In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients—manually annotated by up to four raters—and to 65 comparable scans generated using tumor image simulation software Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%–85%), illustrating the difficulty of this task We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

/pdf/the-multimodal-brain-tumor-image-segmentation-benchmark-2gfraj98dk.pdf

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

https://spiral.imperial.ac.uk/bitstream/10044/1/53839/13/1-s2.0-S1361841516301839-main.pdf

Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation

Brain tumor segmentation with Deep Neural Networks

Artificial intelligence (AI) algorithms, particularly deep learning, have demonstrated remarkable progress in image-recognition tasks. Methods ranging from convolutional neural networks to variational autoencoders have found myriad applications in the medical image analysis field, propelling it forward at a rapid pace. Historically, in radiology practice, trained physicians visually assessed medical images for the detection, characterization and monitoring of diseases. AI methods excel at automatically recognizing complex patterns in imaging data and providing quantitative, rather than qualitative, assessments of radiographic characteristics. In this Opinion article, we establish a general understanding of AI methods, particularly those pertaining to image-based tasks. We explore how these methods could impact multiple facets of radiology, with a general focus on applications in oncology, and demonstrate ways in which these methods are advancing the field. Finally, we discuss the challenges facing clinical implementation and provide our perspective on how the domain could be advanced.

/pdf/artificial-intelligence-in-radiology-2c2bdk1z41.pdf

Artificial intelligence in radiology

MRI-based medical image analysis for brain tumor studies is gaining attention in recent times due to an increased need for efficient and objective evaluation of large amounts of data. While the pioneering approaches applying automated methods for the analysis of brain tumor images date back almost two decades, the current methods are becoming more mature and coming closer to routine clinical application. This review aims to provide a comprehensive overview by giving a brief introduction to brain tumors and imaging of brain tumors first. Then, we review the state of the art in segmentation, registration and modeling related to tumor-bearing brain images with a focus on gliomas. The objective in the segmentation is outlining the tumor including its sub-compartments and surrounding tissues, while the main challenge in registration and modeling is the handling of morphological changes caused by the tumor. The qualities of different approaches are discussed with a focus on methods that can be applied on standard clinical imaging protocols. Finally, a critical assessment of the current state is performed and future developments and trends are addressed, giving special attention to recent developments in radiological tumor assessment guidelines.

/pdf/a-survey-of-mri-based-medical-image-analysis-for-brain-tumor-4mtl4fktmo.pdf

A survey of MRI-based medical image analysis for brain tumor studies

In this paper we propose a novel graph-based concurrent registration and segmentation framework. Registration is modeled with a pairwise graphical model formulation that is modular with respect to the data and regularization term. Segmentation is addressed by adopting a similar graphical model, using image-based classification techniques while producing a smooth solution. The two problems are coupled via a relaxation of the registration criterion in the presence of tumors as well as a segmentation through a registration term aiming the separation between healthy and diseased tissues. Efficient linear programming is used to solve both problems simultaneously. State of the art results demonstrate the potential of our method on a large and challenging low-grade glioma data set.

https://hal.inria.fr/hal-00773618/document

Joint tumor segmentation and dense deformable registration of brain MR images

https://hal.inria.fr/hal-01109692/document

Concurrent tumor segmentation and registration with uncertainty-based sparse non-uniform graphs.

Diffuse WHO grade II gliomas are diffusively infiltrative brain tumors characterized by an unavoidable anaplastic transformation. Their management is strongly dependent on their location in the brain due to interactions with functional regions and potential differences in molecular biology. In this paper, we present the construction of a probabilistic atlas mapping the preferential locations of diffuse WHO grade II gliomas in the brain. This is carried out through a sparse graph whose nodes correspond to clusters of tumors clustered together based on their spatial proximity. The interest of such an atlas is illustrated via two applications. The first one correlates tumor location with the patient's age via a statistical analysis, highlighting the interest of the atlas for studying the origins and behavior of the tumors. The second exploits the fact that the tumors have preferential locations for automatic segmentation. Through a coupled decomposed Markov Random Field model, the atlas guides the segmentation process, and characterizes which preferential location the tumor belongs to and consequently which behavior it could be associated to. Leave-one-out cross validation experiments on a large database highlight the robustness of the graph, and yield promising segmentation results.

/pdf/a-probabilistic-atlas-of-diffuse-who-grade-ii-glioma-2t1uq9lo29.pdf

A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain

Tumor detection in CT liver images is a challenging task. The nature of tumor has a direct effect on the number of voxels being contaminated, as well as on the changes in the observed CT scan. In order to deal with this challenge, in this paper we propose the use of advanced non-linear machine learning techniques to determine the optimal features, as well as the hyperplane that use these features to separate tumoral voxels from voxels corresponding to healthy tissues. Very promising classification results using an important volume of clinically annotated data (86% sensitivity, 82% specificity) demonstrate the potentials of our approach.

Automatic detection of liver tumors

In this paper we propose a novel approach for detection, segmentation and characterization of brain tumors. Our method exploits prior knowledge in the form of a sparse graph representing the expected spatial positions of tumor classes. Such information is coupled with image-based classification techniques along with spatial smoothness constraints towards producing a reliable detection map within a unified graphical model formulation. Towards optimal use of prior knowledge, a two layer interconnected graph is considered with one layer corresponding to the low-grade glioma type (characterization) and the second layer to voxel-based decisions of tumor presence. Efficient linear programming both in terms of performance as well as in terms of computational load is considered to recover the lowest potential of the objective function. The outcome of the method refers to both tumor segmentation as well as their characterization. Promising results on substantial data sets demonstrate the extreme potentials of our method.

https://hal.inria.fr/hal-00712714/document

Stéphane Chemouny

Papers

Joint tumor segmentation and dense deformable registration of brain MR images

Concurrent tumor segmentation and registration with uncertainty-based sparse non-uniform graphs.

A Probabilistic Atlas of Diffuse WHO Grade II Glioma Locations in the Brain

Automatic detection of liver tumors

Graph-based detection, segmentation & characterization of brain tumors