Ischemic stroke is the most common cerebrovascular disease, and its diagnosis, treatment, and study relies on non-invasive imaging. Algorithms for stroke lesion segmentation from magnetic resonance imaging (MRI) volumes are intensely researched, but the reported results are largely incomparable due to different datasets and evaluation schemes. We approached this urgent problem of comparability with the Ischemic Stroke Lesion Segmentation (ISLES) challenge organized in conjunction with the MICCAI 2015 conference. In this paper we propose a common evaluation framework, describe the publicly available datasets, and present the results of the two sub-challenges: Sub-Acute Stroke Lesion Segmentation (SISS) and Stroke Perfusion Estimation (SPES). A total of 16 research groups participated with a wide range of state-of-the-art automatic segmentation algorithms. A thorough analysis of the obtained data enables a critical evaluation of the current state-of-the-art, recommendations for further developments, and the identification of remaining challenges. The segmentation of acute perfusion lesions addressed in SPES was found to be feasible. However, algorithms applied to sub-acute lesion segmentation in SISS still lack accuracy. Overall, no algorithmic characteristic of any method was found to perform superior to the others. Instead, the characteristics of stroke lesion appearances, their evolution, and the observed challenges should be studied in detail. The annotated ISLES image datasets continue to be publicly available through an online evaluation system to serve as an ongoing benchmarking resource (www.isles-challenge.org).

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).

Purpose/objective: Precise delineation of organs at risk (OARs) in head and neck cancer (HNC) is necessary for accurate radiotherapy. Although guidelines exist, significant interobserver variability (IOV) remains. The aim was to validate a 3D convolutional neural network (CNN) for semi-automated delineation of OARs with respect to delineation accuracy, efficiency and consistency compared to manual delineation. Material/Methods: 16 OARs were manually delineated in 15 new HNC patients by two trained radiation oncologists (RO) independently, using international consensus guidelines. OARs were also automatically delineated by applying the CNN and corrected as needed by both ROs separately. Both delineations were performed two weeks apart and blinded to each other. IOV between both ROs was quantified using Dice similarity coefficient (DSC) and average symmetric surface distance (ASSD). To objectify network accuracy, differences between automated and corrected delineations were calculated using the same similarity measures.Results: Average correction time of the automated delineation was 33% shorter than manual delineation (23 vs 34 minutes)(p<10-6). IOV improved significantly with network initialisation for nearly all OARs (p<0.05), resulting in decreased ASSD averaged over all OARs from 1.9 to 1.2 mm. The network achieved an accuracy of 90% and 84% DSC averaged over all OARs for RO1 and RO2 respectively, with an ASSD of 0.7 and 1.5 mm, which was in 93% and 73% of the cases lower than the IOV. Conclusion:The CNN developed for automated OAR delineation in HNC was shown to be more efficient and consistent compared to manual delineation, which justify its implementation in clinical practice.

CT Perfusion (CTP) imaging has gained importance in the diagnosis of acute stroke. Conventional perfusion analysis performs a deconvolution of the measurements and thresholds the perfusion parameters to determine the tissue status. We pursue a data-driven and deconvolution-free approach, where a deep neural network learns to predict the final infarct volume directly from the native CTP images and metadata such as the time parameters and treatment. This would allow clinicians to simulate various treatments and gain insight into predicted tissue status over time. We demonstrate on a multicenter dataset that our approach is able to predict the final infarct and effectively uses the metadata. An ablation study shows that using the native CTP measurements instead of the deconvolved measurements improves the prediction.

Abstract. We present a novel algorithm for the simultaneous segmentation and anatomical labeling of the cerebral vasculature. The method first constructs an overcomplete graph capturing the vasculature. It then selects and labels the subset of edges that most likely represents the true vasculature. Unlike existing approaches that first attempt to obtain a good segmentation and then perform labeling, we jointly optimize for both by simultaneously taking into account the image evidence and the prior knowledge about the geometry and connectivity of the vasculature. This results in an Integer Program (IP), which we solve optimally using a branch-and-cut algorithm. We evaluate our approach on a public dataset of 50 cerebral MRA images, and demonstrate that it compares favorably against state-of-the-art methods.

The main arteries that supply blood to the brain originate from the Circle of Willis (CoW). The CoW exhibits considerable anatomical variations which may have clinical importance, but the variability is insufficiently characterised in the general population. We assessed the anatomical variability of CoW variants in a community-dwelling sample (N = 1,864, 874 men, mean age = 65.4, range 40–87 years), and independent and conditional frequencies of the CoW’s artery segments. CoW segments were classified as present or missing/hypoplastic (w/1mm diameter threshold) on 3T time-of-flight magnetic resonance angiography images. We also examined whether age and sex were associated with CoW variants. We identified 47 unique CoW variants, of which five variants constituted 68.5% of the sample. The complete variant was found in 11.9% of the subjects, and the most common variant (27.8%) was missing both posterior communicating arteries. Conditional frequencies showed patterns of interdependence across most missing segments in the CoW. CoW variants were associated with mean-split age (P = .0147), and there was a trend showing more missing segments with increasing age. We found no association with sex (P = .0526). Our population study demonstrated age as associated with CoW variants, suggesting reduced collateral capacity with older age.

SUMMARYObjective: A prerequisite for the implementation of interictal electroencephalography-correlated functional magnetic resonance imaging (EEG-fMRI) in the presurgical work-up for epilepsy surgery is straightforward processing. We propose a new semiautomatic method as alternative for the challenging and time-consuming visual spike identification. Methods: Our method starts from a patient-specific spike-template, built by averaging spikes recorded on the EEG outside the scanner. Spatiotemporal cross-correlations between the template and the EEG measured during fMRI were calculated. To minimize false-positive detections, this time course of cross-correlations was binarized by means of a spike-template-specific threshold determined in healthy controls. To inform our model for statistical parametric mapping, this binarized regressor was convolved with the canonical hemodynamic response function. We validated our "template-based" method in 21 adult patients with refractory focal epilepsy with a welldefined epileptogenic zone and interictal spikes during EEG-fMRI. Sensitivity and specificity for detecting the epileptogenic zone were calculated and represented in receiver operating characteristic (ROC) curves. Our approach was compared with a previously proposed semiautomatic "topography-based" method that used the topographic amplitude distribution of spikes as a starting point for correlation-based fitting. Results: Good diagnostic performance could be reached with our template-based method. The optimal area under the ROC curve was 0.77. Diagnostic performance of the topography-based method was overall low. Significance: Our new template-based method is more standardized and time-saving than visual spike identification on intra-scanner EEG recordings, and preserves good diagnostic performance for detecting the epileptogenic zone.

Background and Purpose: The ISLES challenge (Ischemic Stroke Lesion Segmentation) enables globally diverse teams to compete to develop advanced tools for stroke lesion analysis with machine learning. Detection of irreversibly damaged tissue on computed tomography perfusion (CTP) is often necessary to determine eligibility for late-time-window thrombectomy. Therefore, the aim of ISLES-2018 was to segment infarcted tissue on CTP based on diffusion-weighted imaging as a reference standard. Methods: The data, from 4 centers, consisted of 103 cases of acute anterior circulation large artery occlusion stroke who underwent diffusion-weighted imaging rapidly after CTP. Diffusion-weighted imaging lesion segmentation was performed manually and acted as a reference standard. The data were separated into 63 cases for training and 40 for testing, upon which quality metrics (dice score coefficient, Hausdorff distance, absolute lesion volume difference, etc) were computed to rank methods based on their overall performance. Results: Twenty-four different teams participated in the challenge. Median time to CTP was 185 minutes (interquartile range, 180–238), the time between CTP and magnetic resonance imaging was 36 minutes (interquartile range, 25–79), and the median infarct lesion size was 15.2 mL (interquartile range, 5.7–45). The best performance for Dice score coefficient and absolute volume difference were 0.51 and 10.1 mL, respectively, from different teams. Based on the ranking criteria, the top team’s algorithm demonstrated for average Dice score coefficient and average absolute volume difference 0.51 and 10.2 mL, respectively, outperforming the conventional threshold-based method (dice score coefficient, 0.3; volume difference, 15.3). Diverse algorithms were used, almost all based on deep learning, with top-ranked approaches making use of the raw perfusion data as well as methods to synthetically generate complementary information to boost prediction performance. Conclusions: Machine learning methods may predict infarcted tissue from CTP with improved accuracy compared with threshold-based methods used in clinical routine. This dataset will remain public and can be used to test improvement in algorithms over time.