Regression is all you need for medical image translation

The acquisition of information-rich images within a limited time budget is crucial in medical imaging. Medical image translation (MIT) can help enhance and supplement existing datasets by generating synthetic images from acquired data. While Generative Adversarial Nets (GANs) and Diffusion Models (DMs) have achieved remarkable success in natural image generation, their benefits - creativity and image realism - do not necessarily transfer to medical applications where highly accurate anatomical information is required. In fact, the imitation of acquisition noise or content hallucination hinder clinical utility. Here, we introduce YODA (You Only Denoise once - or Average), a novel 2.5D diffusion-based framework for volumetric MIT. YODA unites diffusion and regression paradigms to produce realistic or noise-free outputs. Furthermore, we propose Expectation-Approximation (ExpA) DM sampling, which draws inspiration from MRI signal averaging. ExpA-sampling suppresses generated noise and, thus, eliminates noise from biasing the evaluation of image quality. Through extensive experiments on four diverse multi-modal datasets - comprising multi-contrast brain MRI and pelvic MRI-CT - we show that diffusion and regression sampling yield similar results in practice. As such, the computational overhead of diffusion sampling does not provide systematic benefits in medical information translation. Building on these insights, we demonstrate that YODA outperforms several state-of-the-art GAN and DM methods. Notably, YODA-generated images are shown to be interchangeable with, or even superior to, physical acquisitions for several downstream tasks. Our findings challenge the presumed advantages of DMs in MIT and pave the way for the practical application of MIT in medical imaging.

Regression s all you need for medical image translation

The acquisition of information-rich images within a limited time budget is crucial in medical imaging. Medical image translation (MIT) can help enhance and supplement existing datasets by generating synthetic images from acquired data. While Generative Adversarial Nets (GANs) and Diffusion Models (DMs) have achieved remarkable success in natural image generation, their benefits - creativity and image realism - do not necessarily transfer to medical applications where highly accurate anatomical information is required. In fact, the imitation of acquisition noise or content hallucination hinder clinical utility. Here, we introduce YODA (You Only Denoise once - or Average), a novel 2.5D diffusion-based framework for volumetric MIT. YODA unites diffusion and regression paradigms to produce realistic or noise-free outputs. Furthermore, we propose Expectation-Approximation (ExpA) DM sampling, which draws inspiration from MRI signal averaging. ExpA-sampling suppresses generated noise and, thus, eliminates noise from biasing the evaluation of image quality. Through extensive experiments on four diverse multi-modal datasets - comprising multi-contrast brain MRI and pelvic MRI-CT - we show that diffusion and regression sampling yield similar results in practice. As such, the computational overhead of diffusion sampling does not provide systematic benefits in medical information translation. Building on these insights, we demonstrate that YODA outperforms several state-of-the-art GAN and DM methods. Notably, YODA-generated images are shown to be interchangeable with, or even superior to, physical acquisitions for several downstream tasks. Our findings challenge the presumed advantages of DMs in MIT and pave the way for the practical application of MIT in medical imaging.

MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

Learning Anatomical Segmentations for Tractography from Diffusion MRI

Deep learning approaches for diffusion MRI have so far focused primarily on voxel-based segmentation of lesions or white-matter fiber tracts. A drawback of representing tracts as volumetric labels, rather than sets of streamlines, is that it precludes point-wise analyses of microstructural or geometric features along a tract. Traditional tractography pipelines, which do allow such analyses, can benefit from detailed whole-brain segmentations to guide tract reconstruction. Here, we introduce fast, deep learning-based segmentation of 170 anatomical regions directly on diffusion-weighted MR images, removing the dependency of conventional segmentation methods on T 1-weighted images and slow pre-processing pipelines. Working natively in diffusion space avoids non-linear distortions and registration errors across modalities, as well as interpolation artifacts. We demonstrate consistent segmentation results between 0 .70 and 0 .87 Dice depending on the tissue type. We investigate various combinations of diffusion-derived inputs and show generalization across different numbers of gradient directions. Finally, integrating our approach to provide anatomical priors for tractography pipelines, such as TRACULA, removes hours of pre-processing time and permits processing even in the absence of high-quality T 1-weighted scans, without degrading the quality of the resulting tract estimates.