Scaling up fine-grained intracranial vessel annotations in computed tomography angiography

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

Robust automatic brain vessel segmentation in 3D CTA scans using dynamic 4D-CTA data

In this study, we develop a novel methodology for annotating the brain vasculature using dynamic 4D-CTA head scans. By using multiple time points from dynamic CTA acquisitions, we subtract bone and soft tissue to enhance the visualization of arteries and veins, reducing the effort required to obtain manual annotations of brain vessels. We then train deep learning models on our ground truth annotations by using the same segmentation for multiple phases from the dynamic 4D-CTA collection, effectively enlarging our dataset by 4 to 5 times and inducing robustness to contrast phases. In total, our dataset comprises 110 training images from 25 patients and 165 test images from 14 patients. In comparison with two similarly-sized datasets for CTA-based brain vessel segmentation, a nnUNet model trained on our dataset can achieve significantly better segmentations across all vascular regions, with an average mDC of 0.846 for arteries and 0.957 for veins in the TopBrain dataset. Furthermore, metrics such as average directed Hausdorff distance (adHD) and topology sensitivity (tSens) reflected similar trends: using our dataset resulted in low error margins (aDHD of 0.304 mm for arteries and 0.078 for veins) and high sensitivity (tSens of 0.877 for arteries and 0.974 for veins), indicating excellent accuracy in capturing vessel morphology. Our code and model weights are available online: https://github.com/alceballosa/robust-vessel-segmentation

Anatomically-guided masked autoencoder pre-training for aneurysm detection

Intracranial aneurysms are a major cause of morbidity and mortality worldwide, and detecting them manually is a complex, time-consuming task. Albeit automated solutions are desirable, the limited availability of training data makes it difficult to develop such solutions using typical supervised learning frameworks. In this work, we propose a novel pre-training strategy using more widely available unannotated head CT scan data to pre-train a 3D Vision Transformer model prior to fine-tuning for the aneurysm detection task. Specifically, we modify masked auto-encoder (MAE) pre-training in the following ways: we use a factorized self-attention mechanism to make 3D attention computationally viable, we restrict the masked patches to areas near arteries to focus on areas where aneurysms are likely to occur, and we reconstruct not only CT scan intensity values but also artery distance maps, which describe the distance between each voxel and the closest artery, thereby enhancing the backbone's learned representations. Compared with SOTA aneurysm detection models, our approach gains +4-8% absolute Sensitivity at a false positive rate of 0.5. Code and weights will be released.