MRecover: A Conditional Generative Model for Recovering Motion-Corrupted MR images Using AI Generated Contrast

Hippocampal subfield segmentation requires high-resolution T2w turbo spin echo (TSE) MRI, yet this sequence is susceptible to motion artifacts, leading to substantial data loss. We developed a conditional generative model (MRecover) that synthesizes routinely acquired T1w images to create TSE images with autoregressive slice conditioning for volumetric consistency. Trained on 7T MRI data (n=577), the model achieved high in-domain fidelity (n=148, SSIM=0.84, FSIM=0.94) and generalized well to out-of-domain 3T data: subfield volumes from synthesized and the as-acquired images closely matched: (n=416, r=0.87-0.97) and yielded 31.8% more analyzable subjects in the motion-affected ADNI3 dataset after quality control (593 vs 450). The synthesized images also achieved larger effect sizes due to increasing the sample size for diagnostic group differences in hippocampal subfield atrophy (whole hippocampus $ε^2$= 0.121-0.100 vs. 0.086-0.062, left-right hemispheres). Project page: https://jinghangli98.github.io/MRecover/

BM4D-PC: nonlocal volumetric denoising of principal components of diffusion-weighted MR images

Purpose: Noise in diffusion-weighted MRI (dMRI) is often spatially correlated due to different acquisition and reconstruction strategies, which is not fully accounted for in current denoising strategies. Thus, we propose a novel model-based denoising method for dMRI that effectively accounts for the different noise characteristics of data. Methods: We propose a denoising strategy that incorporates full noise statistics, including the noise power spectral density (PSD), by leveraging the BM4D algorithm. Furthermore, to exploit redundancy across the diffusion MRI dataset, BM4D is applied to principal components (PC) of diffusion-weighted images (DWI) obtained through principal component analysis (PCA) decomposition of the entire DWI dataset, an approach we refer to as BM4D-PC. Importantly, our method also allows for direct estimation of both the noise map and PSD. We evaluated BM4D-PC against four existing state-of-the-art methods using in-silico and in vivo datasets, including high-resolution human and marmoset acquisitions. Results: Overall, BM4D-PC presented the best results for the metrics PSNR, SSIM and RMSE on the in-silico experiments. The in-vivo studies also showed that BM4D-PC dramatically enhanced the image quality of raw DWIs, outperforming existing denoising methods in terms of noise suppression and detail preservation, leading to improved quality of diffusion metrics. Conclusion: The proposed BM4D-PC method demonstrated state-of-the-art denoising results for dMRI using datasets from various acquisition strategies and image resolutions, potentially supporting future advances in neuroscience research.

wmh_seg: Transformer based U-Net for Robust and Automatic White Matter Hyperintensity Segmentation across 1.5T, 3T and 7T

White matter hyperintensity (WMH) remains the top imaging biomarker for neurodegenerative diseases. Robust and accurate segmentation of WMH holds paramount significance for neuroimaging studies. The growing shift from 3T to 7T MRI necessitates robust tools for harmonized segmentation across field strengths and artifacts. Recent deep learning models exhibit promise in WMH segmentation but still face challenges, including diverse training data representation and limited analysis of MRI artifacts' impact. To address these, we introduce wmh_seg, a novel deep learning model leveraging a transformer-based encoder from SegFormer. wmh_seg is trained on an unmatched dataset, including 1.5T, 3T, and 7T FLAIR images from various sources, alongside with artificially added MR artifacts. Our approach bridges gaps in training diversity and artifact analysis. Our model demonstrated stable performance across magnetic field strengths, scanner manufacturers, and common MR imaging artifacts. Despite the unique inhomogeneity artifacts on ultra-high field MR images, our model still offers robust and stable segmentation on 7T FLAIR images. Our model, to date, is the first that offers quality white matter lesion segmentation on 7T FLAIR images.