ArteryX: A Reliable End-to-End Toolbox for Standardized Intracranial Artery Feature Extraction from 3D TOF-MRA
Authors: Abrar Faiyaz, Nhat Hoang, Giovanni Schifitto, Md Nasir Uddin
Organizations: Department of Neurology, University of Rochester, Rochester, NY 14642, USA · Department of Physics, University of Rochester, Rochester, NY 14627, USA · Department of Imaging Sciences, University of Rochester, Rochester, NY 14642, USA · Department of Electrical & Computer Engineering, University of Rochester, Rochester, NY 14627, USA · Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
Cerebrovascular research heavily relies on quantitative analysis of intracranial arteries from time-of-flight magnetic resonance angiography, yet existing processing pipelines remain limited by inconsistent artery labeling and a high manual correction burden. We present ArteryX, a toolbox for extracting features that standardizes artery classification across proximal and distal vascular territories. It integrates segmentation handling, isotropic processing, vessel-fused graph construction, and constrained landmark-based classification within a unified artery-specific feature reporting and reproducible workflow. The toolbox extracts morphological, topological, and complexity features including total length, mean radius, volume, surface area, branch count, tortuosity, and fractal dimensionality for standardized artery-segments. Test-and-validation were performed using three complementary datasets: (1)TopBrain-Challenge benchmarking with annotated arteries, (2)synthetic known-reference validation, and (3)exploratory in-vivo cohort of cerebral small vessel disease. In TopBrain analyses, ArteryX with supervised nnUnet segmentation showed minimal bias, while iCafe showed the highest bias and a large limit-of-agreement. ArteryX consistently demonstrated robust downstream quantification performance across segmentation sources (unsupervised/supervised). Agreement analyses showed minimal bias for radius and good sensitivity of extent-dependent metrics throughout the noisier segmentations compared to the state-of-the-art iCafe-toolbox. Furthermore, a stage-wise human-in-the-loop protocol showed lower intervention time than iCafe. In an in-vivo-cohort (48CSVD+, 20CSVD-), ArteryX-derived distal and territory-level features showed group-level differences, not evident with iCafe. To facilitate adoption-and-reproducibility, ArteryX is designed with versioned builds, tutorials, and documentation.
In this work, we present SemanticVessel, a dataset for fine-grained brain vessel segmentation in computed tomography angiography scans. Based on the detailed contrast provided by dynamic 4D-CTA scans, we generate segmentation traces for arteries and veins. We then use intensity-guided region growing to obtain segmentations of the majority of vascular territories in the human brain, which are refined and annotated with 20 unique arterial classes by an expert radiologist. Unlike existing datasets, where minor arteries are discarded as background content, we merge these minor arteries into a generic arterial class. Due to the multiple-phase acquisition of dynamic 4D-CTA, labels for a single phase can be re-used for other phases in the same series, greatly increasing the size of our dataset with no additional annotation cost. The results show that models trained with the additional generic artery class produce better fine-grained segmentations across the board. We will make our code, annotation GUI, and model weights available to the scientific community. Code, weights, and data will be made available on https://github.com/alceballosa/robust-vessel-segmentation
Chu-Hsuan Lin, Alberto Mario Ceballos-Arroyo, Jisoo Kim +4
Mechanical thrombectomy (MT) is a time-critical intervention for acute ischemic stroke; however, access remains limited due to a shortage of neuroradiologists and specialized centers. Reinforcement learning (RL) offers potential to automate endovascular navigation and improve accessibility, yet current models lack standardized frameworks to assess navigation difficulty for model training and evaluation. This study aims to identify vascular metrics associated with navigation difficulty and to develop an automated pipeline for quantitative vascular feature extraction, enabling future complexity grading. Vascular trees were segmented from computed tomography angiograms from 61 patients, and vascular metrics including aortic arch type, presence of bovine arch, vessel length, tortuosity, take-off angle, number of reverse curves, were measured using a custom pipeline. A Soft Actor-Critic RL algorithm was used for 120 s autonomous navigation. Outcomes were analyzed using both mixed effects linear and logistic regression. On the left side, the presence of a bovine arch and aortic arch type II/III increased navigation time by 30.19 s and 37.92 s, respectively, while greater tortuosity (\b{eta} = 118.20) further prolonged the procedure and reduced success probability. On the right side, type II/III arches extended procedure time by 45.94 s, while each additional reverse curve was associated with 3.96 s longer navigation time and lower probability of success. These findings demonstrate for the first time that MT agent navigation difficulty is strongly influenced by vascular geometry. The proposed automated pipeline enables objective and quantitative characterization of vascular features, providing a foundation for future development of standardized complexity grading and RL model evaluation, without aiming to demonstrate clinically generalizable autonomous navigation.
The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to influence the risk, severity, and outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy remains a manual and time-consuming expert task. The CoW is commonly imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), yet few datasets with annotated CoW anatomy exist, and there have been no established benchmarks for comparing CoW segmentation algorithms. We organized the TopCoW benchmark challenge alongside the release of an annotated CoW dataset with 125 paired MRA and CTA scans from the same patients. Voxel-level annotations for 13 vessel components were created using virtual reality technology and verified by clinical experts. Participants submitted algorithms for CoW segmentation and variant classification, which we evaluated on internal and external test sets comprising 226 scans from over five centers. The benchmark includes voxel-level segmentation, CoW component detection, CoW variant classification, and two clinical application tasks. We received submissions from over 250 participants across six continents. Top-performing teams achieved over 90% Dice scores for CoW segmentation, over 80% F1 scores for detecting key vessel components, and over 70% balanced accuracy in CoW variant classification across nearly all test sets. The best algorithms also supported clinically relevant downstream tasks by accurately classifying fetal-type posterior cerebral arteries and localizing aneurysms in relation to CoW anatomy. This benchmark demonstrated the utility of CoW segmentation algorithms for some downstream clinical applications with explainability.