Christian Ewert

Nancy R. Newlin, Kurt Schilling, Serge Koudoro et al.

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.

Sebastian Rassmann, David Kügler, Christian Ewert et al.

While Generative Adversarial Nets (GANs) and Diffusion Models (DMs) have achieved impressive results in natural image synthesis, their core strengths - creativity and realism - can be detrimental in medical applications, where accuracy and fidelity are paramount. These models instead risk introducing hallucinations and replication of unwanted acquisition noise. Here, we propose YODA (You Only Denoise once - or Average), a 2.5D diffusion-based framework for medical image translation (MIT). Consistent with DM theory, we find that conventional diffusion sampling stochastically replicates noise. To mitigate this, we draw and average multiple samples, akin to physical signal averaging. As this effectively approximates the DM's expected value, we term this Expectation-Approximation (ExpA) sampling. We additionally propose regression sampling YODA, which retains the initial DM prediction and omits iterative refinement to produce noise-free images in a single step. Across five diverse multi-modal datasets - including multi-contrast brain MRI and pelvic MRI-CT - we demonstrate that regression sampling is not only substantially more efficient but also matches or exceeds image quality of full diffusion sampling even with ExpA. Our results reveal that iterative refinement solely enhances perceptual realism without benefiting information translation, which we confirm in relevant downstream tasks. YODA outperforms eight state-of-the-art DMs and GANs and challenges the presumed superiority of DMs and GANs over computationally cheap regression models for high-quality MIT. Furthermore, we show that YODA-translated images are interchangeable with, or even superior to, physical acquisitions for several medical applications.

Christian Ewert, David Kügler, Anastasia Yendiki et al.

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.