Brain tumor segmentation 2019

To register for participation and get access to the BraTS data, you can follow the instructions given at the " Registration " page. Specifically, the datasets used in this year's challenge have been updated, since BraTS'18, with more routine clinically-acquired 3T multimodal MRI scans, with accompanying ground truth labels by expert board-certified neuroradiologists.

The ground truth of the validation data will not be provided to the participants, but multiple submissions to the online evaluation platform CBICA's IPP will be allowed. Finally, all participants will be presented with the same test data, which will be made available through email during 26 August-7 September and for a limited controlled time-window 48hbefore the participants are required to upload their final results in CBICA's IPP. The top-ranked participating teams will be invited before the end of September to prepare slides for a short oral presentation of their method during the BraTS challenge.

All the imaging datasets have been segmented manuallyby one to four raters, following the same annotation protocol, and their annotations were approved by experienced neuro-radiologists. The only data that have been previously used and are utilized again during BraTS''19 are the images and annotations of BraTS''13, which have been manually annotated by clinical experts in the past.

Brain Tumor Segmentation and Survival Prediction Using a Cascade of Random Forests

The data used during BraTS''16 from TCIA have been discarded, as they described a mixture of pre- and post-operative scans and their ground truth labels have been annotated by the fusion of segmentation results from algorithms that ranked highly during BraTS'12 and ' The overall survival OS data, defined in days, are included in a comma-separated value. Note that only subjects with resection status of GTR i. Participants are only allowed to use additional private data from their own institutions for data augmentationif they also report results using only the BraTS'19 data and discuss any potential difference in their papers and results.

This is due to our intentions to provide a fair comparison among the participating methods. Menze, A. Jakab, S. Bauer, J. Kalpathy-Cramer, K. Farahani, J. Kirby, et al. Bakas, H. Akbari, A. Sotiras, M. Bilello, M. Rozycki, J. Bakas, M. Reyes, A. Bauer, M. Rempfler, A. Crimi, et al. DOI: Brain tumor segmentation is the process of separating the tumor from normal brain tissues; in clinical routine, it provides useful information for diagnosis and treatment planning. However, it is still a challenging task due to the irregular form and confusing boundaries of tumors.

brain tumor segmentation 2019

Tumor cells thermally represent a heat source; their temperature is high compared to normal brain cells. The main aim of the present paper is to demonstrate that thermal information of brain tumors can be used to reduce false positive and false negative results of segmentation performed in MRI images. Canny edge detector was used to detect tumor contours from the calculated thermal map, as the calculated temperature showed a large gradient in tumor contours.

The proposed method is compared to Chan—Vese based level set segmentation method applied to T1 contrast-enhanced and Flair MRI images of brains containing tumors with ground truth. The obtained results in all patients showed significant improvement using the proposed method compared to segmentation by level set method with an average of 0. We conclude that tumor contours delineation based on tumor temperature changes can be exploited to reinforce and enhance segmentation algorithms in MRI diagnostic.

A brain tumor represents a set of abnormal cells that reproduce in the brain in an uncontrolled way. There are large varieties of brain tumor types that are classified into two categories, benign noncancerous brain tumors are less aggressive, formed slowly, and most often remain isolated from surrounding brain normal tissues; they do not spread to other regions of the brain or other parts in the human body and are generally easier to surgically extract than malignancies.

Malignant brain tumors cancerous are not always easy to distinguish them from surrounding normal tissues. The number of people affected by malignant brain tumors has been increasing in the last few decades. According to the American cancer society [ 12 ] in the US forthere were an estimated number of 23, new cases which increased with 30 cases compared to 23, and 16, estimated deaths with an increase of cases compared to 16, Magnetic Resonance Imaging or MRI is a noninvasive medical imaging modality commonly used in the clinical routine as it offers images with high spatial resolution and high contrast between soft tissues.

MRI provides rich information about shape, size, and localization of brain tumors for more accurate diagnosis and treatment planning [ 34 ]. Therefore, most of the research in medical diagnosis and delineation of brain tumors uses MRI images. T1-weighted image provides a better segmentation for brain tissues due to the high contrast between gray and white matter [ 5 ], T1-weighted contrast-enhanced images and FLAIR are widely used for brain tumors structure diagnostic as it makes tumor region hyperintense.

In this work, we have collected synthetic T1-weighted contrast-enhanced and Flair MRI images of all subjects as experimental data to test our approach. Accurate segmentation of brain tumors from MRI images represents a crucial and challenging task in diagnosis and treatment planning. Image segmentation is an active field in medical imaging, which consists in extracting from the image one or more regions forming the area of interest.

Various algorithms have been developed in the literature to perform brain tumor detection, including threshold-based methods [ 67 ], region-based methods [ 89 ], deformable methods [ 10 — 13 ], classification methods [ 1415 ], and deep learning [ 16 — 18 ].

Deformable models are among the most popular methods used for brain tumor segmentation in MRI images. They are represented by curves 2D or surfaces 3D defined in an image that move by the influence of two forces, internal or local forces defined in the curve to keep it smooth during the deformation process, while external forces are computed from image data in order to move the curve towards the object boundary sought.

In the deformable models, we distinguish two principal categories, parametric deformable models or snakes [ 19 ] and geometric deformable models. The parametric deformable models necessitate a parametric representation during deformation of the curve. These later have difficulty in topology changes to split and merge contours to segment multiple objects. Geometric deformable models or level sets proposed by Osher and Sethian [ 20 ] move based on geometric measurements such as the curve normal and curvature.

The advantage of these models is their capacity for topological changes during curve propagation. Brain tumor segmentation consists of extracting the tumor region from healthy brain tissues; the existence of brain tumors can often be detectable. However, accurate and effective segmentation of tumors remains a challenging task, since the tumors can have different sizes and locations. Their structures are often nonrigid and complex in shape and have various appearance properties.

Besides, they have intensities overlapping with normal brain tissues and especially in tumor borders; they show significant variable appearances from patient to patient [ 21 ], due to the need to add physical information of tumor to reinforce algorithms segmentation for more accurate and effective extraction. In the present work, we investigate the effect of temperature on segmentation in MRI images.Inference of tumor and edema areas from brain magnetic resonance imaging MRI data remains challenging owing to the complex structure of brain tumors, blurred boundaries, and external factors such as noise.

To alleviate noise sensitivity and improve the stability of segmentation, an effective hybrid clustering algorithm combined with morphological operations is proposed for segmenting brain tumors in this paper. Finally, the extracted tumor images are postprocessed using morphological operations and median filtering to obtain accurate representations of brain tumors. In addition, the proposed algorithm was compared with other current segmentation algorithms.

The results show that the proposed algorithm performs better in terms of accuracy, sensitivity, specificity, and recall. Brain tumor is one of the most serious diseases, which often have lethal outcomes.

At present, more and more attention has been paid to the study of brain tumor image. Nowadays, MRI is especially useful for brain imaging [ 1 ], which can be performed without injecting radioisotopes. MRI is based on multiparameter imaging, which can form different images by adjusting different parameters and contains a large amount of information.

As shown in Figure 1MRI images usually have low contrast, and it is difficult to diagnose lesion areas owing to noise accurately.

Therefore, accurate tumor segmentation is essential. Nowadays, many image segmentation techniques have been widely applied to segmentation of medical images. Examples include the threshold segmentation algorithm [ 3 ], edge-based segmentation algorithms [ 4 ], and neural network-based segmentation [ 5 ]. However, there is no efficient and versatile method of brain tumors based on imaging.

The threshold-based segmentation algorithm determines the segmentation threshold based on certain pixel features. This method is simple to implement and execute. Since the characteristics of the boundary pixels are discontinuous, the pixel features on both sides of the boundary will have relatively obvious differences. Therefore, the basic idea of the edge-based segmentation algorithm is to find the boundaries using some method and to specify the directions of the boundary first.

Then, the pixels on one side of the boundary are divided into one subimage, while the pixels on the other side are considered to belong to another subimage. Although this algorithm is fast, it is sensitive to noise and usually obtains incomplete information. In recent years, image segmentation using neural networks has become increasingly popular. New image data are segmented using a trained neural network. Convolutional neural networks CNNs have been particularly popular among different neural network methods [ 5 ].

Yet, one of the most difficult issues related to neural networks is constructing the network. Neural networks are computationally intensive and time-consuming, which hinders implementation.

3D MRI brain tumor segmentation 3D UNET using Tensorflow - +91-7307399944 For query

Clustering algorithms are commonly used for segmentation of medical images. Commonly used clustering algorithms include fuzzy C-means clustering FCMK-means clustering, and expectation maximization EM [ 6 — 8 ]. Fuzzy C-means clustering utilizes the fuzzy set theory, which allows soft segmentation.

The EM algorithm assumes that data can be described as a mixture of probability distributions. Then, the algorithm iteratively calculates the posterior probability and estimates the mean, covariance and mixture coefficients using the maximal likelihood estimation approach and clustering criteria [ 9 ]. However, this clustering algorithm is sensitive to noise.

In order to improve the instability clustering and to alleviate its sensitivity to noise, an effective clustering segmentation algorithm is proposed in this paper. The remainder of the paper is organized as follows: Section 2 depicts the related work of the paper. Section 3 details the methods used in this article. Section 4 presents the experimental results and assessments. Finally, conclusions and outstanding issues are listed in Section 5.

Segmentation of medical images is a very popular research topic, and many methods have been developed. Clustering algorithms for image segmentation are very popular among scholars, and many of these algorithms have been employed for image segmentation. Dhanalakshmi and Kanimozhi [ 10 ] proposed an algorithm for automatic segmentation of brain tumor images based on K-means clustering.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, 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. A brain tumor is a cancerous or noncancerous mass or growth of abnormal cells in the brain.

Originating in the glial cells, gliomas are the most common brain tumor Ferlay et al.

brain tumor segmentation 2019

Glioblastoma is one of the most aggressive and fatal human brain tumors Bleeker et al. Gliomas contain various heterogeneous histological sub-regions, including peritumoral edema, a necrotic core, an enhancing and a non-enhancing tumor core.

For example, the enhancing tumor sub-region is described by areas that show hyper-intensity in a T1Gd scan when compared to a T1 scan. Accurate and robust predictions of overall survival, using automated algorithms, for patients diagnosed with gliomas can provide valuable guidance for diagnosis, treatment planning, and outcome prediction Liu et al.

However, it is difficult to select reliable and potent prognostic features. Medical imaging e. Clinical data, including patient age and resection status, can also provide important information about patients' outcome. Segmentation of gliomas in pre-operative MRI scans, conventionally done by expert board-certified neuroradiologists, can provide quantitative morphological characterization and measurement of glioma sub-regions.

It is also a pre-requisite for survival prediction since most potent features are derived from the tumor region. This quantitative analysis has great potential for diagnosis and research, as it can be used for grade assessment of gliomas and planning of treatment strategies.

But this task is challenging due to the high variance in appearance and shape, ambiguous boundaries and imaging artifacts, while automatic segmentation has the advantage of fast speed, consistency in accuracy and immunity to fatigue Sharma and Aggarwal, Until now, the automatic segmentation of brain tumors in multimodal MRI scans is still one of the most difficult tasks in medical image analysis.

In recent years, deep convolutional neural networks CNNs have achieved great success in the field of computer vision. Inspired by the biological structure of visual cortex Fukushima,CNNs are artificial neural networks with multiple hidden convolutional layers between the input and output layers.

They have non-linear properties and are capable of extracting higher level representative features Gu et al. Deep learning methods with CNN have shown excellent results on a wide variety of other medical imaging tasks, including diabetic retinopathy detection Gulshan et al. In this paper, we present a novel deep learning-based framework for segmentation of a brain tumor and its subregions from multimodal MRI scans, and survival prediction based on radiomic features extracted from segmented tumor sub-regions as well as clinical features.

The proposed framework for brain tumor segmentation and survival prediction using multimodal MRI scans consists of the following steps, as illustrated in Figure 1. First, tumor subregions are segmented using an ensemble model comprising three different convolutional neural network architectures for robust performance through voting majority rule. Then radiomic features are extracted from tumor sub-regions and total tumor volume.

Next, decision tree regression model with gradient boosting is used to fit the training data and rank the importance of features based on variance reduction.In this paper, we propose a U-Net based segmentation network using attention mechanism. As not all the features extracted from the encoders are useful for segmentation, we propose to incorporate an attention mechanism to a U-Net architecture to capture rich contextual relationships for better feature representations.

In addition, the focal tversky loss is introduced to deal with small lesion segmentation. The experiment results, evaluated on a small dataset where only CT slices are available, demonstrate the proposed method can achieve an accurate and rapid segmentation on COVID segmentation. The obtained Dice Score, Sensitivity and Specificity are The pandemic of COVID is spreading all over the world and causes a devastating effect on the global public health.

The number of people infected by the virus is increasing rapidly. Up to April 11,1, cases of COVID have been reported in over countries and territories, resulting in approximately 99, deaths. And there is no efficient treatment at present 1. A critical step in the fight against COVID is to have effective screening and monitoring of infected patients.

In clinical practice, Chest Computed tomography CTas a non-invasive imaging approach, can detect certain characteristic manifestations in the lung associated with COVID It is considered as a low-cost, accurate and efficient method diagnostic tool for early screening and diagnosis of COVID Motivated by this, a number of artificial intelligence AI systems based on deep learning have been proposed and results have been shown to be quite promising.

Compared to the traditional imaging workflow that heavily relies on the human labors, AI enables more safe, accurate and efficient imaging solutions. Recent AI-empowered applications in COVID mainly include the dedicated imaging platform, the lung and infection region segmentation, the clinical assessment and diagnosis, as well as the pioneering basic and clinical research [ 8 ].

It delineates the regions of interest ROIse. For example, Zheng et al. Goze et al. Jin et al.

Robust Semantic Segmentation of Brain Tumor Regions from 3D MRIs

In this paper, we propose a deep learning based segmentation with the attention mechanism. A preliminary conference version appeared at ISBI [ 13 ]which focus on the multi-model fusion issue.Automatic segmentation of brain tumors from medical images is important for clinical assessment and treatment planning of brain tumors. Recent years have seen an increasing use of convolutional neural networks CNNs for this task, but most of them use either 2D networks with relatively low memory requirement while ignoring 3D context, or 3D networks exploiting 3D features while with large memory consumption.

In addition, existing methods rarely provide uncertainty information associated with the segmentation result. In addition, we employ test-time augmentation to achieve improved segmentation accuracy, which also provides voxel-wise and structure-wise uncertainty information of the segmentation result. Experiments with BraTS dataset showed that our cascaded framework with 2.

We also validated our method with BraTS dataset and found that test-time augmentation improves brain tumor segmentation accuracy and that the resulting uncertainty information can indicate potential mis-segmentations and help to improve segmentation accuracy. In adults, gliomas are the most common primary brain tumors. They begin in the brain's glial cells and are typically categorized into different grades: High-Grade Gliomas HGG grow rapidly and are more malignant, while Low-Grade Gliomas LGG are slower growing tumors with a better patient prognosis Louis et al.

Magnetic Resonance Imaging MRI of brain tumors is critical for progression evaluation, treatment planning and assessment of this disease.

T2 and FLAIR images mostly highlight the whole tumor region including infiltrative edemaand T1 and T1ce images give a better contrast for the tumor core region not including infiltrative edema Menze et al.

Therefore, these different sequences providing complementary information can be combined for the analysis of different subregions of brain tumors. Segmenting brain tumors and subregions automatically from multi-modal MRI is important for reproducible and accurate measurement of the tumors, and this can assist better diagnosis, treatment planning and evaluation Menze et al.

However, it remains difficult for automatic methods to accurately segment brain tumors from multi-modal MRI. This is due to the fact that the images often have ambiguous boundaries between normal tissues and brain tumors.

In addition, though prior information of shape and position has been used for segmentation of anatomical structures such as the liver Wang et al. This makes it difficult to use a prior shape and position for robust segmentation of brain tumors.

Recently, deep learning methods with Convolutional Neural Networks CNNs have become the state-of-the-art approaches for brain tumor segmentation Bakas et al. Compared with traditional supervised learning methods such as decision trees Zikic et al.

A key problem for CNN-based segmentation is to design a suitable network structure and training strategy. Using 3D CNNs can better exploit 3D features, but requires a large amount of memory, which may limit the input patch size, depth or feature numbers of the CNNs Kamnitsas et al. As a trade-off, 2. In addition, whole tumor, tumor core and enhancing tumor core follow a hierarchical structure.

brain tumor segmentation 2019

Using the segmentation of whole tumor tumor core to guide the segmentation of tumor core enhancing tumor core can help to reduce false positives. Therefore, in this work, we propose a framework consisting of a cascade of 2. For medical images, uncertainty information of segmentation results is important for clinical decisions as it can help to understand the reliability of the segmentations Shi et al.

For example, for brain tumor images, the low contrast between surrounding tissues and the segmentation target leads voxels around the boundary to be labeled with less confidence.

The uncertainty information of these voxels can indicate regions that have potentially been mis-segmented, and therefore can be employed to guide interactions of human to refine the segmentation results Wang et al. In addition, compared with datasets for natural image recognition Russakovsky et al. Therefore, this work also aims at providing voxel-wise and structure-wise uncertainty information for CNN-based brain tumor segmentation.

Unlike model-based epistemic uncertainty obtained by test-time dropout Gal and Ghahramani, ; Jungo et al. This paper is a combination and an extension of our previous works on brain tumor segmentation Wang et al. We also proposed 2. In this paper, we extend them in two aspects. First, we use test-time augmentation to obtain uncertainty estimation of the segmentation results, and additionally propose an uncertainty-aware conditional random field CRF for post-processing.

The results show that uncertainty estimation not only helps to identify potential mis-segmentations but also can be used to improve segmentation performance. Both voxel-level and structure-level uncertainty are analyzed in this paper.Skip to Main Content.

A not-for-profit organization, IEEE is the world's largest technical professional organization dedicated to advancing technology for the benefit of humanity. Use of this web site signifies your agreement to the terms and conditions. Personal Sign In. For IEEE to continue sending you helpful information on our products and services, please consent to our updated Privacy Policy. Email Address. Sign In. Access provided by: anon Sign Out. To capture the contrast variations of each grade of tumor, currently, the Magnetic Resonance Imaging MRI images are considered as the gold standard and are preferred due to their non-invasive nature.

However, accurate segmentation of these tumors relies on computational models. Existing models use multimodal MRI images for the segmentation of each grade of a tumor which results in downgraded performance in some tumor regions. In this paper, we propose a new method that incorporates a deep learning-based model called U-Net to address the problem of brain tumor segmentation.

The conceptual novelty of our method lies in modifying the U-Net model to make it suitable for multi-grade tumor segmentation task. Additionally, we use this architecture to evaluate individual MRI modalities for the segmentation of brain tumors. Article :. Need Help?

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