Applying Unet for extraction of vascular metrics from T1-weighted and T2-weighted MRI

Abstract

We apply deep learning to the problem of segmenting the arterial system from T1w and T2w images. We use the freely available 7-Tesla ‘forrest’ dataset from OpenNeuro, (which contains TOF, T1w, and T2w) and use supervised learning with T1w or T2w as input, and TOF segmentation as ground truth, to train a Unet architecture capable of segmenting arteries and quantifying arterial diameters from T1w or T2w images alone. We demonstrate arterial segmentations from both T1w and T2w images, and show that T2w images have sufficient vessel contrast to estimate arterial diameters comparable to those estimated from TOF. We then apply our Unet to T2w images from a separate dataset (IXI) and show our model generalizes to images acquired at different field strength. We consider this work proof-of-concept that arterial segmentations can be derived from MRI sequences with poor contrast between arteries and surrounding tissue (T1w and T2w), due to the ability of deep convolutional networks to extract complex features based on local image intensity. Future work will focus on improving the generalizability of the network to non-forrest datasets, with the eventual goal of leveraging the entire pre-existing corpus of neuroimaging data for study of human cerebrovasculature.