High-resolution (HR) MRI acquisition is often hampered by scan time constraints, resulting in anisotropic or low-resolution scans (e.g., thick-slice FLAIR) that limit diagnostic accuracy. While deep learning-based super-resolution (SR) methods show promise, they often hallucinate anatomical details, which can compromise brain structural integrity. To mitigate this limitation, we introduce MR-DiffuSR, a Multi-Resolution Diffusion-based Super-Resolution framework that incorporates HR T1w structural image priors to guide the restoration of thick-slice FLAIR scans and operates in the 3D latent space. Our architecture introduces cross-modality structural swin-attention, which derives structural attention maps from the HR T1w and applies them to the low-resolution FLAIR latent features. This design disentangles anatomical structure from modality-specific contrast, effectively preventing hallucinations. Furthermore, we employ a mixed-scale degradation strategy, training the model on a continuum of downsampling factors to ensure robustness to varying slice thicknesses, while optimizing with a DINOv3-based perceptual loss to preserve high-frequency semantic details. Evaluated on the ADNI-4 dataset, MR-DiffuSR surpasses both CNN and 2D diffusion approaches, achieving an average PSNR of 32.46dB, SSIM of 0.97, and LPIPS of 0.07 across all downsampling factors. In downstream white matter hyperintensity segmentation, our model demonstrates exceptional robustness. While baseline performance collapses at 10x down-sampling (Dice: 0.51), MR-DiffuSR maintains a Dice score of 0.63, preserving utility even at 7mm equivalent slice thickness.
Max Van Puyvelde, Ibrahim Gulluk, Wim Van Criekinge +1cs.AI cs.CV cs.LG
Three-dimensional (3D) brain MRI is central to clinical neurology and neuro-oncology, where generative models could augment under-represented cohorts, simulate disease trajectories, and support privacy-preserving data sharing. Latent diffusion has been the go-to solution for modeling imaging data, but it places two competing demands on the tokenizer: encoder embeddings must retain the clinical information that downstream tasks act on, and the decoder must reconstruct anatomically faithful volumes. Existing reconstruction-driven tokenizers achieve the second at the expense of the first. To address this, we introduce a fully volumetric masked-autoencoder (MAE) based tokenizer for 3D brain MRI latent diffusion, decoupling encoder and decoder: a frozen 3D MAE encoder produces clinically informative embeddings, while a dedicated CNN decoder reconstructs voxels from a linear projection of those embeddings. We pretrain the encoder on 35,309 volumes from 18 public cohorts spanning four modalities, ten disease categories, and 200+ acquisition sites, and demonstrate its dual utility in two settings. First, on a 23-task linear-probing benchmark, the encoder outperforms or matches SOTA models (i.e., BrainIAC, BrainSegFounder, and MedicalNet) on 21 of 23 tasks. Second, a conditional diffusion transformer (DiT) trained on these clinically informative embeddings supports both conditional generation across six variables and patient-specific longitudinal forecasting. Together these results establish a single 3D brain-MRI embedding space capable of both downstream clinical tasks and controllable generation.
Clinical ultrasound images often contain artificial markers, such as measurement calipers and text, to assist diagnostic interpretation and comparison. However, these markers can introduce shortcut bias in downstream automated analysis, encouraging deep learning models to rely on marker-related cues rather than clinically meaningful anatomy. Existing marker removal methods are either mask-dependent and vulnerable to error propagation, or mask-free deterministic restorers that may over-smooth ultrasound texture and perturb unaffected background regions. To address these challenges, we present Echo-DM, a framework for ultrasound marker removal via conditional latent diffusion and region-aware fusion. Echo-DM follows a common encoder-diffusion-decoder pipeline, where a DiT-based conditional latent diffusion network performs global restoration and a region-aware fusion module enforces preservation-aware image-space refinement under end-to-end mask-free inference. Building on this fixed core design, we further instantiate Echo-DM-V and Echo-DM-R with VAE-based and RAE-based latent modules, respectively, which demonstrates that the Echo-DM architecture is compatible with diverse latent-module instantiations. Extensive experiments on Echo-PAIR, a large-scale paired clinical ultrasound dataset, demonstrate superior marker removal and strong anatomical fidelity compared with representative two-stage baselines, while providing favorable quality--efficiency trade-offs across deployment settings. Data, code and models will be released at https://github.com/MiliLab/Echo-DM.