Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network

In this work, we present a method for synthetic CT (sCT) generation from zero-echo-time (ZTE) MRI aimed at structural and quantitative accuracies of the image, with a particular focus on the accurate bone density value prediction. We propose a loss function that favors a spatially sparse region in the image. We harness the ability of a multi-task network to produce correlated outputs as a framework to enable localisation of region of interest (RoI) via classification, emphasize regression of values within RoI and still retain the overall accuracy via global regression. The network is optimized by a composite loss function that combines a dedicated loss from each task. We demonstrate how the multi-task network with RoI focused loss offers an advantage over other configurations of the network to achieve higher accuracy of performance. This is relevant to sCT where failure to accurately estimate high Hounsfield Unit values of bone could lead to impaired accuracy in clinical applications. We compare the dose calculation maps from the proposed sCT and the real CT in a radiation therapy treatment planning setup.

QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation -- Analysis of Ranking Metrics and Benchmarking Results

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder the translation of DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties, could enable clinical review of the most uncertain regions, thereby building trust and paving the way towards clinical translation. Recently, a number of uncertainty estimation methods have been introduced for DL medical image segmentation tasks. Developing metrics to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a metric developed during the BraTS 2019-2020 task on uncertainty quantification (QU-BraTS), and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This metric (1) rewards uncertainty estimates that produce high confidence in correct assertions, and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentages of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, and hence highlight the need for uncertainty quantification in medical image analyses. Our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraTS.

A Data-Adaptive Loss Function for Incomplete Data and Incremental Learning in Semantic Image Segmentation

In the last years, deep learning has dramatically improved the performances in a variety of medical image analysis applications. Among different types of deep learning models, convolutional neural networks have been among the most successful and they have been used in many applications in medical imaging. Training deep convolutional neural networks often requires large amounts of image data to generalize well to new unseen images. It is often time-consuming and expensive to collect large amounts of data in the medical image domain due to expensive imaging systems, and the need for experts to manually make ground truth annotations. A potential problem arises if new structures are added when a decision support system is already deployed and in use. Since the field of radiation therapy is constantly developing, the new structures would also have to be covered by the decision support system. In the present work, we propose a novel loss function, that adapts to the available data in order to utilize all available data, even when some have missing annotations. We demonstrate that the proposed loss function also works well in an incremental learning setting, where it can automatically incorporate new structures as they appear. Experiments on a large in-house data set show that the proposed method performs on par with baseline models, while greatly reducing the training time.

Multi-Decoder Networks with Multi-Denoising Inputs for Tumor Segmentation

Automatic segmentation of brain glioma from multimodal MRI scans plays a key role in clinical trials and practice. Unfortunately, manual segmentation is very challenging, time-consuming, costly, and often inaccurate despite human expertise due to the high variance and high uncertainty in the human annotations. In the present work, we develop an end-to-end deep-learning-based segmentation method using a multi-decoder architecture by jointly learning three separate sub-problems using a partly shared encoder. We also propose to apply smoothing methods to the input images to generate denoised versions as additional inputs to the network. The validation performance indicate an improvement when using the proposed method. The proposed method was ranked 2nd in the task of Quantification of Uncertainty in Segmentation in the Brain Tumors in Multimodal Magnetic Resonance Imaging Challenge 2020.

A Question-Centric Model for Visual Question Answering in Medical Imaging

Deep learning methods have proven extremely effective at performing a variety of medical image analysis tasks. With their potential use in clinical routine, their lack of transparency has however been one of their few weak points, raising concerns regarding their behavior and failure modes. While most research to infer model behavior has focused on indirect strategies that estimate prediction uncertainties and visualize model support in the input image space, the ability to explicitly query a prediction model regarding its image content offers a more direct way to determine the behavior of trained models. To this end, we present a novel Visual Question Answering approach that allows an image to be queried by means of a written question. Experiments on a variety of medical and natural image datasets show that by fusing image and question features in a novel way, the proposed approach achieves an equal or higher accuracy compared to current methods.

Evaluation of Multi-Slice Inputs to Convolutional Neural Networks for Medical Image Segmentation

When using Convolutional Neural Networks (CNNs) for segmentation of organs and lesions in medical images, the conventional approach is to work with inputs and outputs either as single slice (2D) or whole volumes (3D). One common alternative, in this study denoted as pseudo-3D, is to use a stack of adjacent slices as input and produce a prediction for at least the central slice. This approach gives the network the possibility to capture 3D spatial information, with only a minor additional computational cost. In this study, we systematically evaluate the segmentation performance and computational costs of this pseudo-3D approach as a function of the number of input slices, and compare the results to conventional end-to-end 2D and 3D CNNs. The standard pseudo-3D method regards the neighboring slices as multiple input image channels. We additionally evaluate a simple approach where the input stack is a volumetric input that is repeatably convolved in 3D to obtain a 2D feature map. This 2D map is in turn fed into a standard 2D network. We conducted experiments using two different CNN backbone architectures and on five diverse data sets covering different anatomical regions, imaging modalities, and segmentation tasks. We found that while both pseudo-3D methods can process a large number of slices at once and still be computationally much more efficient than fully 3D CNNs, a significant improvement over a regular 2D CNN was only observed for one of the five data sets. An analysis of the structural properties of the segmentation masks revealed no relations to the segmentation performance with respect to the number of input slices. The conclusion is therefore that in the general case, multi-slice inputs appear to not significantly improve segmentation results over using 2D or 3D CNNs.

End-to-End Cascaded U-Nets with a Localization Network for Kidney Tumor Segmentation

Kidney tumor segmentation emerges as a new frontier of computer vision in medical imaging. This is partly due to its challenging manual annotation and great medical impact. Within the scope of the Kidney Tumor Segmentation Challenge 2019, that is aiming at combined kidney and tumor segmentation, this work proposes a novel combination of 3D U-Nets---collectively denoted TuNet---utilizing the resulting kidney masks for the consecutive tumor segmentation. The proposed method achieves a S{\o}rensen-Dice coefficient score of 0.902 for the kidney, and 0.408 for the tumor segmentation, computed from a five-fold cross-validation on the 210 patients available in the data.

TuNet: End-to-end Hierarchical Brain Tumor Segmentation using Cascaded Networks

Glioma is one of the most common types of brain tumors arising in the glial cells in the human brain and spinal cord. In addition to the threat of death, glioma treatment is also very costly. Hence, automatic and accurate segmentation and measurement from the early stages are critical in order to prolong the survival rates of the patients and to reduce the costs of health care. In the present work, we propose a novel end-to-end cascaded network for semantic segmentation that utilizes the hierarchical structure of the tumor sub-regions with ResNet-like blocks and Squeeze-and-Excitation modules after each convolution and concatenation block. By utilizing cross-validation, an average ensemble technique, and a simple post-processing technique, we obtained dice scores of 90.34, 81.12, and 78.42 and Hausdorff Distances (95th percentile) of 4.32, 6.28, and 3.70 for the whole tumor, tumor core, and enhancing tumor, respectively, on the online validation set.

Whole-brain substitute CT generation using Markov random field mixture models

Computed tomography (CT) equivalent information is needed for attenuation correction in PET imaging and for dose planning in radiotherapy. Prior work has shown that Gaussian mixture models can be used to generate a substitute CT (s-CT) image from a specific set of MRI modalities. This work introduces a more flexible class of mixture models for s-CT generation, that incorporates spatial dependency in the data through a Markov random field prior on the latent field of class memberships associated with a mixture model. Furthermore, the mixture distributions are extended from Gaussian to normal inverse Gaussian (NIG), allowing heavier tails and skewness. The amount of data needed to train a model for s-CT generation is of the order of 100 million voxels. The computational efficiency of the parameter estimation and prediction methods are hence paramount, especially when spatial dependency is included in the models. A stochastic Expectation Maximization (EM) gradient algorithm is proposed in order to tackle this challenge. The advantages of the spatial model and NIG distributions are evaluated with a cross-validation study based on data from 14 patients. The study show that the proposed model enhances the predictive quality of the s-CT images by reducing the mean absolute error with 17.9%. Also, the distribution of CT values conditioned on the MR images are better explained by the proposed model as evaluated using continuous ranked probability scores.