Deep learning-based free-water correction for single-shell diffusion MRI

Free-water elimination (FWE) modeling in diffusion magnetic resonance imaging (dMRI) is crucial for accurate estimation of diffusion properties by mitigating the partial volume effects caused by free water, particularly at the interface between white matter and cerebrospinal fluid. The presence of free water partial volume effects leads to biases in estimating diffusion properties. Additionally, the existing mathematical FWE model is a two-compartment model, which can be well posed for multi-shell data. However, single-shell acquisitions are more common in clinical cohorts due to time constraints. To overcome these problems, we proposed a deep-learning framework that focuses on mapping and correcting free-water partial volume contamination in DWI. It utilizes data-driven techniques to infer plausible free-water volumes across different diffusion MRI acquisition schemes, including single-shell acquisitions. In this work, we study the Human Connectome Project Young Adults (HCP-ya), the HCP Aging dataset (HCP-a) as well as Brain Tumor Connectomics Data (BTC). The evaluation demonstrates that it produces more plausible results compared to previous single-shell free water estimation approaches. The proposed method is generalizable through model fine-tuning and b-value re-mapping when dealing with new data. The results have demonstrated improved consistency of properties estimation between scan/rescan data and accuracy in identifying neural pathways, as well as enhanced clarity in the visualization of white matter tracts.