DTI-Guided Volumetric Spherical Harmonics Regression for Single-to-Multi-Shell dMRI Synthesis

Diffusion models have achieved remarkable quality in multi-modal MRI synthesis, but their computational cost (hundreds of sampling steps and separate models per modality) limits clinical deployment. We observe that this inefficiency stems from an unnecessary starting point: diffusion begins from pure noise, discarding the structural information already present in available MRI sequences. We propose WFM (Wavelet Flow Matching), which instead learns a direct flow from an informed prior, the mean of conditioning modalities in wavelet space, to the target distribution. Because the source and target share underlying anatomy and differ primarily in contrast, this formulation enables accurate synthesis in just 1-2 integration steps. A single 82M-parameter model with class conditioning synthesizes all four BraTS modalities (T1, T1c, T2, FLAIR), replacing four separate diffusion models totaling 326M parameters. On BraTS 2024, WFM achieves 26.8 dB PSNR and 0.94 SSIM, within 1-2 dB of diffusion baselines, while running 250-1000x faster (0.16-0.64s vs. 160s per volume). This speed-quality trade-off makes real-time MRI synthesis practical for clinical workflows. Code is available at https://github.com/yalcintur/WFM.

Diffusion MRI (dMRI) probes water diffusion within the brain, providing unique information about tissue microstructure and white matter connectivity. High-quality dMRI enables advanced and accurate analyses but demands dense acquisitions, resulting in long scan times and hardware constraints that are often infeasible. Further, dMRI requires dedicated computational methods to support diverse analysis tasks (e.g., parcellation, registration, and synthesis) for both neuroscientific and clinical applications. Here, we present dMRI-F, a foundation model that unifies dMRI data enhancement and downstream tasks across diverse acquisitions and populations, while requiring only minimal acquisition input. dMRI-F is pre-trained with a q-space masked reconstruction task: predicting densely sampled multi-shell data from only six volumes. It learns generalizable latent feature representations of dMRI data, which serve as a core foundation for adapting to diverse downstream tasks, including brain parcellation, brain registration, and cross-modal synthesis. Across nine independently acquired datasets, we demonstrate that dMRI-F outperforms state-of-the-art methods with robust generalization across acquisitions, populations, and tasks. Our results demonstrate dMRI-F's versatility as a general-purpose framework that enables diverse dMRI applications from low-cost, sparse acquisitions.

Diffusion magnetic resonance imaging is a noninvasive technique that is sensitive to the motion of water molecules in human tissue. The image signal is commonly described in q-space; however, a complete coverage of this space is often infeasible due to hardware and acquisition time limitations. In this work, we propose to represent the entire diffusion signal using an implicit neural representation network with wavelet activation functions. The signal space is encoded using Fourier features and spherical harmonics basis functions for a continuous output distribution of the raw diffusion data, enabling both super-resolution and q-space interpolation. Additionally, we introduce a pretraining strategy using a group template, enabling faster per-subject optimisation when combined with nonlinear registrations of subjects into template space. We tested the method with 10 subjects from the Human Connectome Project and 26 subjects from in-house data (multidimensional diffusion MRI from a Parkinson's disease cohort). The results show that the proposed method yields high-fidelity reconstructions with significantly reduced memory requirements compared to raw diffusion-weighted images. The pretraining scheme showed good generalisability properties on data acquired with very different protocols. We further assess the method on downstream metrics relevant to diffusion MRI data from the learned representations.