Brain Tumor Synthetic Segmentation in 3D Multimodal MRI Scans

The magnetic resonance (MR) analysis of brain tumors is widely used for diagnosis and examination of tumor subregions. The overlapping area among the intensity distribution of healthy, enhancing, non-enhancing, and edema regions makes the automatic segmentation a challenging task. Here, we show that a convolutional neural network trained on high-contrast images can transform the intensity distribution of brain lesions in its internal subregions. Specifically, a generative adversarial network (GAN) is extended to synthesize high-contrast images. A comparison of these synthetic images and real images of brain tumor tissue in MR scans showed significant segmentation improvement and decreased the number of real channels for segmentation. The synthetic images are used as a substitute for real channels and can bypass real modalities in the multimodal brain tumor segmentation framework. Segmentation results on BraTS 2019 dataset demonstrate that our proposed approach can efficiently segment the tumor areas. In the end, we predict patient survival time based on volumetric features of the tumor subregions as well as the age of each case through several regression models

Deep Learning versus Classical Regression for Brain Tumor Patient Survival Prediction

Deep learning for regression tasks on medical imaging data has shown promising results. However, compared to other approaches, their power is strongly linked to the dataset size. In this study, we evaluate 3D-convolutional neural networks (CNNs) and classical regression methods with hand-crafted features for survival time regression of patients with high grade brain tumors. The tested CNNs for regression showed promising but unstable results. The best performing deep learning approach reached an accuracy of 51.5% on held-out samples of the training set. All tested deep learning experiments were outperformed by a Support Vector Classifier (SVC) using 30 radiomic features. The investigated features included intensity, shape, location and deep features. The submitted method to the BraTS 2018 survival prediction challenge is an ensemble of SVCs, which reached a cross-validated accuracy of 72.2% on the BraTS 2018 training set, 57.1% on the validation set, and 42.9% on the testing set. The results suggest that more training data is necessary for a stable performance of a CNN model for direct regression from magnetic resonance images, and that non-imaging clinical patient information is crucial along with imaging information.Comment: Contribution to The International Multimodal Brain Tumor Segmentation (BraTS) Challenge 2018, survival prediction tas

3D Multimodal Brain Tumor Segmentation and Grading Scheme based on Machine, Deep, and Transfer Learning Approaches

Glioma is one of the most common tumors of the brain. The detection and grading of glioma at an early stage is very critical for increasing the survival rate of the patients. Computer-aided detection (CADe) and computer-aided diagnosis (CADx) systems are essential and important tools that provide more accurate and systematic results to speed up the decision-making process of clinicians. In this paper, we introduce a method consisting of the variations of the machine, deep, and transfer learning approaches for the effective brain tumor (i.e., glioma) segmentation and grading on the multimodal brain tumor segmentation (BRATS) 2020 dataset. We apply popular and efficient 3D U-Net architecture for the brain tumor segmentation phase. We also utilize 23 different combinations of deep feature sets and machine learning/fine-tuned deep learning CNN models based on Xception, IncResNetv2, and EfficientNet by using 4 different feature sets and 6 learning models for the tumor grading phase. The experimental results demonstrate that the proposed method achieves 99.5% accuracy rate for slice-based tumor grading on BraTS 2020 dataset. Moreover, our method is found to have competitive performance with similar recent works

Brain Tumor Segmentation from Multi-Spectral MRI Data Using Cascaded Ensemble Learning

Ensemble learning methods are frequently employed in medical decision support. In image segmentation problems the ensemble based decisions require a postprocessing, because the ensemble cannot adequately handle the strong correlation of neighbor voxels. This paper proposes a brain tumor segmentation procedure based on an ensemble cascade. The first ensemble consisting of binary decision trees is trained to separate focal lesions from normal tissues based on four observed and 100 computed features. Starting from the intermediary labels provided by the first ensemble, six local features are computed for each voxel that serve as input for the second ensemble. The second ensemble is a classical random forest that enforces the correlation between neighbor pixels, regularizes the shape of the lesions. The segmentation accuracy is characterized by 85.5% overall Dice Score, 0.5% above previous solutions