Automatic Brain Tumor Segmentation Method Research Articles

MRI Brain Tumor Segmentation Using 3D U-Net with Dense Encoder Blocks and Residual Decoder Blocks

The main task of magnetic resonance imaging (MRI) automatic brain tumor segmentation is to automatically segment the brain tumor edema, peritumoral edema, endoscopic core, enhancing tumor core and nonenhancing tumor core from 3D MR images. Because the location, size, shape and intensity of brain tumors vary greatly, it is very difficult to segment these brain tumor regions automatically. In this paper, by combining the advantages of DenseNet and ResNet, we proposed a new 3D U-Net with dense encoder blocks and residual decoder blocks. We used dense blocks in the encoder part and residual blocks in the decoder part. The number of output feature maps increases with the network layers in contracting path of encoder, which is consistent with the characteristics of dense blocks. Using dense blocks can decrease the number of network parameters, deepen network layers, strengthen feature propagation, alleviate vanishing-gradient and enlarge receptive fields. The residual blocks were used in the decoder to replace the convolution neural block of original U-Net, which made the network performance better. Our proposed approach was trained and validated on the BraTS2019 training and validation data set. We obtained dice scores of 0.901, 0.815 and 0.766 for whole tumor, tumor core and enhancing tumor core respectively on the BraTS2019 validation data set. Our method has the better performance than the original 3D U-Net. The results of our experiment demonstrate that compared with some state-of-the-art methods, our approach is a competitive automatic brain tumor segmentation method.

Automatic Brain Tumor Segmentation Method Based on Modified Convolutional Neural Network.

In the domain of brain diseases, it is difficult for image registration after some brain structures are severely deformed because of diseases. Fortunately, convolutional neural network have gained many promising results in semantic segmentation challenging tasks in recent years. To enhance the performance of automatic brain tumor segmentation, this paper presents a robust segmentation algorithm based on convolutional neural network, which achieved improvement of 3.84% in segmenting the enhancing tumor. Our network architecture is developed from the prevalent U-Net. We combined it with ResNet and modified it to maximize its performance in our brain tumor segmentation task. In this work, BraTS 2017 dataset was employed to train and test the proposed network. Data imbalance was dealt with using a weighted cross entropy loss function. The problem of overfitting was handled through data augmentation. The proposed method achieved averaged dice scores of 0.883, 0.781 and 0.748 for whole tumor, tumor core and enhancing tumor respectively in the validation set and 0.877, 0.774, 0.757 respectively in the testing set.

MRI brain tumor segmentation based on texture features and kernel sparse coding

Abstract An automatic brain tumor segmentation method based on texture feature and kernel sparse coding from FLAIR (fluid attenuated inversion recovery) contrast-enhanced MRIs (magnetic resonance imaging) is presented in this paper. First, the MRIs are pre-processed to reduce noise, enhance contrast and correct the intensity non-uniformity. Then sparse coding is performed on the first order and second order statistical eigenvector extracted from original MRIs which is a patch of 3 × 3 around the voxel. The kernel dictionary learning is used to extract the non-linear features to construct two adaptive dictionaries for healthy and pathologically tissues respectively. A kernel-clustering algorithm based on dictionary learning is developed to code the voxels, then the linear discrimination method is used to classify the target pixels. In the end, the flood-fill operation is used to improve the segmentation quality. The results demonstrate that the method based on kernel sparse coding has better capacity and higher segmentation accuracy with low computation cost.

Kernel sparse representation for MRI image analysis in automatic brain tumor segmentation

The segmentation of brain tumor plays an important role in diagnosis, treatment planning, and surgical simulation. The precise segmentation of brain tumor can help clinicians obtain its location, size, and shape information. We propose a fully automatic brain tumor segmentation method based on kernel sparse coding. It is validated with 3D multiple-modality magnetic resonance imaging (MRI). In this method, MRI images are pre-processed first to reduce the noise, and then kernel dictionary learning is used to extract the nonlinear features to construct five adaptive dictionaries for healthy tissues, necrosis, edema, non-enhancing tumor, and enhancing tumor tissues. Sparse coding is performed on the feature vectors extracted from the original MRI images, which are a patch of m×m×m around the voxel. A kernel-clustering algorithm based on dictionary learning is developed to code the voxels. In the end, morphological filtering is used to fill in the area among multiple connected components to improve the segmentation quality. To assess the segmentation performance, the segmentation results are uploaded to the online evaluation system where the evaluation metrics dice score, positive predictive value (PPV), sensitivity, and kappa are used. The results demonstrate that the proposed method has good performance on the complete tumor region (dice: 0.83; PPV: 0.84; sensitivity: 0.82), while slightly worse performance on the tumor core (dice: 0.69; PPV: 0.76; sensitivity: 0.80) and enhancing tumor (dice: 0.58; PPV: 0.60; sensitivity: 0.65). It is competitive to the other groups in the brain tumor segmentation challenge. Therefore, it is a potential method in differentiation of healthy and pathological tissues.

Segmentation of Brain Tumor Tissues in HGG and LGG MR Images Using 3D U-net Convolutional Neural Network

The quantitative assessment of tumor extent is necessary for surgical planning, as well as monitoring of tumor growth or shrinkage, and radiotherapy planning. For brain tumors, magnetic resonance imaging (MRI) is used as a standard for diagnosis and prognosis. Manually segmenting brain tumors from 3D MRI volumes is tedious and depends on inter and intra observer variability. In the clinical facilities, a reliable fully automatic brain tumor segmentation method is necessary for the accurate delineation of tumor sub regions. This article presents a 3D U-net Convolutional Neural Network for segmentation of a brain tumor. The proposed method achieves a mean dice score of 0.83, a specificity of 0.80 and a sensitivity of 0.81 for segmenting the whole tumor, and for the tumor core region a mean dice score of 0.76, a specificity of 0.79 and a sensitivity of 0.73. For the enhancing region, the mean dice score is 0.68, a specificity of 0.73 and a sensitivity of 0.77. From the experimental analysis, the proposed U-net model achieved considerably good results compared to the other segmentation models.

Brain Tumor Segmentation Using Deep Belief Networks and Pathological Knowledge.

In this paper, we propose an automatic brain tumor segmentation method based on Deep Belief Networks (DBNs) and pathological knowledge. The proposed method is targeted against gliomas (both low and high grade) obtained in multi-sequence magnetic resonance images (MRIs). Firstly, a novel deep architecture is proposed to combine the multi-sequences intensities feature extraction with classification to get the classification probabilities of each voxel. Then, graph cut based optimization is executed on the classification probabilities to strengthen the spatial relationships of voxels. At last, pathological knowledge of gliomas is applied to remove some false positives. Our method was validated in the Brain Tumor Segmentation Challenge 2012 and 2013 databases (BRATS 2012, 2013). The performance of segmentation results demonstrates our proposal providing a competitive solution with stateof- the-art methods.

Brain tumor segmentation with Deep Neural Networks.

In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.

Multiscale CNNs for Brain Tumor Segmentation and Diagnosis.

Early brain tumor detection and diagnosis are critical to clinics. Thus segmentation of focused tumor area needs to be accurate, efficient, and robust. In this paper, we propose an automatic brain tumor segmentation method based on Convolutional Neural Networks (CNNs). Traditional CNNs focus only on local features and ignore global region features, which are both important for pixel classification and recognition. Besides, brain tumor can appear in any place of the brain and be any size and shape in patients. We design a three-stream framework named as multiscale CNNs which could automatically detect the optimum top-three scales of the image sizes and combine information from different scales of the regions around that pixel. Datasets provided by Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized by MICCAI 2013 are utilized for both training and testing. The designed multiscale CNNs framework also combines multimodal features from T1, T1-enhanced, T2, and FLAIR MRI images. By comparison with traditional CNNs and the best two methods in BRATS 2012 and 2013, our framework shows advances in brain tumor segmentation accuracy and robustness.

3D variational brain tumor segmentation using Dirichlet priors on a clustered feature set

Brain tumor segmentation is a required step before any radiation treatment or surgery. When performed manually, segmentation is time consuming and prone to human errors. Therefore, there have been significant efforts to automate the process. But, automatic tumor segmentation from MRI data is a particularly challenging task. Tumors have a large diversity in shape and appearance with intensities overlapping the normal brain tissues. In addition, an expanding tumor can also deflect and deform nearby tissue. In our work, we propose an automatic brain tumor segmentation method that addresses these last two difficult problems. We use the available MRI modalities (T1, T1c, T2) and their texture characteristics to construct a multidimensional feature set. Then, we extract clusters which provide a compact representation of the essential information in these features. The main idea in this work is to incorporate these clustered features into the 3D variational segmentation framework. In contrast to previous variational approaches, we propose a segmentation method that evolves the contour in a supervised fashion. The segmentation boundary is driven by the learned region statistics in the cluster space. We incorporate prior knowledge about the normal brain tissue appearance during the estimation of these region statistics. In particular, we use a Dirichlet prior that discourages the clusters from the normal brain region to be in the tumor region. This leads to a better disambiguation of the tumor from brain tissue. We evaluated the performance of our automatic segmentation method on 15 real MRI scans of brain tumor patients, with tumors that are inhomogeneous in appearance, small in size and in proximity to the major structures in the brain. Validation with the expert segmentation labels yielded encouraging results: Jaccard (58%), Precision (81%), Recall (67%), Hausdorff distance (24mm). Using priors on the brain/tumor appearance, our proposed automatic 3D variational segmentation method was able to better disambiguate the tumor from the surrounding tissue.