scholarly journals MRI Modality-based Brain Tumor Segmentation Using Deep Neural Networks

2021 ◽  
Author(s):  
Pankaj Eknath Kasar ◽  
Shivajirao M. Jadhav ◽  
Vineet Kansal
Keyword(s):  
Neural Networks ◽  
Brain Tumor ◽  
Clinical Practice ◽  
Brain Tumors ◽  
Deep Neural Networks ◽  
Automatic Segmentation ◽  
Brain Mri ◽  
Tumor Segmentation ◽  
Dice Similarity Coefficient ◽  
Manual Segmentation

Abstract The tumor detection is major challenging task in brain tumor quantitative evaluation. In recent years, owing to non-invasive and strong soft tissue comparison, Magnetic Resonance Imaging (MRI) has gained great interest. MRI is a commonly used image modality technique to locate brain tumors. An immense amount of data is produced by the MRI. Heterogeneity, isointense and hypointense tumor properties restrict manual segmentation in a fair period of time, thus restricting the use of reliable quantitative measures in clinical practice. In the clinical practice manual segmentation task is quite time consuming and their performance is highly depended on the operator’s experience. Accurate and automated tumor segmentation techniques are also needed; however, the severe spatial and structural heterogeneity of brain tumors makes automatic segmentation a difficult job. This paper proposes fully automatic segmentation of brain tumors using encoder-decoder based convolutional neural networks. The paper focuses on well-known semantic segmentation deep neural networks i.e., UNET and SEGNET for segmenting tumors from Brain MRI images. The networks are trained and tested using freely accessible standard dataset, with Dice Similarity Coefficient (DSC) as metric for whole predicted image i.e., including tumor and background. UNET’s average DSC on test dataset is 0.76 whereas for SEGNET we got average DSC 0.67. The evaluation of results proves that UNET is having better performance than SEGNET.

P04.06 Can BraTS Toolkit Brain Tumor Segmentation Algorithms be relevant when dealing with post-operative MRI in clinical practice?

2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii19-ii20
Author(s):  
L Piram ◽  
C Acquitter ◽  
U Sabatini ◽  
B Lemasson ◽  
E Moyal ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Clinical Practice ◽  
Brain Tumors ◽  
Hausdorff Distance ◽  
De Novo ◽  
Automatic Segmentation ◽  
Outcome Evaluation ◽  
Tumor Segmentation ◽  
Brain Tumor Segmentation ◽  
Image Conversion

Abstract BACKGROUND Segmentation of brain tumors is crucial for radiotherapy plans and treatment outcome evaluation. As manual segmentation (MS) is a time-consuming task, many algorithms to automate the process were proposed over the past decades. BraTS toolkit (BTK) offers a solution for automatic brain tumor segmentation in 3 steps: a Preprocessor for image conversion and registration, a Segmentor generating segmentations from 4 deep-learning based algorithms and a Fusionator combining the results. As most algorithms published, BTK was trained on pre-operative data. Yet, as surgery is the first treatment of glioblastomas, most MRIs in clinical practice are post-operative images. This study aimed to assess whether segmentation of post-operative brain tumors could benefit from an initial automatic segmentation (AS) using BTK. MATERIAL AND METHODS MRI dataset from the multicenter, STERIMGLI clinical trial provided 92 series from 25 patients with a unifocal recurrence of glioblastoma. AS were generated using BTK Preprocessor and Segmentor. Out of the 4 algorithms output, the best AS was selected after visual appraisal. AS contained 3 labels: T1w contrast enhanced tumor (ET), flair edema (ED) and non-enhanced tumor (NET). AS were then reviewed by a radiation oncologist and a neuroradiologist to produce the MS. ET and ED were corrected; surgical cavity (SC) was also segmented, either from the NET label or de novo. Dice-score, Hausdorff Distance (HD) and Average Hausdorff Distance (AHD) were used to quantify the similarity between AS and MS for each label. RESULTS AS succeeded to label 89.3% (82/92), 100% (92/92) and 85.8% (79/92) of ET, ED and NET respectively. Among the 4 algorithms in BTK, Zyx_2019 produced 36% of AS, mic-dkfz 32%, xfeng 18%, lfb_rwth 14%. Mean Dice-scores of 75.8%, 94.8% were found for ET and ED respectively. Mean HD and AHD were 25.2mm (±39.7), 2.8mm (±10.9) for ET; 14.9mm (±25.8), 0.9mm (±5.8) for ED. Concerning SC, Dice-scores were <0.1 for 49% (39/79), >0.6 for 30% (42/79). CONCLUSION BraTS Toolkit was trained to segment necrosis as the label NET. Still, it detected the surgical cavity and saved time for the MS in 51% of post-operative cases. Even though BTK was designed to segment pre-operative brain tumors, similarity metrics show that minimal or no manual corrections are necessary most of the time when used to segment ET and ED on post-operative MRI acquired in clinical routine. The development of a unique AS tool for pre and post-operative images would be useful in clinical practice.

Recent advancements in Fuzzy C-means based techniques for brain MRI Segmentation

2021 ◽  
Vol 16 ◽  
Author(s):  
Ghazanfar Latif ◽  
Jaafar Alghazo ◽  
Fadi N. Sibai ◽  
D.N.F. Awang Iskandar ◽  
Adil H. Khan
Keyword(s):  
Brain Tumor ◽  
Brain Tumors ◽  
Brain Mri ◽  
Tumor Segmentation ◽  
Brain Anatomy ◽  
Mri Segmentation ◽  
Brain Tumor Segmentation ◽  
Brain Images ◽  
Low Contrast ◽  
Fuzzy C Means

Background: Variations of image segmentation techniques, particularly those used for Brain MRI segmentation, vary in complexity from basic standard Fuzzy C-means (FCM) to more complex and enhanced FCM techniques. Objective: In this paper, a comprehensive review is presented on all thirteen variations of FCM segmentation techniques. In the review process, the concentration is on the use of FCM segmentation techniques for brain tumors. Brain tumor segmentation is a vital step in the process of automatically diagnosing brain tumors. Unlike segmentation of other types of images, brain tumor segmentation is a very challenging task due to the variations in brain anatomy. The low contrast of brain images further complicates this process. Early diagnosis of brain tumors is indeed beneficial to patients, doctors, and medical providers. Results: FCM segmentation works on images obtained from magnetic resonance imaging (MRI) scanners, requiring minor modifications to hospital operations to early diagnose tumors as most, if not all, hospitals rely on MRI machines for brain imaging. In this paper, we critically review and summarize FCM based techniques for brain MRI segmentation.

Brain Tumor Segmentation Based on Region of Interest-Aided Localization and Segmentation U-Net

2021 ◽  
Author(s):  
Shidong Li ◽  
Jianwei Liu ◽  
Zhanjie Song
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Brain Tumor ◽  
Medical Image ◽  
Brain Mri ◽  
Medical Image Processing ◽  
Tumor Segmentation ◽  
Dice Similarity Coefficient ◽  
Brain Tumor Segmentation ◽  
The Impact

Abstract Since magnetic resonance imaging (MRI) has superior soft tissue contrast, contouring (brain) tumor accurately by MRI images is essential in medical image processing. Segmenting tumor accurately is immensely challenging, since tumor and normal tissues are often inextricably intertwined in the brain. It is also extremely time consuming manually. Late deep learning techniques start to show reasonable success in brain tumor segmentation automatically. The purpose of this study is to develop a new region-ofinterest-aided (ROI-aided) deep learning technique for automatic brain tumor MRI segmentation. The method consists of two major steps. Step one is to use a 2D network with U-Net architecture to localize the tumor ROI, which is to reduce the impact of normal tissue’s disturbance. Then a 3D U-Net is performed in step 2 for tumor segmentation within identified ROI. The proposed method is validated on MICCAI BraTS 2015 Challenge with 220 high Gliomas grade (HGG) and 54 low Gliomas grade (LGG) patients’ data. The Dice similarity coefficient and the Hausdorff distance between the manual tumor contour and that segmented by the proposed method are 0.876 ±0.068 and 3.594±1.347 mm, respectively. These numbers are indications that our proposed method is an effective ROI-aided deep learning strategy for brain MRI tumor segmentation, and a valid and useful tool in medical image processing.

scholarly journals BRAIN TUMOR SEGMENTATION BASED ON U-NET WITH IMAGE DRIVEN LEVEL SET LOSS

2021 ◽  
Vol 59 (5) ◽  
Author(s):  
Truong Van Pham ◽  
Thao Thi Tran
Keyword(s):  
Brain Tumor ◽  
Level Set ◽  
Loss Function ◽  
High Performance ◽  
Deep Neural Networks ◽  
Brain Mri ◽  
Tumor Segmentation ◽  
Dice Coefficient ◽  
Brain Tumor Segmentation ◽  
Mri Scans

This paper presents an approach for brain tumor segmentation based on deep neural networks. The paper proposes to utilize U-Net as an architecture of the approach to capture the fine and soars information from input images. Especially, to train the network, instead of using commonly used cross-entropy loss, dice loss or both, in this study, we propose to employ a new loss function including Level set loss and Dice loss function. The level set loss is inspired from Mumford-Shah functional for unsupervised task. Meanwhile, the Dice loss function measures the similarity between the predicted mask and desired mask. The proposed approach is then applied to segment brain tumor from MRI images as well as evaluated and compared with other approaches on a dataset of nearly 4000 brain MRI scans. Experiment results show that the proposed approach achieves high performance in terms of Dice coefficient and Intersection over Union (IoU) scores.

scholarly journals Brain MRI Images Segmentation Based on U-Net Architecture

2021 ◽  
Vol 18 (1) ◽  
pp. 21-27
Author(s):  
Assalah Atiyah ◽  
Khawla Ali
Keyword(s):  
Brain Tumor ◽  
Brain Tumors ◽  
Performance Metrics ◽  
Brain Mri ◽  
Regular Function ◽  
Survival Rates ◽  
Tumor Segmentation ◽  
Brain Tumor Segmentation ◽  
Edge Based ◽  
The Brain

Brain tumors are collections of abnormal tissues within the brain. The regular function of the brain may be affected as it grows within the region of the skull. Brain tumors are critical for improving treatment options and patient survival rates to prevent and treat them. The diagnosis of cancer utilizing manual approaches for numerous magnetic resonance imaging (MRI) images is the most complex and time-consuming task. Brain tumor segmentation must be carried out automatically. A proposed strategy for brain tumor segmentation is developed in this paper. For this purpose, images are segmented based on region-based and edge-based. Brain tumor segmentation 2020 (BraTS2020) dataset is utilized in this study. A comparative analysis of the segmentation of images using the edge-based and region-based approach with U-Net with ResNet50 encoder, architecture is performed. The edge-based segmentation model performed better in all performance metrics compared to the region-based segmentation model and the edge-based model achieved the dice loss score of 0. 008768, IoU score of 0. 7542, f1 score of 0. 9870, the accuracy of 0. 9935, the precision of 0. 9852, recall of 0. 9888, and specificity of 0. 9951.

Automatic MRI Brain Tumor Segmentation System Based on Localizing Active Contour Models

2011 ◽  
Vol 219-220 ◽  
pp. 1342-1346 ◽  
Author(s):  
Ying Wang ◽  
Zhi Xian Lin ◽  
Jian Guo Cao ◽  
Mao Qing Li
Keyword(s):  
Brain Tumor ◽  
Active Contour ◽  
Automatic Segmentation ◽  
Brain Mri ◽  
Initial Contour ◽  
Tumor Segmentation ◽  
Brain Tumor Segmentation ◽  
Active Contour Models ◽  
Mri Brain ◽  
Contour Models

In this paper, an automatic segmentation system was developed for MRI brain tumor. Local region-based active contour models were suitable for heterogeneous features of brain MRI image. But the models are sensitive to initial contour, which generally requires manual setting. An automatic MRI brain tumor segmentation system were developed based on localized contour models, which can identify tumor-dominant slice, set initial contour automatically and segment tumor’s contours from all MRI slices autonomously. K-means clustering and grayscale analysis were combined to identify tumor-dominant slice. Multi-threshold algorithm with the aid of erosion and dilation operators was adopted to obtain an initial contour for the tumor-dominant slice. The segmentation contour from the local active contour models was applied as initial contours of two-side neighboring slices. MRI brain tumor data were applied to validate the automatic segmentation system.

scholarly journals Brain tumor segmentation with Deep Neural Networks

2017 ◽  
Vol 35 ◽  
pp. 18-31 ◽  
Author(s):  
Mohammad Havaei ◽  
Axel Davy ◽  
David Warde-Farley ◽  
Antoine Biard ◽  
Aaron Courville ◽  
...  
Keyword(s):  
Neural Networks ◽  
Brain Tumor ◽  
Deep Neural Networks ◽  
Tumor Segmentation ◽  
Brain Tumor Segmentation
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