Brain Tumor Segmentation Challenge Research Articles

Brain Tumor Segmentation Using an Ensemble of 3D U-Nets and Overall Survival Prediction Using Radiomic Features.

Accurate segmentation of different sub-regions of gliomas such as peritumoral edema, necrotic core, enhancing, and non-enhancing tumor core from multimodal MRI scans has important clinical relevance in diagnosis, prognosis and treatment of brain tumors. However, due to the highly heterogeneous appearance and shape of these tumors, segmentation of the sub-regions is challenging. Recent developments using deep learning models has proved its effectiveness in various semantic and medical image segmentation tasks, many of which are based on the U-Net network structure with symmetric encoding and decoding paths for end-to-end segmentation due to its high efficiency and good performance. In brain tumor segmentation, the 3D nature of multimodal MRI poses challenges such as memory and computation limitations and class imbalance when directly adopting the U-Net structure. In this study we aim to develop a deep learning model using a 3D U-Net with adaptations in the training and testing strategies, network structures, and model parameters for brain tumor segmentation. Furthermore, instead of picking one best model, an ensemble of multiple models trained with different hyper-parameters are used to reduce random errors from each model and yield improved performance. Preliminary results demonstrate the effectiveness of this method and achieved the 9th place in the very competitive 2018 Multimodal Brain Tumor Segmentation (BraTS) challenge. In addition, to emphasize the clinical value of the developed segmentation method, a linear model based on the radiomics features extracted from segmentation and other clinical features are developed to predict patient overall survival. Evaluation of these innovations shows high prediction accuracy in both low-grade glioma and glioblastoma patients, which achieved the 1st place in the 2018 BraTS challenge.

Three-Plane-assembled Deep Learning Segmentation of Gliomas.

To design a computational method for automatic brain glioma segmentation of multimodal MRI scans with high efficiency and accuracy. The 2018 Multimodal Brain Tumor Segmentation Challenge (BraTS) dataset was used in this study, consisting of routine clinically acquired preoperative multimodal MRI scans. Three subregions of glioma-the necrotic and nonenhancing tumor core, the peritumoral edema, and the contrast-enhancing tumor-were manually labeled by experienced radiologists. Two-dimensional U-Net models were built using a three-plane-assembled approach to segment three subregions individually (three-region model) or to segment only the whole tumor (WT) region (WT-only model). The term three-plane-assembled means that coronal and sagittal images were generated by reformatting the original axial images. The model performance for each case was evaluated in three classes: enhancing tumor (ET), tumor core (TC), and WT. On the internal unseen testing dataset split from the 2018 BraTS training dataset, the proposed models achieved mean Sørensen-Dice scores of 0.80, 0.84, and 0.91, respectively, for ET, TC, and WT. On the BraTS validation dataset, the proposed models achieved mean 95% Hausdorff distances of 3.1 mm, 7.0 mm, and 5.0 mm, respectively, for ET, TC, and WT and mean Sørensen-Dice scores of 0.80, 0.83, and 0.91, respectively, for ET, TC, and WT. On the BraTS testing dataset, the proposed models ranked fourth out of 61 teams. The source code is available at https://github.com/GuanLab/Brain_Glioma. This deep learning method consistently segmented subregions of brain glioma with high accuracy, efficiency, reliability, and generalization ability on screening images from a large population, and it can be efficiently implemented in clinical practice to assist neuro-oncologists or radiologists. Supplemental material is available for this article. © RSNA, 2020.

Novel Volumetric Sub-region Segmentation in Brain Tumors.

A novel deep learning based model called Multi-Planar Spatial Convolutional Neural Network (MPS-CNN) is proposed for effective, automated segmentation of different sub-regions viz. peritumoral edema (ED), necrotic core (NCR), enhancing and non-enhancing tumor core (ET/NET), from multi-modal MR images of the brain. An encoder-decoder type CNN model is designed for pixel-wise segmentation of the tumor along three anatomical planes (axial, sagittal, and coronal) at the slice level. These are then combined, by incorporating a consensus fusion strategy with a fully connected Conditional Random Field (CRF) based post-refinement, to produce the final volumetric segmentation of the tumor and its constituent sub-regions. Concepts, such as spatial-pooling and unpooling are used to preserve the spatial locations of the edge pixels, for reducing segmentation error around the boundaries. A new aggregated loss function is also developed for effectively handling data imbalance. The MPS-CNN is trained and validated on the recent Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018 dataset. The Dice scores obtained for the validation set for whole tumor (WT :NCR/NE +ET +ED), tumor core (TC:NCR/NET +ET), and enhancing tumor (ET) are 0.90216, 0.87247, and 0.82445. The proposed MPS-CNN is found to perform the best (based on leaderboard scores) for ET and TC segmentation tasks, in terms of both the quantitative measures (viz. Dice and Hausdorff). In case of the WT segmentation it also achieved the second highest accuracy, with a score which was only 1% less than that of the best performing method.

CGHF: A Computational Decision Support System for Glioma Classification Using Hybrid Radiomics- and Stationary Wavelet-Based Features

Brain tumors are the most prominent neurologically malignant cancers with the highest injury and death rates worldwide. Glioma classification is crucial for the prognosis, assessment of prognostication and the planning of clinical guidelines before surgery. Herein, we introduce a novel stationary wavelet-based radiomics approach to classify the grade of glioma more accurately and in a non-invasive manner. The training dataset of Brain Tumor Segmentation (BraTS) Challenge 2018 is used for performance evaluation and calculation is done based on the radiomics features for three different regions of interest. The classifier, Random Forest, is trained on these features and predicted the grade of glioma. At last, the performance is validated by usingfive-fold cross-validation scheme. The state-of-the-art performance is achieved considering metric (Acc, Sens, Spec, Score, MCC, AUC) ≡ (97.54%, 97.62%, 97.33%, 98.3%, 94.12%, 97.48%) with machine learning predictive model Random Forest (RF) for brain tumor patients' classification. Considering the importance of glioma classification for the assessment of prognosis, our approach could be useful in the planning of clinical guidelines prior to surgery.

Task Decomposition and Synchronization for Semantic Biomedical Image Segmentation

Semantic segmentation is essentially important to biomedical image analysis. Many recent works mainly focus on integrating the Fully Convolutional Network (FCN) architecture with sophisticated convolution implementation and deep supervision. In this paper, we propose to decompose the single segmentation task into three subsequent sub-tasks, including (1) pixel-wise image segmentation, (2) prediction of the class labels of the objects within the image, and (3) classification of the scene the image belonging to. While these three sub-tasks are trained to optimize their individual loss functions of different perceptual levels, we propose to let them interact by the task-task context ensemble. Moreover, we propose a novel sync-regularization to penalize the deviation between the outputs of the pixel-wise segmentation and the class prediction tasks. These effective regularizations help FCN utilize context information comprehensively and attain accurate semantic segmentation, even though the number of the images for training may be limited in many biomedical applications. We have successfully applied our framework to three diverse 2D/3D medical image datasets, including Robotic Scene Segmentation Challenge 18 (ROBOT18), Brain Tumor Segmentation Challenge 18 (BRATS18), and Retinal Fundus Glaucoma Challenge (REFUGE18). We have achieved top-tier performance in all three challenges.

Data Augmentation for Brain-Tumor Segmentation: A Review.

Data augmentation is a popular technique which helps improve generalization capabilities of deep neural networks, and can be perceived as implicit regularization. It plays a pivotal role in scenarios in which the amount of high-quality ground-truth data is limited, and acquiring new examples is costly and time-consuming. This is a very common problem in medical image analysis, especially tumor delineation. In this paper, we review the current advances in data-augmentation techniques applied to magnetic resonance images of brain tumors. To better understand the practical aspects of such algorithms, we investigate the papers submitted to the Multimodal Brain Tumor Segmentation Challenge (BraTS 2018 edition), as the BraTS dataset became a standard benchmark for validating existent and emerging brain-tumor detection and segmentation techniques. We verify which data augmentation approaches were exploited and what was their impact on the abilities of underlying supervised learners. Finally, we highlight the most promising research directions to follow in order to synthesize high-quality artificial brain-tumor examples which can boost the generalization abilities of deep models.

Divide and Conquer: Stratifying Training Data by Tumor Grade Improves Deep Learning-Based Brain Tumor Segmentation.

It is a general assumption in deep learning that more training data leads to better performance, and that models will learn to generalize well across heterogeneous input data as long as that variety is represented in the training set. Segmentation of brain tumors is a well-investigated topic in medical image computing, owing primarily to the availability of a large publicly-available dataset arising from the long-running yearly Multimodal Brain Tumor Segmentation (BraTS) challenge. Research efforts and publications addressing this dataset focus predominantly on technical improvements of model architectures and less on properties of the underlying data. Using the dataset and the method ranked third in the BraTS 2018 challenge, we performed experiments to examine the impact of tumor type on segmentation performance. We propose to stratify the training dataset into high-grade glioma (HGG) and low-grade glioma (LGG) subjects and train two separate models. Although we observed only minor gains in overall mean dice scores by this stratification, examining case-wise rankings of individual subjects revealed statistically significant improvements. Compared to a baseline model trained on both HGG and LGG cases, two separately trained models led to better performance in 64.9% of cases (p < 0.0001) for the tumor core. An analysis of subjects which did not profit from stratified training revealed that cases were missegmented which had poor image quality, or which presented clinically particularly challenging cases (e.g., underrepresented subtypes such as IDH1-mutant tumors), underlining the importance of such latent variables in the context of tumor segmentation. In summary, we found that segmentation models trained on the BraTS 2018 dataset, stratified according to tumor type, lead to a significant increase in segmentation performance. Furthermore, we demonstrated that this gain in segmentation performance is evident in the case-wise ranking of individual subjects but not in summary statistics. We conclude that it may be useful to consider the segmentation of brain tumors of different types or grades as separate tasks, rather than developing one tool to segment them all. Consequently, making this information available for the test data should be considered, potentially leading to a more clinically relevant BraTS competition.

Research on glioma magnetic resonance imaging segmentation based on dual-channel three-dimensional densely connected network

Focus on the inconsistency of the shape, location and size of brain glioma, a dual-channel 3-dimensional (3D) densely connected network is proposed to automatically segment brain glioma tumor on magnetic resonance images. Our method is based on a 3D convolutional neural network frame, and two convolution kernel sizes are adopted in each channel to extract multi-scale features in different scales of receptive fields. Then we construct two densely connected blocks in each pathway for feature learning and transmission. Finally, the concatenation of two pathway features was sent to classification layer to classify central region voxels to segment brain tumor automatically. We train and test our model on open brain tumor segmentation challenge dataset, and we also compared our results with other models. Experimental results show that our algorithm can segment different tumor lesions more accurately. It has important application value in the clinical diagnosis and treatment of brain tumor diseases.

Automated brain tumor segmentation and classification for MRI analysis system

&lt;span&gt;This paper proposed a new analysis technique of brain tumor segmentation and classification for Fluid Attenuated Inversion Recovery (FLAIR) Magnetic Resonance Images (MRI). 25 FLAIR MRI images were collected from online database of Multimodal Brain Tumor Segmentation Challenge 2015 (BRaTS’15). The analysis comprised four stages which are preprocessing, segmentation, feature extraction and classification. Fuzzy C-Means (FCM) was proposed for brain tumor segmentation. Mean, median, mode, standard deviation, area and perimeter were calculated and utilized as the features to be fed into a rule-based classifier. The segmentation performances were assessed based on Jaccard, Dice, False Positive and False Negative Rates (FPR and FNR). The results indicate that FCM offered high similarity indices which were 0.74 and 0.83 for Jaccard and Dice indices, respectively. The technique can possibly provide high accuracy and has the potential to detect and classify brain tumor from FLAIR MRI database.&lt;/span&gt;

Brain Tumor Segmentation and Survival Prediction Using Multimodal MRI Scans With Deep Learning.

Gliomas are the most common primary brain malignancies. Accurate and robust tumor segmentation and prediction of patients' overall survival are important for diagnosis, treatment planning and risk factor identification. Here we present a deep learning-based framework for brain tumor segmentation and survival prediction in glioma, using multimodal MRI scans. For tumor segmentation, we use ensembles of three different 3D CNN architectures for robust performance through a majority rule. This approach can effectively reduce model bias and boost performance. For survival prediction, we extract 4,524 radiomic features from segmented tumor regions, then, a decision tree and cross validation are used to select potent features. Finally, a random forest model is trained to predict the overall survival of patients. The 2018 MICCAI Multimodal Brain Tumor Segmentation Challenge (BraTS), ranks our method at 2nd and 5th place out of 60+ participating teams for survival prediction tasks and segmentation tasks respectively, achieving a promising 61.0% accuracy on the classification of short-survivors, mid-survivors and long-survivors.

Abstract 3351: Overall survival prediction of glioblastoma patients combining clinical factors with texture features extracted from 3-D convolutional neural networks

Abstract Objective: We aim to predict overall survival (OS) in Glioblastoma treated with gross total resection (GTR) using pre-operative MRI images. Methods: A cohort of 87 GBM patients (59 patients for training and 28 patients for validation) who underwent GTR was analyzed using multi-institutional data from brain tumor segmentation (BraTS) challenge 2018 (Menze BH, et al. TMI 2015; Bakas S, et al. NSD 2017). Each patient consisted of a series of pre-surgical MR images including T1 pre contrast, T1-Contrast Enhanced, T2 and Flair images. A group of experienced radiologists delineated edema, tumor core and enhanced tumor for each testing patient using these image sequences. A 2D U-net was trained to segment these structures on the validation cohort. A 3D CNN model with orthogonalized random filters was used to learn images features from the three segmented subregions including texture, size, location, etc. Global maximum pooling was performed on intermediate convolutional layers to obtain representative image features for each patient. Since mid-term survivors (6-18 months) outnumbered short (&amp;lt;6 months) and long term (&amp;gt;18 months) survivors for a large margin, the MR images from both short and long term survivors were augmented with random rotations to balance the number of patients among three cohorts of patients. The extracted image features was then fed into an RBF-kernel based L-2 norm regression algorithm (Huang GB, IEEE SMC, 2012) to predict patient’s OS. Results: The average [standard deviation] of dice similarity coefficient (DSC) for the whole tumor, enhanced tumor, and tumor core contours were 0.882[0.080], 0.712 [0.294], and 0.769 [0.263], respectively for the validation cohort. Parameters of regression algorithm was optimized using leave one out cross validation. One convolutional layer was used in the CNN archietecture due to limited training samples. The model performance deteriorated when using deeper layers. The best architecture to classify patients into short, mid and long term survivors was one convolutional layer with 30 filters. The prediction accuracy was 64.3%, and the spearman’r sank correlation was 0.395. The model performance was slightly improved by including clinical factors such as age, tumor location, ratio of the whole tumor size to the entire brain etc. The Spearman’s rank correlation coefficient was increased to 0.432 while the accuracy maintained the same. Conclusions: We developed a 3D CNN model followd with kernel regression to extract image features from pre-operative MR images and predict OS of GBM patients after GTR. These signatures have shown potential values as biomarkers to predict OS. Citation Format: Weiwei Zong, Joon Lee, Chang Liu, James Snyder, Ning Wen. Overall survival prediction of glioblastoma patients combining clinical factors with texture features extracted from 3-D convolutional neural networks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3351.

A deep learning model integrating SK-TPCNN and random forests for brain tumor segmentation in MRI

The segmentation of brain tumors in magnetic resonance imaging (MRI) images plays an important role in early diagnosis, treatment planning and outcome evaluation. However, due to gliomas’ significant diversity in structure, the segmentation accuracy is low. In this paper, an automatic segmentation method integrating the small kernels two-path convolutional neural network (SK-TPCNN) and random forests (RF) is proposed, the feature extraction ability of SK-TPCNN and the joint optimization capability of model are presented respectively. The SK-TPCNN structure combining the small convolutional kernels and large convolutional kernels can enhance the nonlinear mapping ability and avoid over-fitting, the multiformity of features is also increased. The learned features from SK-TPCNN are then applied to the RF classifier to implement the joint optimization. RF classifier effectively integrates redundancy features and classify each MRI image voxel into normal brain tissues and different parts of tumor. The proposed algorithm is validated and evaluated in the Brain Tumor Segmentation Challenge (Brats) 2015 challenge Training dataset and the better performance is achieved.

Brain tumor detection using statistical and machine learning method

Background and ObjectiveBrain tumor occurs because of anomalous development of cells. It is one of the major reasons of death in adults around the globe. Millions of deaths can be prevented through early detection of brain tumor. Earlier brain tumor detection using Magnetic Resonance Imaging (MRI) may increase patient's survival rate. In MRI, tumor is shown more clearly that helps in the process of further treatment. This work aims to detect tumor at an early phase. MethodsIn this manuscript, Weiner filter with different wavelet bands is used to de-noise and enhance the input slices. Subsets of tumor pixels are found with Potential Field (PF) clustering. Furthermore, global threshold and different mathematical morphology operations are used to isolate the tumor region in Fluid Attenuated Inversion Recovery (Flair) and T2 MRI. For accurate classification, Local Binary Pattern (LBP) and Gabor Wavelet Transform (GWT) features are fused. ResultsThe proposed approach is evaluated in terms of peak signal to noise ratio (PSNR), mean squared error (MSE) and structured similarity index (SSIM) yielding results as 76.38, 0.037 and 0.98 on T2 and 76.2, 0.039 and 0.98 on Flair respectively. The segmentation results have been evaluated based on pixels, individual features and fused features. At pixels level, the comparison of proposed approach is done with ground truth slices and also validated in terms of foreground (FG) pixels, background (BG) pixels, error region (ER) and pixel quality (Q). The approach achieved 0.93 FG and 0.98 BG precision and 0.010 ER on a local dataset. On multimodal brain tumor segmentation challenge dataset BRATS 2013, 0.93 FG and 0.99 BG precision and 0.005 ER are acquired. Similarly on BRATS 2015, 0.97 FG and 0.98 BG precision and 0.015 ER are obtained. In terms of quality, the average Q value and deviation are 0.88 and 0.017. At the fused feature based level, specificity, sensitivity, accuracy, area under the curve (AUC) and dice similarity coefficient (DSC) are 1.00, 0.92, 0.93, 0.96 and 0.96 on BRATS 2013, 0.90, 1.00, 0.97, 0.98 and 0.98 on BRATS 2015 and 0.90, 0.91, 0.90, 0.77 and 0.95 on local dataset respectively. ConclusionThe presented approach outperformed as compared to existing approaches.

Glioma grading using structural magnetic resonance imaging and molecular data.

A glioma grading method using conventional structural magnetic resonance image (MRI) and molecular data from patients is proposed. The noninvasive grading of glioma tumors is obtained using multiple radiomic texture features including dynamic texture analysis, multifractal detrended fluctuation analysis, and multiresolution fractal Brownian motion in structural MRI. The proposed method is evaluated using two multicenter MRI datasets: (1)the brain tumor segmentation (BRATS-2017) challenge for high-grade versus low-grade (LG) and (2)the cancer imaging archive (TCIA) repository for glioblastoma (GBM) versus LG glioma grading. The grading performance using MRI is compared with that of digital pathology (DP) images in the cancer genome atlas (TCGA) data repository. The results show that the mean area under the receiver operating characteristic curve (AUC) is 0.88 for the BRATS dataset. The classification of tumor grades using MRI and DP images in TCIA/TCGA yields mean AUC of 0.90 and 0.93, respectively. This work further proposes and compares tumor grading performance using molecular alterations (IDH1/2 mutations) along with MRI and DP data, following the most recent World Health Organization grading criteria, respectively. The overall grading performance demonstrates the efficacy of the proposed noninvasive glioma grading approach using structural MRI.

Supervised Brain Tumor Segmentation Based on Gradient and Context-Sensitive Features.

Gliomas have the highest mortality rate and prevalence among the primary brain tumors. In this study, we proposed a supervised brain tumor segmentation method which detects diverse tumoral structures of both high grade gliomas and low grade gliomas in magnetic resonance imaging (MRI) images based on two types of features, the gradient features and the context-sensitive features. Two-dimensional gradient and three-dimensional gradient information was fully utilized to capture the gradient change. Furthermore, we proposed a circular context-sensitive feature which captures context information effectively. These features, totally 62, were compressed and optimized based on an mRMR algorithm, and random forest was used to classify voxels based on the compact feature set. To overcome the class-imbalanced problem of MRI data, our model was trained on a class-balanced region of interest dataset. We evaluated the proposed method based on the 2015 Brain Tumor Segmentation Challenge database, and the experimental results show a competitive performance.

Detection of HGG and LGG Brain Tumors using U-Net

Background/Objectives: Advancement in medical equipment has enabled accurate and quick diagnosis in medical field. However, an increase in the number of medical staff is slower than the rate of medical equipment development. It has resulted in increased risk of diagnostic misinterpretation. The purpose of this paper is to help diagnosis of medical staff through artificial neural network (ANN).Method/Statistical Analysis: We selected U-Net among artificial neural networks. U-Net is highly accurate in medical imaging. The dataset for learning the network was obtained from the Brain Tumor Segmentation Challenge (BraTS). This dataset contains four classes of brain tumor data and it is suitable for learning variety of brain tumors. We used F-Score to measure the accuracy of the learned network.Findings: In this paper, we compare the performance of the network by conducting two experiments. First, we checked the learning progress of the network. Second, we compared the results of learning with mixed and single datasets. In the first experiment, when allowing the network to learn for a total of 200 generations, it was confirmed that the results of 100 generations were the most accurate. In the second experiment, the network learned by three groups of datasets. The first group consisted of HGG data only, and the second group was composed of LGG data only, and the last group was made up of mixing HGG and LGG data. When comparing the results of the first group with the third group, the accuracy of HGG patient was 0.6696 and 0.6222, respectively. Subsequently, the results of the second and the third group were 0.6315 and 0.6228, respectively.Improvements/Applications: In this experiment, we compared the results obtained when the datasets were mixed and when they were used singly. The results show similar accuracy. However, when using a mixture of datasets, the accuracy is lower, which is enough to assist the diagnosis of the medical staff. It is expected that this will help the development of the medical image processing field by confirming the position and size of the brain tumor accurately regardless of the data of any grade for brain tumor.

Brain abnormality detection using template matching

Abstract Magnetic resonance imaging (MRI) is a widely used imaging modality to evaluate brain disorders. MRI generates huge volumes of data, which consist of a sequence of scans taken at different instances of time. As the presence of brain disorders has to be evaluated on all magnetic resonance (MR) sequences, manual brain disorder detection becomes a tedious process and is prone to inter- and intra-rater errors. A technique for detecting abnormalities in brain MRI using template matching is proposed. Bias filed correction is performed on volumetric scans using N4ITK filter, followed by volumetric registration. Normalized cross-correlation template matching is used for image registration taking into account, the rotation and scaling operations. A template of abnormality is selected which is then matched in the volumetric scans, if found, the corresponding image is retrieved. Post-processing of the retrieved images is performed by the thresholding operation; the coordinates and area of the abnormality are reported. The experiments are carried out on the glioma dataset obtained from Brain Tumor Segmentation Challenge 2013 database (BRATS 2013). Glioma dataset consisted of MR scans of 30 real glioma patients and 50 simulated glioma patients. NVIDIA Compute Unified Device Architecture framework is employed in this paper, and it is found that the detection speed using graphics processing unit is almost four times faster than using only central processing unit. The average Dice and Jaccard coefficients for a wide range of trials are found to be 0.91 and 0.83, respectively.

A Novel Tool for Supervised Segmentation Using 3D Slicer

The rather impressive extension library of medical image-processing platform 3D Slicer lacks a wide range of machine-learning toolboxes. The authors have developed such a toolbox that incorporates commonly used machine-learning libraries. The extension uses a simple graphical user interface that allows the user to preprocess data, train a classifier, and use that classifier in common medical image-classification tasks, such as tumor staging or various anatomical segmentations without a deeper knowledge of the inner workings of the classifiers. A series of experiments were carried out to showcase the capabilities of the extension and quantify the symmetry between the physical characteristics of pathological tissues and the parameters of a classifying model. These experiments also include an analysis of the impact of training vector size and feature selection on the sensitivity and specificity of all included classifiers. The results indicate that training vector size can be minimized for all classifiers. Using the data from the Brain Tumor Segmentation Challenge, Random Forest appears to have the widest range of parameters that produce sufficiently accurate segmentations, while optimal Support Vector Machines’ training parameters are concentrated in a narrow feature space.

AdaptAhead Optimization Algorithm for Learning Deep CNN Applied to MRI Segmentation.

Deep learning is one of the subsets of machine learning that is widely used in artificial intelligence (AI) field such as natural language processing and machine vision. The deep convolution neural network (DCNN) extracts high-level concepts from low-level features and it is appropriate for large volumes of data. In fact, in deep learning, the high-level concepts are defined by low-level features. Previously, in optimization algorithms, the accuracy achieved for network training was less and high-cost function. In this regard, in this study, AdaptAhead optimization algorithm was developed for learning DCNN with robust architecture in relation to the high volume data. The proposed optimization algorithm was validated in multi-modality MR images of BRATS 2015 and BRATS 2016 data sets. Comparison of the proposed optimization algorithm with other commonly used methods represents the improvement of the performance of the proposed optimization algorithm on the relatively large dataset. Using the Dice similarity metric, we report accuracy results on the BRATS 2015 and BRATS 2016 brain tumor segmentation challenge dataset. Results showed that our proposed algorithm is significantly more accurate than other methods as a result of its deep and hierarchical extraction.

User-Guided Segmentation of Multi-modality Medical Imaging Datasets with ITK-SNAP.

ITK-SNAP is an interactive software tool for manual and semi-automatic segmentation of 3D medical images. This paper summarizes major new features added to ITK-SNAP over the last decade. The main focus of the paper is on new features that support semi-automatic segmentation of multi-modality imaging datasets, such as MRI scans acquired using different contrast mechanisms (e.g., T1, T2, FLAIR). The new functionality uses decision forest classifiers trained interactively by the user to transform multiple input image volumes into a foreground/background probability map; this map is then input as the data term to the active contour evolution algorithm, which yields regularized surface representations of the segmented objects of interest. The new functionality is evaluated in the context of high-grade and low-grade glioma segmentation by three expert neuroradiogists and a non-expert on a reference dataset from the MICCAI 2013 Multi-Modal Brain Tumor Segmentation Challenge (BRATS). The accuracy of semi-automatic segmentation is competitive with the top specialized brain tumor segmentation methods evaluated in the BRATS challenge, with most results obtained in ITK-SNAP being more accurate, relative to the BRATS reference manual segmentation, than the second-best performer in the BRATS challenge; and all results being more accurate than the fourth-best performer. Segmentation time is reduced over manual segmentation by 2.5 and 5 times, depending on the rater. Additional experiments in interactive placenta segmentation in 3D fetal ultrasound illustrate the generalizability of the new functionality to a different problem domain.