NeuroGAN-3D: Enhancing Intrinsic Functional Brain Networks via High-Fidelity 3D Generative Super-Resolution
Authors: M. Moein Esfahani, Sepehr Salem Ghahfarokhi, Mohammed Alser, Jingyu Liu, Vince Calhoun
Organizations: 1 2 Georgia State University, Atlanta, GA, USA · 2 1 Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
Abstract
Recent advances in neuroimaging have deepened our understanding of the brain's complex functional and structural organization. Among these, functional Magnetic Resonance Imaging (fMRI) - particularly resting-state fMRI (rs-fMRI) - has emerged as a tool for identifying biomarkers of intrinsic brain connectivity and delineating large-scale neural networks. These networks are typically represented as volumetric spatial maps that capture functionally coherent brain regions and reflect individual differences in brain activity and structure. The spatial resolution of these maps plays an important role, as it determines the ability to localize functional units with precision, perform reliable brain parcellation, and detect subtle, spatially specific neurobiological alterations associated with development, aging, or disease. Therefore, improving the effective resolution of neuroimaging-derived maps holds significant promise for enabling more detailed insights into brain architecture and its relationship to behavior and pathology. To address this need, we propose NeuroGAN-3D, a novel 3D generative super-resolution model tailored to the computational demands of volumetric neuroimaging. Our model leverages a generative adversarial network architecture to enhance the spatial resolution of rs-fMRI spatial maps, significantly outperforming a conventional baseline.
Resolving complex fiber geometries in brain white matter requires high-resolution diffusion MRI at the cost of long acquisition times. This leads many clinical protocols to opt for low-resolution scans, making downstream microstructure estimation and tractography challenging. Implicit neural representations (INRs) can model the diffusion signal continuously, enabling native single-subject super-resolution by querying the network at arbitrary spatial coordinates, yet existing methods often suffer from long training times and lack a mechanism to incorporate anatomical priors to regularize super-resolution by constraining the space of plausible reconstructions. To address these limitations, we propose a novel transfer-learning framework that pre-trains an INR on a high-resolution template and then adapts it to subject-specific scans via registration and fine-tuning. For 4× through-plane super-resolution from 5 mm to 1.25 mm on Human Connectome Project (HCP) data, our method reduces NRMSE by 36-49% and increases FSIM by 24-43% over a recent baseline with 6× faster training, outperforming competing INR-based methods across both image quality and domain-specific metrics. Code is available on the project page at https://abdulkaderghandoura.github.io/research/msc-thesis/ .
Abdulkader Ghandoura, Marsil Zakour, William Consagra +1
The success of large-scale deep learning models in neuroscience is fundamentally constrained by severe data heterogeneity. Native fMRI data aggregated from diverse sources exhibit substantial variation in both spatial and temporal resolutions. Consequently, most existing frameworks rely on lengthy, rigid preprocessing pipelines that enforce uniformity across datasets. This practice introduces two critical limitations: (1) potential degradation of subject-specific anatomical information; (2) significant computational overhead, often requiring hours of processing per subject. Here, we propose FlexiBrain, a resolution-agnostic voxel-level encoding framework for native fMRI based on Mamba-JEPA. FlexiBrain defines patch sizes in real-world physical units and employs a dynamic patch resizing, thereby bypassing destructive spatial standardization while enabling direct ingestion of data in native space. We instantiate the framework using an efficient Mamba-JEPA backbone to model high-dimensional 4D fMRI signals. Across five diverse downstream neuroscience tasks, FlexiBrain consistently outperforms recent state-of-the-art methods, achieving gains of up to 12 percentage points without external data augmentation. Importantly, FlexiBrain functions as a seamless plug-in module, substantially reducing preprocessing costs and accelerating the development of robust voxel-level fMRI foundation models. Code is available at https://github.com/OneMore1/FlexiBrain.
Three-dimensional (3D) medical image enhancement, including denoising and super-resolution, is critical for clinical diagnosis in CT, PET, and MRI. Although diffusion models have shown remarkable success in 2D medical imaging, scaling them to high-resolution 3D volumes remains computationally prohibitive due to lengthy diffusion trajectories over high-dimensional volumetric data. We observe that in conditional enhancement, strong anatomical priors in the degraded input render dense noise schedules largely redundant. Leveraging this insight, we propose a sparse voxel-space diffusion framework that trains and samples on a compact set of uniformly subsampled timesteps. The network predicts clean data directly on the data manifold, supervised in velocity space for stable gradient scaling. A lightweight Structure-aware Trajectory Modulation (STM) module recalibrates time embeddings at each network block based on local anatomical content, enabling structure-adaptive denoising over the shared sparse schedule. Operating directly in voxel space, our framework preserves fine anatomical detail without lossy compression while achieving up to 10× training acceleration. Experiments on four datasets spanning CT, PET, and MRI demonstrate state-of-the-art performance on both denoising and super-resolution tasks. Our code is publicly available at: https://github.com/mirthAI/sparse-3d-diffusion.