scholarly journals Brain Tumor Segmentation From Multi-Modal MR Images via Ensembling UNets

2021 ◽  
Vol 1 ◽  
Author(s):  
Yue Zhang ◽  
Pinyuan Zhong ◽  
Dabin Jie ◽  
Jiewei Wu ◽  
Shanmei Zeng ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Network Architecture ◽  
Biological Properties ◽  
Training Data ◽  
Validation Dataset ◽  
Tumor Segmentation ◽  
Post Processing ◽  
Mr Images ◽  
Brain Tumor Segmentation ◽  
The Third

Glioma is a type of severe brain tumor, and its accurate segmentation is useful in surgery planning and progression evaluation. Based on different biological properties, the glioma can be divided into three partially-overlapping regions of interest, including whole tumor (WT), tumor core (TC), and enhancing tumor (ET). Recently, UNet has identified its effectiveness in automatically segmenting brain tumor from multi-modal magnetic resonance (MR) images. In this work, instead of network architecture, we focus on making use of prior knowledge (brain parcellation), training and testing strategy (joint 3D+2D), ensemble and post-processing to improve the brain tumor segmentation performance. We explore the accuracy of three UNets with different inputs, and then ensemble the corresponding three outputs, followed by post-processing to achieve the final segmentation. Similar to most existing works, the first UNet uses 3D patches of multi-modal MR images as the input. The second UNet uses brain parcellation as an additional input. And the third UNet is inputted by 2D slices of multi-modal MR images, brain parcellation, and probability maps of WT, TC, and ET obtained from the second UNet. Then, we sequentially unify the WT segmentation from the third UNet and the fused TC and ET segmentation from the first and the second UNets as the complete tumor segmentation. Finally, we adopt a post-processing strategy by labeling small ET as non-enhancing tumor to correct some false-positive ET segmentation. On one publicly-available challenge validation dataset (BraTS2018), the proposed segmentation pipeline yielded average Dice scores of 91.03/86.44/80.58% and average 95% Hausdorff distances of 3.76/6.73/2.51 mm for WT/TC/ET, exhibiting superior segmentation performance over other state-of-the-art methods. We then evaluated the proposed method on the BraTS2020 training data through five-fold cross validation, with similar performance having also been observed. The proposed method was finally evaluated on 10 in-house data, the effectiveness of which has been established qualitatively by professional radiologists.

scholarly journals Fully Automated Brain Tumor Segmentation and Survival Prediction of Gliomas using Deep Learning and MRI

2019 ◽  
Author(s):  
Chandan Ganesh Bangalore Yogananda ◽  
Sahil S. Nalawade ◽  
Gowtham K. Murugesan ◽  
Ben Wagner ◽  
Marco C. Pinho ◽  
...  
Keyword(s):  
Deep Learning ◽  
Brain Tumor ◽  
Texture Features ◽  
Response To Therapy ◽  
Validation Dataset ◽  
Tumor Segmentation ◽  
Survival Prediction ◽  
Accuracy Score ◽  
Mr Images ◽  
Brain Tumor Segmentation

ABSTRACTTumor segmentation of magnetic resonance (MR) images is a critical step in providing objective measures of predicting aggressiveness and response to therapy in gliomas. It has valuable applications in diagnosis, monitoring, and treatment planning of brain tumors. The purpose of this work was to develop a fully automated deep learning method for brain tumor segmentation and survival prediction. Well curated brain tumor cases with multi-parametric MR Images from the BraTS2019 dataset were used. A three-group framework was implemented, with each group consisting of three 3D-Dense-UNets to segment whole tumor (WT), tumor core (TC) and enhancing tumor (ET). This method was implemented to decompose the complex multi-class segmentation problem into individual binary segmentation problems for each sub-component. Each group was trained using different approaches and loss functions. The output segmentations of a particular label from their respective networks from the 3 groups were ensembled and post-processed. For survival analysis, a linear regression model based on imaging texture features and wavelet texture features extracted from each of the segmented components was implemented. The networks were tested on the BraTS2019 validation dataset including 125 cases for the brain tumor segmentation task and 29 cases for the survival prediction task. The segmentation networks achieved average dice scores of 0.901, 0.844 and 0.801 for WT, TC and ET respectively. The survival prediction network achieved an accuracy score of 0.55 and mean squared error (MSE) of 119244. This method could be implemented as a robust tool to assist clinicians in primary brain tumor management and follow-up.

scholarly journals Multidimensional and Multiresolution Ensemble Networks for Brain Tumor Segmentation

2019 ◽  
Author(s):  
Gowtham Krishnan Murugesan ◽  
Sahil Nalawade ◽  
Chandan Ganesh ◽  
Ben Wagner ◽  
Fang F. Yu ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Learning Algorithm ◽  
Validation Dataset ◽  
Tumor Segmentation ◽  
Mr Images ◽  
3D Segmentation ◽  
Brain Tumor Segmentation ◽  
Robust Segmentation ◽  
2D And 3D ◽  
Segmentation Models

AbstractIn this work, we developed multiple 2D and 3D segmentation models with multiresolution input to segment brain tumor components, and then ensembled them to obtain robust segmentation maps. This reduced overfitting and resulted in a more generalized model. Multiparametric MR images of 335 subjects from BRATS 2019 challenge were used for training the models. Further, we tested a classical machine learning algorithm (xgboost) with features extracted from the segmentation maps to classify subject survival range. Preliminary results on the BRATS 2019 validation dataset demonstrasted this method can achieve excellent performance with DICE scores of 0.898, 0.784, 0.779 for whole tumor, tumor core and enhancing tumor respectively and accuracy 34.5 % for survuval prediction.

scholarly journals Recurrent Multi-Fiber Network for 3D MRI Brain Tumor Segmentation

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 320
Author(s):  
Yue Zhao ◽  
Xiaoqiang Ren ◽  
Kun Hou ◽  
Wentao Li
Keyword(s):  
Brain Tumor ◽  
Network Architecture ◽  
Contextual Information ◽  
Computational Cost ◽  
Disease Diagnosis ◽  
Tumor Segmentation ◽  
Brain Tumor Segmentation ◽  
Fiber Network ◽  
3D Network ◽  
The Brain

Automated brain tumor segmentation based on 3D magnetic resonance imaging (MRI) is critical to disease diagnosis. Moreover, robust and accurate achieving automatic extraction of brain tumor is a big challenge because of the inherent heterogeneity of the tumor structure. In this paper, we present an efficient semantic segmentation 3D recurrent multi-fiber network (RMFNet), which is based on encoder–decoder architecture to segment the brain tumor accurately. 3D RMFNet is applied in our paper to solve the problem of brain tumor segmentation, including a 3D recurrent unit and 3D multi-fiber unit. First of all, we propose that recurrent units segment brain tumors by connecting recurrent units and convolutional layers. This quality enhances the model’s ability to integrate contextual information and is of great significance to enhance the contextual information. Then, a 3D multi-fiber unit is added to the overall network to solve the high computational cost caused by the use of a 3D network architecture to capture local features. 3D RMFNet combines both advantages from a 3D recurrent unit and 3D multi-fiber unit. Extensive experiments on the Brain Tumor Segmentation (BraTS) 2018 challenge dataset show that our RMFNet remarkably outperforms state-of-the-art methods, and achieves average Dice scores of 89.62%, 83.65% and 78.72% for the whole tumor, tumor core and enhancing tumor, respectively. The experimental results prove our architecture to be an efficient tool for brain tumor segmentation accurately.

A Deep Adaptive Convolutional Network for Brain Tumor Segmentation from Multimodal MR Images

2019 ◽  
Author(s):  
Palash Ghosal ◽  
Shanmukha Reddy ◽  
Charan Sai ◽  
Vikas Pandey ◽  
Jayasree Chakraborty ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Tumor Segmentation ◽  
Mr Images ◽  
Convolutional Network ◽  
Brain Tumor Segmentation

scholarly journals Improving Brain Tumor Segmentation with Data Augmentation Strategies

2021 ◽  
Author(s):  
Radhika Malhotra ◽  
Jasleen Saini ◽  
Barjinder Singh Saini ◽  
Savita Gupta
Keyword(s):  
Brain Tumor ◽  
Data Augmentation ◽  
Large Data ◽  
Training Data ◽  
Tumor Segmentation ◽  
Biomedical Image Processing ◽  
Brain Tumor Segmentation ◽  
Biomedical Image ◽  
Augmentation Strategies ◽  
Unseen Data

In the past decade, there has been a remarkable evolution of convolutional neural networks (CNN) for biomedical image processing. These improvements are inculcated in the basic deep learning-based models for computer-aided detection and prognosis of various ailments. But implementation of these CNN based networks is highly dependent on large data in case of supervised learning processes. This is needed to tackle overfitting issues which is a major concern in supervised techniques. Overfitting refers to the phenomenon when a network starts learning specific patterns of the input such that it fits well on the training data but leads to poor generalization abilities on unseen data. The accessibility of enormous quantity of data limits the field of medical domain research. This paper focuses on utility of data augmentation (DA) techniques, which is a well-recognized solution to the problem of limited data. The experiments were performed on the Brain Tumor Segmentation (BraTS) dataset which is available online. The results signify that different DA approaches have upgraded the accuracies for segmenting brain tumor boundaries using CNN based model.

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