrid algorithm using Cuckoo Based Search (CBS) and interval type‐2 fuzzy based clustering, so as to exhibit efficient magnetic resonance (MR) brain image segmentation. An automatic MR brain image segmentation facilitates and enables a radiologist to have a brief review and easy analysis of complicated tumor regions of imprecise gray level regions with minimal user interface. The tumor region having severe intensity variations and suffering from poor boundaries are to be detected by the proposed hybrid technique that could ease the process of clinical diagnosis and this tends to be the core subject of this article. The ability of the proposed technique is compared using standard comparison parameters such as mean squared error, peak signal to noise ratio, computational time, Dice Overlap Index, and Jaccard T animoto C oefficient Index. The proposed CBS combined with interval type‐2 fuzzy based clustering produces a sensitivity of 0.7143 and specificity of 0.9375, which are far better than the conventional techniques such as kernel based, entropy based, graph‐cut based, and self‐organizing maps based clustering. Appreciable segmentation results of tumor region that enhances clinical diagnosis is made available through this article and two of the radiologists who have hands on experience in the field of radiology have extended their support in validating the efficiency of the proposed methodology and have given their consent in utilizing the proposed methodology in the processes of clinical oncology.     

Magnetic resonance brain image classification based on weighted‐type fractional Fourier transform and nonparallel support vector machine

To classify brain images into pathological or healthy is a key pre‐clinical state for patients. Manual classification is tiresome, expensive, time‐consuming, and irreproducible. In this study, we aimed to present an automatic computer‐aided system for brain‐image classification. We used 90 T2‐weighted images obtained by magnetic resonance images. First, we used weighted‐type fractional Fourier transform (WFRFT) to extract spectrums from each magnetic resonance image. Second, we used principal component analysis (PCA) to reduce spectrum features to only 26. Third, those reduced spectral features of different samples were combined and were fed into support vector machine (SVM) and its two variants: generalized eigenvalue proximal SVM and twin SVM. A 5 × 5‐fold cross‐validation results showed that this proposed “WFRFT + PCA + generalized eigenvalue proximal SVM” yielded sensitivity of 99.53%, specificity of 92.00%, precision of 99.53%, and accuracy of 99.11%, which are comparable with the proposed “WFRFT + PCA + twin SVM” and better than the proposed “WFRFT + PCA + SVM.” Besides, all three proposed methods were superior to eight state‐of‐the‐art algorithms. Thus, WFRFT is effective, and the proposed methods can be used in practical. © 2015 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 25, 317–327, 2015