Deep learning-based 3D cerebrovascular segmentation workflow on bright and black blood sequences magnetic resonance angiography

Abstract

Background: Cerebrovascular diseases have emerged as significant threats to human life and health. Effectively segmenting brain blood vessels has become a crucial scientific challenge. We aimed to develop a fully automated deep learning workflow that achieves accurate 3D segmentation of cerebral blood vessels by incorporating classic convolutional neural networks (CNNs) and transformer models.

Methods: We used a public cerebrovascular segmentation dataset (CSD) containing 45 volumes of 1.5 T time-of-flight magnetic resonance angiography images. We collected data from another private middle cerebral artery (MCA) with lenticulostriate artery (LSA) segmentation dataset (MLD), which encompassed 3.0 T three-dimensional T1-weighted sequences of volumetric isotropic turbo spin echo acquisition MRI images of 107 patients aged 62 ± 11 years (42 females). The workflow includes data analysis, preprocessing, augmentation, model training with validation, and postprocessing techniques. Brain vessels were segmented using the U-Net, V-Net, UNETR, and SwinUNETR models. The model performances were evaluated using the dice similarity coefficient (DSC), average surface distance (ASD), precision (PRE), sensitivity (SEN), and specificity (SPE).

Results: During 4-fold cross-validation, SwinUNETR obtained the highest DSC in each fold. On the CSD test set, SwinUNETR achieved the best DSC (0.853), PRE (0.848), SEN (0.860), and SPE (0.9996), while V-Net achieved the best ASD (0.99). On the MLD test set, SwinUNETR demonstrated good MCA segmentation performance and had the best DSC, ASD, PRE, and SPE for segmenting the LSA.

Conclusions: The workflow demonstrated excellent performance on different sequences of MRI images for vessels of varying sizes. This method allows doctors to visualize cerebrovascular structures.

Critical relevance statement: A deep learning-based 3D cerebrovascular segmentation workflow is feasible and promising for visualizing cerebrovascular structures and monitoring cerebral small vessels, such as lenticulostriate arteries.

Key points: • The proposed deep learning-based workflow performs well in cerebrovascular segmentation tasks. • Among comparison models, SwinUNETR achieved the best DSC, ASD, PRE, and SPE values in lenticulostriate artery segmentation. • The proposed workflow can be used for different MR sequences, such as bright and black blood imaging.

Keywords: Angiography; Black blood imaging; Cerebrovascular segmentation; Deep learning; Magnetic resonance.

Fig. 1

3D deep learning-based cerebrovascular segmentation workflow

Fig. 2

Mean DSC metrics for different models on two fourfold cross-validation sets

Fig. 3

Distributions of the evaluation results of the four best-validated models on the test sets. The first row shows the results for CSD, and the second and third rows show the results for MLD

Fig. 4

Visualizations of the ground truth and four model segmentation results. Red indicates true positives, green indicates false positives, and blue indicates false negatives. The first row shows the entire brain vessel in CSD, and the second and third rows show the middle cerebral artery (MCA M1) and the lenticulostriate artery (LSA) in MLD