Generalized Diffusion MRI Denoising and Super-Resolution using Swin Transformers

Abstract

Diffusion MRI is a non-invasive, in-vivo medical imaging method able to map tissue microstructure and structural connectivity of the human brain, as well as detect changes, such as brain development and injury, not visible by other clinical neuroimaging techniques. However, acquiring high signal-to-noise ratio (SNR) datasets with high angular and spatial sampling requires prohibitively long scan times, limiting usage in many important clinical settings, especially children, the elderly, and emergency patients with acute neurological disorders who might not be able to cooperate with the MRI scan without conscious sedation or general anesthesia. Here, we propose to use a Swin UNEt TRansformers (Swin UNETR) model, trained on augmented Human Connectome Project (HCP) data and conditioned on registered T1 scans, to perform generalized denoising and super-resolution of diffusion MRI invariant to acquisition parameters, patient populations, scanners, and sites. We qualitatively demonstrate super-resolution with artificially downsampled HCP data in normal adult volunteers. Our experiments on two other unrelated datasets, one of children with neurodevelopmental disorders and one of traumatic brain injury patients, show that our method demonstrates superior denoising despite wide data distribution shifts. Further improvement can be achieved via finetuning with just one additional subject. We apply our model to diffusion tensor (2nd order spherical harmonic) and higher-order spherical harmonic coefficient estimation and show results superior to current state-of-the-art methods. Our method can be used out-of-the-box or minimally finetuned to denoise and super-resolve a wide variety of diffusion MRI datasets. The code and model are publicly available at https://github.com/ucsfncl/dmri-swin