In the recent years there have been a number of studies that applied deep learning algorithms to neuroimaging data. Pipelines used in those studies mostly require multiple processing steps for feature extraction, although modern advancements in deep learning for image classification can provide a powerful framework for automatic feature generation and more straightforward analysis. In this paper, we show how similar performance can be achieved skipping these feature extraction steps with the residual and plain 3D convolutional neural network architectures. We demonstrate the performance of the proposed approach for classification of Alzheimer's disease versus mild cognitive impairment and normal controls on the Alzheimers Disease National Initiative (ADNI) dataset of 3D structural MRI brain scans.

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. The automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their methods on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge. Sixty T1 + FLAIR images from three MR scanners were released with the manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. The segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: 1) Dice similarity coefficient; 2) modified Hausdorff distance (95th percentile); 3) absolute log-transformed volume difference; 4) sensitivity for detecting individual lesions; and 5) F1-score for individual lesions. In addition, the methods were ranked on their inter-scanner robustness; 20 participants submitted their methods for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all the methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.

Performance of models highly depend not only on the used algorithm but also the data set it was applied to. This makes the comparison of newly developed tools to previously published approaches difficult. Either researchers need to implement others' algorithms first, to establish an adequate benchmark on their data, or a direct comparison of new and old techniques is infeasible. The Ischemic Stroke Lesion Segmentation (ISLES) challenge, which has ran now consecutively for 3 years, aims to address this problem of comparability. ISLES 2016 and 2017 focused on lesion outcome prediction after ischemic stroke: By providing a uniformly pre-processed data set, researchers from all over the world could apply their algorithm directly. A total of nine teams participated in ISLES 2015, and 15 teams participated in ISLES 2016. Their performance was evaluated in a fair and transparent way to identify the state-of-the-art among all submissions. Top ranked teams almost always employed deep learning tools, which were predominately convolutional neural networks (CNNs). Despite the great efforts, lesion outcome prediction persists challenging. The annotated data set remains publicly available and new approaches can be compared directly via the online evaluation system, serving as a continuing benchmark (www.isles-challenge.org).

The current COVID-19 pandemic overloads healthcare systems, including radiology departments. Though several deep learning approaches were developed to assist in CT analysis, nobody considered study triage directly as a computer science problem. We describe two basic setups: Identification of COVID-19 to prioritize studies of potentially infected patients to isolate them as early as possible; Severity quantification to highlight patients with severe COVID-19, thus direct them to a hospital or provide emergency medical care. We formalize these tasks as binary classification and estimation of affected lung percentage. Though similar problems were well-studied separately, we show that existing methods could provide reasonable quality only for one of these setups. We employ a multitask approach to consolidate both triage approaches and propose a convolutional neural network to leverage all available labels within a single model. In contrast with the related multitask approaches, we show the benefit from applying the classification layers to the most spatially detailed feature map at the upper part of U-Net instead of the less detailed latent representation at the bottom. We train our model on approximately 1500 publicly available CT studies and test it on the holdout dataset that consists of 123 chest CT studies of patients drawn from the same healthcare system, specifically 32 COVID-19 and 30 bacterial pneumonia cases, 30 cases with cancerous nodules, and 31 healthy controls. The proposed multitask model outperforms the other approaches and achieves ROC AUC scores of 0.87±0.01 vs. bacterial pneumonia, 0.93±0.01 vs. cancerous nodules, and 0.97±0.01 vs. healthy controls in Identification of COVID-19, and achieves 0.97±0.01 Spearman Correlation in Severity quantification. We have released our code and shared the annotated lesions masks for 32 CT images of patients with COVID-19 from the test dataset.

We perform 2.5D axisymmetric simulations of the pulsar magnetosphere (aligned dipole rotator) using the charge conservative, relativistic, electromagnetic particle in cell code picsar. Particle in cell codes are a powerful tool to use for studying the pulsar magnetosphere, because they can handle the force-free and vacuum limits and provide a self-consistent treatment of magnetic reconnection. In the limit of dense plasma throughout the magnetosphere, our solutions are everywhere in the force-free regime except for dissipative regions at the polar caps, in the current layers, and at the Y-point. These dissipative regions arise self-consistently, since we do not have any explicit dissipation in the code. A minimum of ≈15–20 per cent of the electromagnetic spin-down luminosity is transferred to the particles inside 5 light cylinder radii. However, the particles can carry as much as ≳ 50 per cent of the spin-down luminosity if there is insufficient plasma in the outer magnetosphere to screen the component of electric field parallel to the magnetic field. In reality, the component of the spin-down luminosity carried by the particles could be radiated as gamma-rays, but high-frequency synchrotron emission would need to be implemented as a sub-grid process in our simulations and is not present for the current suite of runs. The value of the spin-down luminosity in our simulations is within ≈10 per cent of the force-free value, and the structure of the electromagnetic fields in the magnetosphere is on the whole consistent with the force-free model.