BACKGROUND: Existing methods to reconstruct vascular structures from a computerized tomography (CT) angiogram rely on contrast injection to enhance the radio-density within the vessel lumen. However, pathological changes in the vasculature may be present that prevent accurate reconstruction. In aortic aneurysmal disease, a thrombus adherent to the aortic wall within the expanding aneurysmal sac is present in > 90% of cases. These deformations prevent the automatic extraction of vital clinical information by existing image reconstruction methods. AIM: In this study, a deep learning architecture consisting of a modified U-Net with attention-gating was implemented to establish a high-throughput and automated segmentation pipeline of pathological blood vessels in CT images acquired with or without the use of a contrast agent. METHODS AND RESULTS: Seventy-Five patients with paired non-contrast and contrast-enhanced CT images were randomly selected from an ongoing study (Ethics Ref 13/SC/0250), manually annotated and used for model training and evaluation. Data augmentation was implemented to diversify the training data set in a ratio of 10:1. The performance of our Attention-based U-Net in extracting both the inner (blood flow) lumen and the wall structure of the aortic aneurysm from CT angiograms (CTA) was compared against a generic 3-D U-Net and displayed superior results. Implementation of this network within the aortic segmentation pipeline for both contrast and non-contrast CT images has allowed for accurate and efficient extraction of the morphological and pathological features of the entire aortic volume. CONCLUSION: This extraction method can be used to standardize aneurysmal disease management and sets the foundation for complex geometric and morphological analysis. Furthermore, this pipeline can be extended to other vascular pathologies.