AA-ViT: Anatomically Aware Vision Transformer with Structural and Frequency Guidance for Contrast Enhanced Brain MRI Synthesis
Authors: Talha Meraj, Tom Flannery, Charlie Cummins, Matt Townend, Thomas C Booth, Peter Crossley, Michael McCann, Ian Overton, +1 more
Organizations: Department of Computing and Electronic Engineering, Atlantic Technological University, Sligo, Ireland · Mathematical Modelling and Intelligent Systems for Health and Environment (MISHE), Faculty of Engineering and Design, Atlantic Technological University, Sligo, Ireland · JANUS Research Centre, Atlantic Technological University, Letterkenny, Ireland · Johnston Cancer Research Centre, Queen’s University Belfast, Belfast, BT9 7AE, UK · Department of Neurosurgery, Belfast Health and Social Care Trust, Belfast, BT12 6BA, UK · Department of Neuroradiology, Ruskin Wing, King’s College Hospital NHS Foundation Trust, London, SE5 9RS, UK · School of Biomedical Engineering & Imaging Sciences, King’s College London, UK · Department of Computing, Atlantic Technological University, Letterkenny, Ireland
Accurate tumour localization and diagnosis is a critical component of clinical care for brain cancers. Magnetic Resonance Imaging (MRI) is the most commonly used imaging modality due to its superior soft-tissue contrast. However, standard MRI often exhibits limited contrast and imaging artifacts, which necessitates the use of contrast agents to enhance lesion visibility. The administration of chemical contrast agents is not always feasible and may be contraindicated in patients with renal impairment or other health conditions. As a result, developing accurate and non-invasive contrast enhanced MRI (CEMRI) synthesis methods has clinical importance. In recent years, numerous approaches for CEMRI synthesis have been proposed, predominantly relying on generative artificial intelligence models. While these methods demonstrate promising performance, their dependence on implicit feature learning often limits their ability to preserve anatomical boundaries and tumour-specific fine structures. To address these challenges, we propose an anatomically aware frequency-and-structure-guided vision transformer (AA-ViT), for CEMRI synthesis using pre-contrast MRI modalities (T1, T2, and FLAIR). Experiments on the BraTS 2021 dataset demonstrate that the proposed method preserves anatomical and lesion boundaries, achieving higher PSNR and SSIM than state-of-the-art approaches. Clinical evaluation by three neuroradiologists and a neurosurgeon on 19 randomly selected cases across diverse gliomas yielded a mean score of 3.94/5, providing preliminary clinical validation rarely seen in prior studies. Synthetic post-contrast scans from our model could lower scanning costs, shorten imaging time, and avoid the potential risks of using gadolinium-based contrast agents.
Multi-contrast brain MRI provide complementary soft-tissue characteristics that aid in the screening and diagnosis of diseases. However, limited scanning time, image corruption and various imaging protocols often result in incomplete multi-contrast images. While current approaches excel in image synthesis, they often struggle to synthesize critical tumor regions and exploit contextual information in multi-contrast brain MRI effectively. To address this issue, we propose a synthesis-centric, segmentation-assisted closed-loop framework with retrieval augmentation synthesis. Our method overall takes a generative adversarial architecture, which aims to synthesize missing contrasts from any combination of available ones with a single model. To explicitly capture tumor semantics and focus synthesis on tumor regions, we add an auxiliary segmentation branch that predicts tumor masks and feeds them back as semantic conditioning in synthesis branch, thereby learning tumor-aware representations in the model and improving synthesis fidelity. Furthermore, we propose a dual-bank retrieval augmentation strategy. It dynamically queries two external knowledge bases, namely a tumor masks memory bank for crucial tumor context and cross-image contrast feature memory bank for global style information, to augment synthesis. Verified on two public multi-contrast magnetic resonance brain datasets: BraTs2020 and UCSF-BMSR, the proposed method is effective in handling medical brain images synthesis tasks and shows superior performance compared to previous methods. Code is available at:https://github.com/iBizzard/SSCF.git
Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is essential for breast cancer management, but reliance on gadolinium-based contrast agents (GBCAs) restricts use in contraindicated populations, prolongs scan protocols, and presents environmental toxicity concerns. Contrast synthesis offers a non-invasive alternative; however, existing approaches struggle to balance spatial realism with temporal continuity, suffer from slow iterative sampling, underutilize structural priors, and lack clinical validation. We propose a novel conditioned latent transport framework that predicts contrast enhancement in a single forward pass. By anchoring the latent trajectory to the pre-contrast anatomy and applying continuous time conditioning, the model synthesizes patient-specific contrast evolution at any acquisition time. The proposed approach outperforms baseline and the state-of-the-art models across spatial, perceptual, temporal, and distributional metrics. Evaluated on an independent external cohort, the method demonstrates robustness to domain shifts induced by scanner noise as well as differing acquisition protocol. Furthermore, our synthetic contrast enhancement significantly improved downstream tumor segmentation performance, yielding a 22.4% relative increase in Dice coefficient (0.60 vs. 0.49 baseline pre-contrast, p < 0.01), reducing boundary segmentation error by over 39%, while outperforming all other generative model baselines. Finally, a reader study involving four breast radiologists evaluated the image quality, kinetic fidelity, and diagnostic viability of our synthesized sequences across 40 randomly selected cases. The results demonstrated that in 70% of cases, synthesized images provided sufficient clinical information to support the same management decisions as real DCE-MRI, suggesting a path toward safer and faster contrast-free or contrast-reduced imaging workflows.
Smriti Joshi, Apostolia Tsirikoglou, Daniel M. Lang +15
We developed an anatomy-aware deep learning framework to synthesize post-contrast breast MRI from pre-contrast images, emphasizing tumor and background parenchymal enhancement (BPE) regions. This retrospective study included 649 patients with 6,251 paired pre-contrast and post-contrast images. The framework integrates breast mask consistency, lesion-region supervision, and BPE-region supervision into an image-to-image translation model. Evaluation included quantitative image quality metrics, a reader study with two breast radiologists, and downstream Ki-67 classification. The proposed method outperformed Pix2Pix, Pix2PixHD, diffusion-based synthesis, and mask-supervised baselines in whole-image and regional evaluations. Ki-67 classification showed no statistically significant performance differences across real- and synthetic-image training and testing settings, although this does not establish equivalence. These findings suggest that anatomy-aware supervision improves synthesis fidelity and support further investigation of synthetic post-contrast MRI for contrast-free imaging workflows.