Neuroimaging

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Overview

Neuroimaging studies the brain using modalities such as MRI, functional MRI, diffusion imaging, PET, EEG, and MEG, to understand brain organization and support diagnosis and treatment. Methods range from image registration, segmentation, and signal modeling to machine learning that predicts clinical outcomes or decodes responses to stimuli; newer work also combines modalities and models brain changes over time. Self-supervised and foundation models, generative methods, and graph-based analyses are being explored to make better use of large, heterogeneous datasets and capture brain structure and dynamics. A central challenge is whether gains on familiar datasets generalize across scanners, sites, and populations while producing reliable, interpretable results that can be validated in clinical settings.

Latest papers

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235 papers30 papers in the last four weeks, up 15% on the four weeks before. 0.2% of all new papers.

Mar 10, 2026

BrainSTR: Spatio-Temporal Contrastive Learning for Interpretable Dynamic Brain Network Modeling

Dynamic functional connectivity captures time-varying brain states for better neuropsychiatric diagnosis and spatio-temporal interpretability, i.e., identifying when discriminative disease signatures emerge and where they reside in the connectivity topology. Reliable interpretability faces major challenges: diagnostic signals are often subtle and sparsely distributed across both time and topology, while nuisance fluctuations and non-diagnostic connectivities are pervasive. To address these issues, we propose BrainSTR, a spatio-temporal contrastive learning framework for interpretable dynamic brain network modeling. BrainSTR learns state-consistent phase boundaries via a data-driven Adaptive Phase Partition module, identifies diagnostically critical phases with attention, and extracts disease-related connectivity within each phase using an Incremental Graph Structure Generator regularized by binarization, temporal smoothness, and sparsity. Then, we introduce a spatio-temporal supervised contrastive learning approach that leverages diagnosis-relevant spatio-temporal patterns to refine the similarity metric between samples and capture more discriminative spatio-temporal features, thereby constructing a well-structured semantic space for coherent and interpretable representations. Experiments on ASD, BD, and MDD validate the effectiveness of BrainSTR, and the discovered critical phases and subnetworks provide interpretable evidence consistent with prior neuroimaging findings. Our code: https://anonymous.4open.science/r/BrainSTR1.

Guiliang Guo, Guangqi Wen, Lingwen Liu +6

Computer Science and Engineering, Northeastern University, Shenyang, China · School of Computer Science and Artificial Intelligence, Shandong Normal University, Jinan, China · Graduate School of Information, Production and Systems, Waseda University, Kitakyushu, Fukuoka, Japan +3

Dynamic Functional ConnectivityBrain Network AnalysisNeuroimagingDynamic Graph LearningNeural Network InterpretabilityGraph Contrastive Learning+1
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Mar 9, 2026

Multimodal Deep Learning for Dynamic and Static Neuroimaging: Integrating MRI and fMRI for Alzheimer Disease Analysis

Magnetic Resonance Imaging (MRI) provides detailed structural information, while functional MRI (fMRI) captures temporal brain activity. In this work, we present a multimodal deep learning framework that integrates MRI and fMRI for multi-class classification of Alzheimer Disease (AD), Mild Cognitive Impairment, and Normal Cognitive State. Structural features are extracted from MRI using 3D convolutional neural networks, while temporal features are learned from fMRI sequences using recurrent architectures. These representations are fused to enable joint spatial-temporal learning. Experiments were conducted on a small paired MRI-fMRI dataset (29 subjects), both with and without data augmentation. Results show that data augmentation substantially improves classification stability and generalization, particularly for the multimodal 3DCNN-LSTM model. In contrast, augmentation was found to be ineffective for a large-scale single-modality MRI dataset. These findings highlight the importance of dataset size and modality when designing augmentation strategies for neuroimaging-based AD classification.

Anima Kujur, Zahra Monfared

Interdisciplinary Centre for Scientific Computing (IWR), Department of Mathematics and Computer Science, Heidelberg University, Germany

Alzheimer's Disease ClassificationNeuroimagingMultimodal ClassificationMultimodal FusionData Augmentation
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Mar 9, 2026

BrainCast: A Spatio-Temporal Forecasting Model for Whole-Brain fMRI Time Series Prediction

Functional magnetic resonance imaging (fMRI) enables noninvasive investigation of brain function, while short clinical scan durations, arising from human and non-human factors, usually lead to reduced data quality and limited statistical power for neuroimaging research. In this paper, we propose BrainCast, a novel spatio-temporal forecasting framework specifically tailored for whole-brain fMRI time series forecasting, to extend informative fMRI time series without additional data acquisition. It formulates fMRI time series forecasting as a multivariate time series prediction task and jointly models temporal dynamics within regions of interest (ROIs) and spatial interactions across ROIs. Specifically, BrainCast integrates a Spatial Interaction Awareness module to characterize inter-ROI dependencies via embedding every ROI time series as a token, a Temporal Feature Refinement module to capture intrinsic neural dynamics within each ROI by enhancing both low- and high-energy temporal components of fMRI time series at the ROI level, and a Spatio-temporal Pattern Alignment module to combine spatial and temporal representations for producing informative whole-brain features. Experimental results on resting-state and task fMRI datasets from the Human Connectome Project demonstrate the superiority of BrainCast over state-of-the-art time series forecasting baselines. Moreover, fMRI time series extended by BrainCast improve downstream cognitive ability prediction, highlighting the clinical and neuroscientific impact brought by whole-brain fMRI time series forecasting in scenarios with restricted scan durations.

Yunlong Gao, Jinbo Yang, Li Xiao +5

Institute of Advanced Technology, University of Science and Technology of China, Hefei 230052, China. · MoE Key Laboratory of Brain-Inspired Intelligence Perception and Cognition, University of Science and Technology of China, Hefei 230052, China. · School of Mathematics and Computer Sciences, Nanchang University, Nanchang 330031, China. +3

Time Series ForecastingSpatiotemporal ForecastingNeuroimagingFunctional Magnetic Resonance ImagingMultivariate Time Series Forecasting
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Mar 8, 2026

Neural Dynamics-Informed Pre-trained Framework for Personalized Brain Functional Network Construction

Brain activity is intrinsically a neural dynamic process constrained by anatomical space. This leads to significant variations in spatial distribution patterns and correlation patterns of neural activity across variable and heterogeneous scenarios. However, dominant brain functional network construction methods, which relies on pre-defined brain atlases and linear assumptions, fails to precisely capture varying neural activity patterns in heterogeneous scenarios. This limits the consistency and generalizability of the brain functional networks constructed by dominant methods. Here, a neural dynamics-informed pre-trained framework is proposed for personalized brain functional network construction. The proposed framework extracts personalized representations of neural activity patterns in heterogeneous scenarios. Personalized brain functional networks are obtained by utilizing these representations to guide brain parcellation and neural activity correlation estimation. Systematic evaluations were employed on 18 datasets across tasks, such as virtual neural modulation and abnormal neural circuit identification. Experimental results demonstrate that the proposed framework attains superior performance in heterogeneous scenarios. Overall, the proposed framework challenges the dominant brain functional network construction method.

Hongjie Jiang, Yifei Tang, Shuqiang Wang

Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.

Brain Network AnalysisFunctional ConnectivityNeuroimaging
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Mar 5, 2026

An Approach to Simultaneous Acquisition of Real-Time MRI Video, EEG, and Surface EMG for Articulatory, Brain, and Muscle Activity During Speech Production

Speech production is a complex process spanning neural planning, motor control, muscle activation, and articulatory kinematics. While the acoustic speech signal is the most accessible product of the speech production act, it does not directly reveal its causal neurophysiological substrates. We present the first simultaneous acquisition of real-time (dynamic) MRI, EEG, and surface EMG, capturing several key aspects of the speech production chain: brain signals, muscle activations, and articulatory movements. This multimodal acquisition paradigm presents substantial technical challenges, including MRI-induced electromagnetic interference and myogenic artifacts. To mitigate these, we introduce an artifact suppression pipeline tailored to this tri-modal setting. Once fully developed, this framework is poised to offer an unprecedented window into speech neuroscience and insights leading to brain-computer interface advances. The source code and data are available.

Jihwan Lee, Parsa Razmara, Kevin Huang +16

Signal Analysis and Interpretation Laboratory, University of Southern California · Ming Hsieh Dept. of Electrical and Computer Engineering, University of Southern California · Dept. of Linguistics, University of Southern California

NeuroimagingSpeech Production
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Mar 5, 2026

LUMINA: Laplacian-Unifying Mechanism for Interpretable Neurodevelopmental Analysis via Quad-Stream GCN

Functional Magnetic Resonance Imaging(fMRI) has now become a classic way for measuring brain activity, and recent trend is shifting toward utilizing fMRI brain data for AI-driven diagnosis. Given that the brain functions as not a discrete but interconnected whole, Graph-based architectures represented by Graph Convolutional Network(GCN) has emerged as a dominant framework for such task, since they are capable of treating ROIs as dynamically interconnected nodes and extracting relational architecture between them. Ironically, however, it is the very nature of GCN's architecture that acts as an obstacle to its performance. The mathematical foundation of GCN, effective for capturing global regularities, acts as a tradeoff; by smoothing features across the connected nodes repeatedly, traditional GCN tend to blur out the contrastive dynamics that might be crucial in identifying certain neurological disorders. In order to break through this structural bottleneck, we propose LUMINA, a Laplacian-Unifying Mechanism for Interpretable Neurodevelopmental Analysis. Our model is a Quad-Stream GCN that employs a bipolar RELU activation and a dual-spectrum graph Laplacian filtering mechanism, thereby capturing heterogeneous dynamics that were often blurred out in conventional GCN. By doing so, we can preserve the diverse range and characteristics of neural connections in each fMRI data. Through 5-fold cross validation on the ADHD200(N=144) and ABIDE(N=579) dataset, LUMINA demonstrates stable diagnostic performance in two of the most critical neurodevelopmental disorder in childhood, ADHD and ASD, outperforming existing models with an accuracy of 84.66% and 88.41% each.

Minkyung Cha, Jooyoung Bae, Jaewon Jung +3

Seoul National University, Seoul, Republic of Korea · NVIDIA AI Technology Center HK, Hong Kong

GNN OversmoothingGraph Neural NetworksMedical DiagnosisNeuroimagingFunctional Connectivity
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Mar 4, 2026

A Unified Framework for Joint Detection of Lacunes and Enlarged Perivascular Spaces

Cerebral small vessel disease (CSVD) markers, specifically enlarged perivascular spaces (EPVS) and lacunae, present a unique challenge in medical image analysis due to their radiological mimicry. Standard segmentation networks struggle with feature interference and extreme class imbalance when handling these divergent targets simultaneously. To address these issues, we propose a morphology-decoupled framework where Zero-Initialized Gated Cross-Task Attention exploits dense EPVS context to guide sparse lacune detection. Furthermore, biological and topological consistency are enforced via a mixed-supervision strategy integrating Mutual Exclusion and Centerline Dice losses. Finally, we introduce an Anatomically-Informed Inference Calibration mechanism to dynamically suppress false positives based on tissue semantics. Extensive 5-folds cross-validation on the VALDO 2021 dataset (N=40) demonstrates state-of-the-art performance, notably surpassing task winners in lacunae detection precision (71.1%, p=0.01) and F1-score (62.6%, p=0.03). Furthermore, evaluation on the external EPAD cohort (N=1762) confirms the model's robustness for large-scale population studies. Code will be released upon acceptance.

Lucas He, Krinos Li, Hanyuan Zhang +7

Hawkes Institute, University College London, UK · Unit for Lifelong Health and Aging, University College London, UK · Bioengineering Department and Imperial-X, Imperial College London, UK +6

NeuroimagingBrain MRIMulti-Task Learning
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Mar 3, 2026

Beyond Anatomy: Explainable ASD Classification from rs-fMRI via Functional Parcellation and Graph Attention Networks

Anatomical brain parcellations dominate rs-fMRI-based Autism Spectrum Disorder (ASD) classification, yet their rigid boundaries may fail to capture the idiosyncratic connectivity patterns that characterise ASD. We present a graph-based deep learning framework comparing anatomical (AAL, 116 ROIs) and functionally-derived (MSDL, 39 ROIs) parcellation strategies on the ABIDE I dataset. Our FSL preprocessing pipeline handles multi-site heterogeneity across 400 balanced subjects, with site-stratified 70/15/15 splits to prevent data leakage. Gaussian noise augmentation within training folds expands samples from 280 to 1,680. A three phase pipeline progresses from a baseline GCN with AAL (73.3% accuracy, AUC=0.74), to an optimised GCN with MSDL (84.0%, AUC=0.84), to a Graph Attention Network ensemble achieving 95.0% accuracy (AUC=0.98), outperforming all recent GNN-based benchmarks on ABIDE I. The 10.7-point gain from atlas substitution alone demonstrates that functional parcellation is the most impactful modelling decision. Gradient-based saliency and GNNExplainer analyses converge on the Posterior Cingulate Cortex and Precuneus as core Default Mode Network hubs, validating that model decisions reflect ASD neuropathology rather than acquisition artefacts. All code and datasets will be publicly released upon acceptance.

Syeda Hareem Madani, Noureen Bibi, Adam Rafiq Jeraj +3

Salim Habib University · VentureDive · National University of Computer and Emerging Sciences

Autism Spectrum DisorderNeuroimagingExplainable Medical Image AnalysisGraph Attention NetworksFunctional Connectivity
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Feb 28, 2026

Multiple Inputs and Mixwd data for Alzheimer's Disease Classification Based on 3D Vision Transformer

The current methods for diagnosing Alzheimer Disease using Magnetic Resonance Imaging (MRI) have significant limitations. Many previous studies used 2D Transformers to analyze individual brain slices independently, potentially losing critical 3D contextual information. Region of interest-based models often focus on only a few brain regions despite Alzheimer's affecting multiple areas. Additionally, most classification models rely on a single test, whereas diagnosing Alzheimer's requires a multifaceted approach integrating diverse data sources for a more accurate assessment. This study introduces a novel methodology called the Multiple Inputs and Mixed Data 3D Vision Transformer (MIMD-3DVT). This method processes consecutive slices together to capture the feature dimensions and spatial information, fuses multiple 3D ROI imaging data inputs, and integrates mixed data from demographic factors, cognitive assessments, and brain imaging. The proposed methodology was experimentally evaluated using a combined dataset that included the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Australian Imaging, Biomarker, and Lifestyle Flagship Study of Ageing (AIBL), and the Open Access Series of Imaging Studies (OASIS). Our MIMD-3DVT, utilizing single or multiple ROIs, achieved an accuracy of 97.14%, outperforming the state-of-the-art methods in distinguishing between Normal Cognition and Alzheimer's Disease.

Juan A. Castro-Silva, Maria N. Moreno Garcia, Diego H. Peluffo-Ordoñez

Faculty of Engineering, Universidad Surcolombiana, Neiva 410002, Colombia · College of Computing, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco

Alzheimer's Disease ClassificationMultimodal Classification3D ViTsNeuroimaging
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Feb 27, 2026

SHINE: Sequential Hierarchical Integration Network for EEG and MEG

How natural speech is represented in the brain constitutes a major challenge for cognitive neuroscience. Reconstructing the speech envelope and Mel spectrogram from EEG and MEG provides a time-resolved way to study its temporal and spectral structure. Speech-related neural activity spans sensors and temporal scales; extracting these representations while adapting the use of context to each acoustic target is a central problem in speech reconstruction. We propose SHINE, a Sequential Hierarchical Integration Network for EEG and MEG. A residual sensor adapter unifies input dimensions, intermediate dilated-block states retain temporal depth, and a target- and time-dependent gate fuses local hierarchical and attention-enhanced context predictions. Across two EEG and two MEG datasets, SHINE has the highest mean envelope and mean-Mel Pearson correlations among nine local baseline implementations on all eight dataset-metric combinations. SHINE also placed second in the speech-detection Extended Track of the NeurIPS 2025 PNPL Competition. Code will be released at https://github.com/xuxiran/SHINE.

Xiran Xu, Yujie Yan, Songyi Li +4

Speech and Hearing Research Center, School of Intelligence Science and Technology, Peking University, China · National Key Laboratory of General Artificial Intelligence, China · Center for BioMed-X Research, Academy for Advanced Interdisciplinary Studies, Peking University, China

ElectroencephalographyNeural ProcessesNeural DecodingEEG DecodingAttention MechanismsNeuroimaging+1
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Feb 24, 2026

PIME: Prototype-based Interpretable MCTS-Enhanced Brain Network Analysis for Disorder Diagnosis

Recent deep learning methods for fMRI-based diagnosis have achieved promising accuracy by modeling functional connectivity networks. However, standard approaches often struggle with noisy interactions, and conventional post-hoc attribution methods may lack reliability, potentially highlighting dataset-specific artifacts. To address these challenges, we introduce PIME, an interpretable framework that bridges intrinsic interpretability with minimal-sufficient subgraph optimization by integrating prototype-based classification and consistency training with structural perturbations during learning. This encourages a structured latent space and enables Monte Carlo Tree Search (MCTS) under a prototype-consistent objective to extract compact minimal-sufficient explanatory subgraphs post-training. Experiments on three benchmark fMRI datasets demonstrate that PIME achieves state-of-the-art performance. Furthermore, by constraining the search space via learned prototypes, PIME identifies critical brain regions that are consistent with established neuroimaging findings. Stability analysis shows 90% reproducibility and consistent explanations across atlases.

Kunyu Zhang, Yanwu Yang, Jing Zhang +2

Zhengzhou University, Zhengzhou, China · University Hospital Tübingen, Tübingen, Germany · China University of Geosciences, Wuhan, China +3

Brain Network AnalysisInterpretable MLNeuroimagingFunctional Connectivity
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Feb 23, 2026

Token-UNet: A New Case for Transformers Integration in Efficient and Interpretable 3D UNets for Brain Imaging Segmentation

We present Token-UNet, adopting the TokenLearner and TokenFuser modules to encase Transformers into UNets. While Transformers have enabled global interactions among input elements in medical imaging, current computational challenges hinder their deployment on common hardware. Models like (Swin)UNETR adapt the UNet architecture by incorporating (Swin)Transformer encoders, which process tokens that each represent small subvolumes (838^3 voxels) of the input. The Transformer attention mechanism scales quadratically with the number of tokens, which is tied to the cubic scaling of 3D input resolution. This work reconsiders the role of convolution and attention, introducing Token-UNets, a family of 3D segmentation models that can operate in constrained computational environments and time frames. To mitigate computational demands, our approach maintains the convolutional encoder of UNet-like models, and applies TokenLearner to 3D feature maps. This module pools a preset number of tokens from local and global structures. Our results show this tokenization effectively encodes task-relevant information, yielding naturally interpretable attention maps. The memory footprint, computation times at inference, and parameter counts of our heaviest model are reduced to 33%, 10%, and 35% of the SwinUNETR values, with better average performance (86.75% ±0.19%\pm 0.19\% Dice score for SwinUNETR vs our 87.21% ±0.35%\pm 0.35\%). This work opens the way to more efficient trainings in contexts with limited computational resources, such as 3D medical imaging. Easing model optimization, fine-tuning, and transfer-learning in limited hardware settings can accelerate and diversify the development of approaches, for the benefit of the research community.

Louis Fabrice Tshimanga, Andrea Zanola, Federico Del Pup +1

3D Medical Image SegmentationHybrid CNN-Transformer ArchitecturesEfficient ViTsNeuroimaging
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Feb 21, 2026

A Data-Driven Method to Map the Functional Organisation of Human Brain White Matter

The white matter of the brain is organised into axonal bundles that support long-range neural communication. Although diffusion MRI (dMRI) enables detailed mapping of these pathways through tractography, how white matter pathways directly facilitate large-scale neural synchronisation remains poorly understood. We developed a data-driven framework that integrates dMRI and functional MRI (fMRI) to model the dynamic coupling supported by white matter tracks. Specifically, we employed track dynamic functional connectivity (Track-DFC) to characterise functional coupling of remote grey matter connected by individual white matter tracks. Using independent component analysis followed by k-medoids clustering, we derived functionally-coherent clusters of white matter tracks from the Human Connectome Project young adult cohort. When applied to the HCP ageing cohort, these clusters exhibited widespread age-related declines in both functional coupling strength and temporal variability. Importantly, specific clusters encompassing pathways linking control, default mode, attention, and visual systems significantly mediated the relationship between age and cognitive performance. Together, these findings depict the functional organisation of white matter tracks and provide a powerful tool to study brain ageing and cognitive decline.

Yifei Sun, James M. Shine, Robert D. Sanders +4

School of Biomedical Engineering, The University of Sydney, Sydney, 2050, Australia. · Brain and Mind Centre, The University of Sydney, Sydney, 2050, Australia. · School of Medical Science, The University of Sydney, Sydney, 2050, Australia. +5

Functional ConnectivityNeuroimagingDynamic Functional Connectivity
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Feb 13, 2026

Machine Learning-Based Classification of Jhana Advanced Concentrative Absorption Meditation Using 7 Tesla Functional Magnetic Resonance Imaging

Introduction: Jhana advanced concentrative absorption meditation (ACAM-J) involves profound changes in consciousness, making its neural correlates important for understanding consciousness and well-being. Prior neuroimaging has relied on univariate, group-level contrasts, leaving open whether ACAM-J carries distributed neural signatures decodable from individual scans. This study evaluates whether fMRI-derived regional homogeneity (ReHo) can classify ACAM-J using machine learning. Methods: We analysed 7T fMRI data from 20 advanced meditators who progressed through their standard ACAM-J sequence and two matched control tasks, plus intensive data from one case-study participant held out for final evaluation. ReHo maps were computed per segment and parcellated into 498 regions spanning cortex, subcortex, brainstem, and cerebellum. Within subject-wise stratified cross-validation, feature ranking, recursive feature elimination, and class balancing were applied to training data only; six classifier families were fitted, and the top three per contrast were combined by probability averaging. Results: Across 19 binary comparisons, the ensemble reached an overall average accuracy of 65.87% before and 66.82% after regressing out phenomenology-related variance, with an average Cohen's \k{appa} of 0.2443. Discrimination was strongest for the most separated states (ACAM-J1 vs ACAM-J6, 74.33% accuracy, \k{appa} = 0.5158), while adjacent states were harder to separate. Prefrontal and anterior cingulate areas contributed most to model decisions. Conclusion: ReHo patterns measured at 7T carry information distinguishing ACAM-J from control states and, more modestly, from one another, supporting the feasibility of multivariate decoding of advanced meditation and informing future work on its mechanisms and neuromodulation.

Puneet Kumar, Winson F. Z. Yang, Alakhsimar Singh +2

School of AI and Data Engineering, Indian Institute of Technology Ropar 140001, India · Meditation Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA · Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA +2

Functional Magnetic Resonance ImagingNeural DecodingNeuroimaging
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Feb 9, 2026

Data-Driven Registration and Modeling of Brain Deformation for Image-Guided Neurosurgery: A Systematic Review

Accurate compensation of brain deformation is critical for reliable image-guided neurosurgery. Surgical manipulation and tumor resection induce tissue motion, causing preoperative planning images to become misaligned with the intraoperative anatomy. In this systematic review, we examine data-driven methods developed between 2020 and 2025 for brain deformation registration and modeling, with a particular focus on learning-based approaches. A comprehensive literature search was conducted in PubMed, IEEE Xplore, Scopus, and Web of Science using predefined inclusion and exclusion criteria for computational methods addressing brain deformation in neurosurgical imaging, resulting in 46 eligible studies. We provide a unified analysis of methodological strategies, including deep learning-based image registration, direct deformation field regression, synthesis-driven multimodal alignment, resection-aware architectures for handling missing correspondences, and hybrid models integrating biomechanical priors. We also examine dataset utilization, evaluation metrics, validation protocols, and the assessment of uncertainty and generalization across studies. While learning-based methods demonstrate promising accuracy and computational efficiency, current approaches remain limited by out-of-distribution robustness, standardized benchmarking, interpretability, and readiness for clinical deployment. Our review highlights these gaps and outlines future directions toward more robust, generalizable, and clinically translatable solutions for neurosurgical guidance. By organizing recent advances and critically assessing evaluation practices, this work provides a comprehensive reference for researchers and clinicians working on data-driven registration and modeling of brain deformation.

Tiago Assis, Colin P. Galvin, Joshua P. Castillo +12

LASIGE, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal · Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA · Gina Cody School of Engineering and Computer Science, Concordia University, Montreal, QC H3G 2W1, Canada +5

NeuroimagingDeformable Image Registration
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Nov 17, 2025

BrainNormalizer: Anatomy-Informed Pseudo-Healthy Brain Reconstruction from Tumor MRI via Edge-Guided ControlNet

Brain tumors induce complex structural deformations that obscure the patient' s original neuroanatomy, making it difficult to distinguish tumor-induced changes from inherent anatomical variability. Reconstructing a subject-specific pseudo-healthy brain can provide a critical reference for such analysis, but this task is inherently counterfactual, as paired pre-tumor scans and explicit healthy guidance are unavailable. We propose BrainNormalizer, a diffusion-based framework for subject-specific pseudo-healthy brain MRI reconstruction that enables anatomy-informed reconstruction without requiring paired data or explicit healthy references. The framework learns anatomical priors and edge-based structural conditioning through a two-stage training strategy consisting of inpainting-based diffusion fine-tuning and ControlNet-based edge conditioning. At inference, counterfactual pseudo-healthy reconstruction is achieved through a deliberate misalignment strategy, where tumorous inputs are paired with non-tumorous prompts and mirrored contralateral edge maps. This allows subject-specific anatomical guidance to be constructed from the patient's own anatomy, enabling anatomically consistent pseudo-healthy reconstruction that preserves individual structural characteristics. Experiments on the BraTS2020 dataset demonstrate that BrainNormalizer achieves improved distributional realism, symmetry-based structural consistency, and reduced false positive detection compared to existing methods. These results indicate that the proposed framework provides a principled approach for subject-specific counterfactual reconstruction and supports downstream analysis of tumor-induced deformation.

Min Gu Kwak, Yeonju Lee, Hairong Wang +2

Department of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh, PA, USA · H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA,2026 USA · Operations Research and Industrial Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, USAJul +2

Diffusion Models for Image RestorationMedical Image SynthesisDiffusion MRINeuroimagingBrain MRI
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Nov 14, 2025

Hi-DREAM: Brain-Inspired Hierarchical Diffusion for fMRI-to-Image Reconstruction via ROI Encoder and VisuAl Mapping

Reconstructing natural images from fMRI requires bridging neural activity with both the structural and semantic representations used by modern generative models. Existing diffusion-based decoders often condition on a single global fMRI embedding, which limits their ability to exploit the hierarchical organization of the visual cortex and makes the contribution of different visual areas difficult to inspect. We propose Hi-DREAM, a brain-inspired hierarchical diffusion framework that structures fMRI conditioning according to early, middle, and late visual Regions of Interest (ROI) streams. A ROI adapter converts these streams into a multi-scale cortical pyramid, and a lightweight ROI-conditioned ControlNet injects the resulting anatomy-aware priors into matched U-Net depths during denoising. Experiments on the Natural Scenes Dataset (NSD) show that Hi-DREAM achieves state-of-the-art high-level semantic reconstruction while retaining strong low-level structure. Further ablation and attribution analyses show that the proposed hierarchy-aware conditioning is effective, and that different ROI streams provide complementary, inspectable contributions to reconstruction.

Guowei Zhang, Yun Zhao, Kai Sun +4

Dept of Data Science and AI, Monash University, Melbourne, Australia · Brain and Mind Centre, University of Sydney, Sydney, Australia · School of Psychological Sciences, Monash University, Melbourne, Australia

Visual NeuroscienceConditional Image GenerationImage ReconstructionNeural DecodingConditional Diffusion ModelsNeuroimaging+1
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Oct 15, 2025

Scaling Vision Transformers for Functional MRI with Flat Maps

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

Connor Lane, Mihir Tripathy, Leema Krishna Murali +15

MedARC · Sophont · Baylor College of Medicine +3

fMRI Foundation ModelsMasked AutoencodersNeuroimagingMedical Image BenchmarksMedical Imaging Foundation ModelsfMRI Representation Learning+1
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Sep 12, 2025

On a Geometry of Interbrain Networks

Effective analysis in neuroscience benefits significantly from robust conceptual frameworks. Traditional metrics of interbrain synchrony in social neuroscience typically depend on fixed, correlation-based approaches, restricting their explanatory capacity to descriptive observations. Inspired by the successful integration of geometric insights in network science, we propose leveraging discrete geometry to examine the dynamic reconfigurations in neural interactions during social exchanges. Unlike conventional synchrony approaches, our method interprets inter-brain connectivity changes through the evolving geometric structures of neural networks. This geometric framework is realized through a pipeline that identifies critical transitions in network connectivity using entropy metrics derived from curvature distributions. By doing so, we significantly enhance the capacity of hyperscanning methodologies to uncover underlying neural mechanisms in interactive social behavior.

Nicolás Hinrichs, Noah Guzmán, Melanie Weber

Neural Data Science and Statistical Computing Group, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany · Embodied Cognitive Science Unit, Okinawa Institute of Science and Technology, Okinawa, Japan · Independent Scholar +1

Neuroimaging
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Sep 11, 2025

Reduced NEXI protocol for the quantification of human gray matter microstructure on the Connectome 2.0 scanner

Biophysical diffusion MRI models like Neurite Exchange Imaging (NEXI) are essential for probing gray matter microstructure, estimating compartment diffusivities, neurite fraction, and exchange time. However, NEXI's multi-shell, multi-diffusion-time requirements cause prohibitively long acquisitions. Leveraging the Connectome 2.0 ultra-high gradient scanner, we developed a time-efficient protocol using an Explainable AI (XAI) framework. Combining XGBoost, SHAP, and Recursive Feature Elimination trained on synthetic signals, XAI identified an optimal 8-feature subset, cutting scan time from 27 to 14 minutes. Validated in vivo in seven healthy participants, the XAI protocol was benchmarked against the full 15-feature acquisition, a Cram'er-Rao Lower Bound (CRLB) theoretical optimum, and two heuristics ("Mid-Range" and "Corner"). It robustly reproduced parameter estimates and maintained test-retest reproducibility. Remarkably, the XAI selection converged to the CRLB optimum. This validates XAI's optimality while highlighting its main advantage: achieving gold-standard optimization without complex analytical Jacobians, making it easily adaptable to numerical models or complex noise where CRLB is intractable. Furthermore, XAI showed superior in vivo robustness over heuristics: "Mid-Range" sampling yielded biased exchange time estimates from insufficient temporal diversity, while "Corner" sampling gave unstable intra-neurite diffusivity estimates (5-fold higher CV) due to noise sensitivity. Ultimately, this robust 14-minute protocol accelerates exchange-sensitive microstructural mapping, establishing a model-agnostic optimization framework adaptable to future ultra-high gradient systems and existing clinical scanners.

Quentin Uhl, Tommaso Pavan, Julianna Gerold +10

Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland · Department of Radiology, Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Boston, MA, USA

Magnetic Resonance ImagingNeuroimaging
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Sep 5, 2025

Uncertain but Useful: Leveraging CNN Training Variability into Data Augmentation

Deep learning (DL) has transformed neuroimaging by delivering state-of-the-art performance with reduced computation times. Yet, the numerical uncertainty inherent to DL training remains largely underexplored despite its potential to significantly impact the reliability of model outcomes. We show that training the FastSurfer segmentation model introduces substantial numerical uncertainty that exceeds its non-DL counterpart (FreeSurfer 7.3.2) in cortical regions, potentially impacting downstream clinical results. We also characterize this training-time uncertainty using random seed perturbations and demonstrate that seed-induced variability is structurally comparable to numerical variability. We then show that seed variability can be leveraged as a data augmentation technique through ensembling to improve downstream brain age regression performance. These findings position numerical uncertainty during DL training as a substantive factor in neuroimaging reliability, with measurable consequences for downstream tasks, and demonstrate that it can simultaneously be harnessed as a data augmentation technique.

Inés Gonzalez-Pepe, Vinuyan Sivakolunthu, Yohan Chatelain +1

Department of Computer Science Concordia University Montreal, QC H3G 1M8, Canada · Department of Computer Science Concordia University2026 Montreal, QC H3G 1M8, Canada · Krembil Centre for Neuroinformatics Centre for Addiction and Mental Health Toronto, ON M5T 0S8, Canada +1

Image SegmentationData AugmentationNeuroimagingNeural Network Training DynamicsSegmentation Uncertainty EstimationBrain MRI
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Aug 24, 2025

Achieving detailed medial temporal lobe segmentation with upsampled isotropic training from implicit neural representation

Imaging biomarkers in magnetic resonance imaging (MRI) are important tools for diagnosing, tracking and treating Alzheimer's disease (AD). Neurofibrillary tau pathology in AD is closely linked to neurodegeneration and generally follows a pattern of spread in the brain, with early stages involving subregions of the medial temporal lobe (MTL). Accurate segmentation of MTL subregions is needed to extract granular biomarkers of AD progression. MTL subregions are often imaged using T2-weighted (T2w) MRI scans that are highly anisotropic due to constraints of MRI physics and image acquisition, making it difficult to reliably model MTL subregions geometrically and extract morphological measures, such as thickness. In this study, we propose a segmentation framework for MTL subregions in isotropic space, in which an implicit neural representation is used to construct the isotropic training atlas from the anisotropic low-resolution T2w data, with T1w MRI as an auxiliary modality to support the INR and segmentation. In an independent test set, the morphological measures extracted using this isotropic model showed stronger effect sizes than those from models trained on anisotropic data in distinguishing participants with mild cognitive impairment (MCI) from cognitively unimpaired individuals. In the test-retest analysis, the morphological measures extracted using the isotropic model showed greater stability than those from the anisotropic segmentation. This study demonstrates improved reliability of MRI-derived MTL subregion biomarkers without additional atlas annotation effort, which may more accurately quantify and track the relationship between AD pathology and brain atrophy for monitoring disease progression.

Yue Li, Pulkit Khandelwal, Rohit Jena +8

University of Pennsylvania, Philadelphia, United States · Siemens Healthineers, Princeton, United States · Lund University, Lund, Sweden

Alzheimer's DiseaseImage SegmentationMedical Image SegmentationNeuroimagingBrain MRI
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Jul 24, 2025

A Multimodal Sequence-to-Sequence Model for Cross-Subject Prediction of Brain Responses to Naturalistic Stimuli

Brain encoding models predict time-resolved neural activity from computational representations of ongoing experience, providing a principled framework for testing how information is represented and transformed across cortical systems. Naturalistic audiovisual narratives are a particularly rich but challenging testbed for these models, requiring integration of multimodal inputs over long temporal horizons and generalization across individuals with substantial response variability. We introduce a multimodal sequence-to-sequence Transformer with a hybrid cross-subject parameterization that predicts cortex-wide parcel-wise fMRI time series autoregressively from visual, audio, language, and vision--language representations. We evaluate the approach on data from the Courtois NeuroMod project, where four deeply-sampled participants viewed six seasons of Friends and four feature-length films during fMRI. Sequence-to-sequence temporal modeling yields consistent improvements over single-frame prediction across cortical networks, with gains extending to novel stimuli. A hybrid architecture that pairs a shared stimulus encoder with lightweight subject-specific decoder components outperforms both fully shared and fully individual models, indicating complementary advantages of learning shared stimulus representations across subjects and fitting individual neural readouts. Finally, we show that in data-scarce settings, hybrid models can be personalized to new individuals with limited fMRI data, demonstrating that multi-subject pretraining serves as a strong inductive prior for building individual-specific encoding models. Together, these results indicate that combining multimodal sequence modeling with a hybrid cross-subject architecture offers a scalable framework for personalized brain encoding under naturalistic conditions.

Qianyi He, Monica D. Rosenberg, Yuan Chang Leong

Data Science Institute University of Chicago, USA · Department of Psychology, Neuroscience Institute University of Chicago, USA

Neural DecodingNeuroimagingMultimodal Learning
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Mar 20, 2025

Explainable Graph-theoretical Machine Learning with Application to Alzheimer's Disease Prediction

Dementia affects over 55 million people worldwide, projected to reach 139 million by 2050, with Alzheimer's disease (AD) accounting for 60-70% of cases. AD is associated with disruptions in metabolic brain connectivity. Detecting these disruptions early is crucial for AD management. FDG-PET is a useful tool for identifying such impairments. However, most studies rely on group-level analyses or thresholding, potentially masking individual differences and overlooking weaker yet biologically critical brain connections. Moreover, AD prediction largely focuses on univariate rather than multivariate outcomes. To address this, we introduce explainable graph-theoretical machine learning (XGML), a framework for constructing individual metabolic brain graphs and identifying subgraphs most predictive of multivariate disease-related outcomes. Using Alzheimer's Disease Neuroimaging Initiative (ADNI) FDG-PET data, we compared six graph representations against three non-graph baselines, each with six machine learning models using repeated stratified 3-fold cross-validation (10 repeats). The best configuration combined kernel density estimation with Hellinger distance and random forest. Across eight cognitive scores, it reached an overall Fisher-z-averaged Pearson correlation of r=0.595, with strongest performance for ADAS13 (r=0.67), ADAS11 (r=0.65), and ADASQ4 (r=0.62). We identified key edges that were jointly but differentially predictive across outcomes, suggesting their potential as network biomarkers of cognitive decline. Preliminary external feasibility validation on an OASIS3 cohort yielded weak predictive performance for CDRSB (r=0.26) and MMSE (r=0.18), likely reflecting cohort, protocol, and diagnostic differences. Overall, our results suggest the promise of graph-theoretical machine learning for biomarker discovery, disease prediction, and understanding the neural mechanisms underlying AD.

Narmina Baghirova, Duy-Thanh Vũ, Duy-Cat Can +6

Department of Informatics, University of Fribourg, Fribourg, Switzerland · Platform of Bioinformatics, Lausanne University Hospital (CHUV), Lausanne, Switzerland · Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland

Clinical Outcome PredictionNeuroimaging
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Jul 22, 2024

Enhancing Cognitive Workload Classification Using Integrated LSTM Layers and CNNs for fNIRS Data Analysis

Functional near-infrared spectroscopy (fNIRS) is employed as a non-invasive method to monitor functional brain activation by capturing changes in the concentrations of oxygenated haemoglobin (HbO) and deoxygenated haemo-globin (HbR). Various machine learning classification techniques have been utilized to distinguish cognitive states. However, conventional machine learning methods, although simpler to implement, undergo a complex pre-processing phase before network training and demonstrate reduced accuracy due to inadequate data preprocessing. Additionally, previous research in cog-nitive load assessment using fNIRS has predominantly focused on differ-sizeentiating between two levels of mental workload. These studies mainly aim to classify low and high levels of cognitive load or distinguish between easy and difficult tasks. To address these limitations associated with conven-tional methods, this paper conducts a comprehensive exploration of the im-pact of Long Short-Term Memory (LSTM) layers on the effectiveness of Convolutional Neural Networks (CNNs) within deep learning models. This is to address the issues related to spatial features overfitting and lack of tem-poral dependencies in CNN in the previous studies. By integrating LSTM layers, the model can capture temporal dependencies in the fNIRS data, al-lowing for a more comprehensive understanding of cognitive states. The primary objective is to assess how incorporating LSTM layers enhances the performance of CNNs. The experimental results presented in this paper demonstrate that the integration of LSTM layers with Convolutional layers results in an increase in the accuracy of deep learning models from 97.40% to 97.92%.

Mehshan Ahmed Khan, Houshyar Asadi, Mohammad Reza Chalak Qazani +6

Institute for Intelligent Systems Research and Innovation, Deakin University, 75 Pigdons Rd, Waurn Ponds, VIC, 3216, Geelong, Australia

Recurrent Neural NetworksConvolutional Neural NetworksNeuroimaging
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