Brain Magnetic Resonance Imaging

Generating signals on graphs requires permutation-equivariant models that exhibit stability with respect to relative structural perturbations. While recent graph-aware Schrödinger bridge models incorporate topology information directly into their reference dynamics, it is unclear how perturbations of the graph propagate through these dynamics and affect the resulting generated distributions. In this paper, we analyze the structural stability of graph-aware continuous-time generative models whose drift combines a graph filter with a learned graph neural network. We derive explicit Wasserstein stability bounds that quantify the effect of relative graph perturbations on the generated distributions. Motivated by these bounds, we introduce a principled framework for designing stable graph filters that preserve the smoothing behavior of graph heat diffusion, while boosting structural stability. Experiments on synthetic and fMRI signals show our stable filters enhance structural robustness while matching or exceeding the generative quality of the heat equation baseline.

We developed BrainVLM to classify all 12 World Health Organization (WHO) 2021 brain tumor types. BrainVLM integrates an uncertainty quantification strategy to indicate prediction reliability and a module for generating radiology reports to elucidate the clinical rationale. BrainVLM was trained on multi-modal data (MRI scans, demographics, and radiology reports) from 40,043 individuals. It was validated on 5,211 patients with pathologically confirmed brain tumors, including 3,877 held-out patients from the primary hospital and 1,334 patients from 11 independent hospitals. We further conducted two proof-of-concept studies to validate its clinical utility in AI-clinician workflows: 1) a blinded multireader study where 12 neuroradiologists across varying experience levels interpreted 248 retrospective cases with or without AI assistance, and 2) a real-world prospective study in which 1,009 patients were independently and blindly assessed by BrainVLM and radiologists before surgery. Additionally, we demonstrated BrainVLM's utility in preoperative molecular subgroup prediction for adult-type diffuse gliomas, using a multi-center cohort of 632 patients. In primary evaluation, BrainVLM achieved an area under the curve (macro-AUC) of 0.85 (95% CI: 0.84-0.86), and an F1 score of 0.82 (95% CI: 0.81-0.83), surpassing neuroradiologists (F1 = 0.80 (95% CI: 0.79-0.81)). In external validation across 11 centers, BrainVLM achieved an AUC = 0.80 (95% CI: 0.79-0.82) and F1 = 0.75 (95% CI: 0.73-0.78), compared with F1 = 0.71 (95% CI: 0.69-0.73) for neuroradiologists. In prospective real-world evaluation, BrainVLM maintained performance comparable to neuroradiologists.

Most knowledge of graphical perception comes from behavioral studies. Understanding from a neural perspective is much more limited due in part to neuroimaging studies' expensiveness and difficulty to conduct. In this paper, we evaluate whether Meta's Tribe V2 neural encoding model can recover neural contrasts from a visualization fMRI study. Specifically, we evaluate Tribe V2 through a conceptual replication of the visualization-viewing component of a prior comparison of Bubble charts and three-dimensional Surface charts in color and grayscale. We generate TRIBE-predicted cortical responses for the original stimuli and compare the resulting contrasts with those reported in the human study. The model reproduced the direction of 11 of 14 reported cortical effects, with agreement concentrated in visual-processing regions. This agreement characterizes the model's alignment with the prior human-generated fMRI results rather than independently confirming them. We discuss the limitations encountered when working with this model for in-silico replication and hope to encourage future work exploring this new avenue for neuroimaging studies in visualization. Supplemental materials are available at https://osf.io/8a96x/.

fMRI foundation models increasingly aggregate heterogeneous data across brain states, cohorts, and acquisition settings, yet pretraining domains are commonly treated as a flat mixture and downstream tasks are adapted independently. We study whether measured learning relations can organize both stages without modifying the backbone. During pretraining, a lightweight Brain-DiT proxy estimates difficulty and directed facilitation across ten fMRI domains, yielding a priority-guided cumulative domain curriculum combined with high-to-low-noise timestep scheduling and joint consolidation. During adaptation, controlled first- and higher-order transfer across fifteen tasks constructs a directed taskonomy, from which budgeted integer programming (BIP) selects directly supervised source tasks and target-specific routes. The joint priority-domain and high-to-low-timestep curriculum reduces v-NMSE, PSD-NMSE, and FC-MSE by 6.5%, 16.3%, and 10.5%, respectively, relative to uniform sampling over both dimensions, and shows strong downstream performance across six in- and out-of-domain tasks. The taskonomy reveals asymmetric, target-dependent transfer, while exploratory sealed-test evaluation shows larger descriptive gains for BIP policies when higher-order route spaces are available than for matched random controls. Together, these findings support organizing fMRI pretraining and adaptation by measured learning relations rather than treating domains and tasks as independent flat sets.

Medical image inpainting has the potential to improve automated brain MRI analysis by reconstructing healthy tissue within pathological regions. We introduce RARF, a task-agnostic region-aware rectified flow framework for masked data generation. We instantiate the framework for 3D brain MRI inpainting as our submission to the BraTS Inpainting Challenge 2026. RARF restricts the stochastic interpolation process to the inpainting region, while the observed voxels remain fixed and provide patient-specific anatomical context. A three-dimensional neural network receives the partially voided image, with Gaussian noise filling the missing region, together with the inpainting mask and the corresponding timestep. The model is trained using masked flow-matching and reconstruction-consistency objectives, combined with mask-aware preprocessing and data augmentation. During inference, the learned velocity field transports the initial noise toward a plausible reconstruction of the missing tissue, which is then combined with the unchanged observed anatomy. Experiments under the BraTS evaluation protocol show that the proposed approach produces competitive reconstructions while maintaining anatomical consistency. Source code is available at: https://github.com/TomasGuija/rarf.

Neuroradiologists rarely read a brain MRI in isolation, yet automated brain-MRI report generation has been built almost entirely for single studies. Temporal analysis has been explored on chest radiography and chest CT, but to our knowledge, longitudinal reporting for brain MRI, where interval change is often subtle and spatially distributed, remains unaddressed. We present BrainDiff, the first longitudinal vision-language system for brain MRI. BrainDiff outperforms both frontier general-purpose and single-study neuroimaging models on the same patient pairs. Moreover, BrainDiff retains 91% of internal RadGraph-XL entity+relation F1 (rg_er) on an external, cross-hospital cohort. Beyond the system, we contribute three analyses. First, we identify two independent grounding levers: a counterfactual objective with prior-report dropout, which increases measured image reliance by ~47%, and a staged curriculum. Together, these interventions raise image reliance 2.5-fold from the baseline. Second, we provide a factorial over prior-report availability and image identity, isolating a visual contribution of +0.0387 rg_er, which grows when the prior report is withheld. Third, a cheap change-decodability test for candidate backbones shows that interval change is decodable far more weakly than single-study pathology (0.60 vs. 0.77 AUROC). Code is publicly available at https://github.com/jhuldr/BrainDiff.

3D brain MRI generation has made significant advances in medical imaging, simulation, and controllable anatomical analysis. However, existing generative models typically synthesize 3D volumes monolithically, often overlooking regional anatomical structures and limiting local controllability. To address these limitations, we introduce AnaDiffusion, an anatomically compositional latent diffusion framework that factorizes the generation process into distinct, anatomically meaningful regions, followed by part-to-whole assembly and global refinement. Our approach first trains part diffusion models to capture local structural priors. We then inject an assembled anatomical composite of the parts into the whole-brain latent representation and continue denoising. This mechanism enables the model to resolve global context while preserving the injected anatomy. As a result, AnaDiffusion produces both explicit part assets and a globally coherent volume, thereby enabling controllable part editing without requiring subject-specific dense segmentation maps at inference time while maintaining consistent part-to-whole brain structure. On the subject-disjoint ADNI test split, AnaDiffusion achieves the lowest FID across the whole brain, left and right hemispheres, cerebellar-brainstem complex, and seam regions. It also achieves the best cerebellar and second-best ventricular and brainstem absolute Cohen's d values among the evaluated methods. In localized editing experiments, paired MS-SSIM demonstrates high target transfer and off-target preservation, supporting controllable part replacement with minimal unintended anatomical alterations.

Deep learning models for neuroimaging have largely been developed for individual tasks, limiting knowledge transfer across applications. Here we introduce GenFAR, a modular deep learning framework that learns general, clinically informed features from brain MRIs. We trained this modular architecture on 49,246 individuals across 11 cohorts, using 17 diverse classification and regression tasks spanning cognition, clinical, diagnosis, demographics, and biomarkers. This yields aggregated, focused feature sets that capture rich, clinically- and biologically-relevant brain representations. We developed a sequential learning approach where tasks progressively build on previously learned representations. Through an analysis of 5,000 task sequences, we identified an optimal sequence length of six tasks and introduced a Donor Score metric to quantify each task's contribution to downstream performance. This analysis revealed five consistently strong donor tasks (Age, AD/MCI, MMSE, Hypertension, Hyperlipidemia) that formed the base of our sequential model. We demonstrated the utility of our learned representation, in various tasks beyond those included in the training set, to serve as the foundation for specialized secondary predictors. We further showed that using the learned feature representation can substantially increase the sample efficiency of secondary deep learning training tasks and models, as well as improve their accuracy.

Alzheimer's disease is a leading cause of death with no cure. Therefore, early detection is critical to slow progression and preserve quality of life. Diagnosis relies on medical history, cognitive tests, physical exams, and MRI brain scans, making deep learning suitable for Alzheimer's classification. This work proposes a benchmark that evaluates ten different convolutional neural network (CNN) architectures (including ResNet, DenseNet, MobileNet, EfficientNet, and VGG family models) under the same held-out test split protocol. A two-stage transfer learning and full fine-tuning pipeline is introduced to perform training using a class-balanced subset (3,900 images) derived from the OASIS medical imaging dataset, comprising 86,437 single-view MRI brain scans labeled into four classifications of Alzheimer's disease: Non-Demented, Very Mild Dementia, Mild Dementia, and Moderate Dementia. The best results were achieved by VGG16, with a 0.9637 validation accuracy and a 0.9533 test accuracy score. A key finding documented in this work is the difficulty of classifying the transition from Non-Demented to Very Mild Demented stages, observed consistently across all ten architectures.

Frozen foundation-model (FM) embeddings are increasingly used as off-the-shelf brain-MRI representations, on the assumption that they capture anatomy. We audit what they actually encode and find that acquisition site is a large, intrinsic component of the representation. Across two independent cohorts (ABIDE-I, ABIDE-II), three frozen 3-D encoders (brain-pretrained, CT-pretrained, and randomly initialized), and every network depth, site is linearly decodable at roughly 0.9 balanced accuracy at deep layers, exceeding the decodability of every clinical or demographic variable (sex, age, autism diagnosis) at every layer. The effect is intrinsic rather than learned: a randomly initialized encoder is already a ~0.9 site classifier on both cohorts and across three architecture families (Swin, ViT, ResNet), and site is decodable at ~0.95 directly from the raw downsampled image with no encoder, so the fingerprint reflects low-level image statistics that any encoder preserves rather than a product of pretraining. Residualizing measured population covariates leaves site decodability essentially unchanged, indicating an acquisition- rather than population-driven effect. A nonlinear probe matches the linear one, so the fingerprint is fully linearly accessible. The site subspace is removable post hoc by iterative null-space projection or ComBat (site decodability 0.94 -> 0.07/0.00), and is a site-attribution concern for shared or federated embeddings; but for dense segmentation this removal is not free, because site and anatomy occupy an entangled linear subspace (a matched-rank random-direction projection is Dice-neutral, whereas removing the site subspace is destructive). We recommend site-audited use of frozen brain-MRI FMs and release an open audit toolkit.

Large-scale multi-modal MRI datasets impose substantial storage and I/O costs, limiting the training of 3D generative models on commodity infrastructure. While lossy compression is known to preserve accuracy for discriminative segmentation networks, its effect on generative models, which must learn the full data distribution rather than a decision boundary, is unexplored. We study whether standard image codecs can effectively compress semantically rich brain tumor MRI while preserving the fidelity required to train and deploy a 3D MRI generative model. Each 3D volume is compressed with JPEG2000 or a near-lossless JPEG-LS pipeline. Next, a Wavelet Flow Matching model, conditioned on BraTS image sequences (T1n, T1c, T2, T2f), is trained on compressed data, and the resulting models are evaluated on the validation set. At a 20:1 compression ratio, synthesis quality is statistically equivalent to a model trained on uncompressed data within a pre-specified margin ($Δ$PSNR $<1$,dB, $Δ$SSIM $<0.02$; paired TOST $p=[[p]]$): mean PSNR is 27.3,dB vs. 27.0,dB and mean SSIM is 0.95 vs. 0.96 across modalities. Our results indicate that JPEG2000 compression is a practical step toward scalable 3D MRI generative modeling without degrading synthesis quality. The codebase is available at https://github.com/lisafis/MRIComp4Flow .

Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.

T2-weighted (T2w) brain MRI provides fluid-sensitive soft-tissue contrast that is important for neuro-oncology and radiotherapy planning. However, T2w scans are acquired with anisotropic voxels and appear blurred or stair-stepped on coronal and sagittal views, which obscures small structures and weakens any downstream 3D analysis. We propose VIPP-SR (View-Independent Patched Projection Super-Resolution), a cross-contrast guided super-resolution framework that restores the inter-plane resolution of an existing anisotropic T2w volume without an isotropic ground-truth T2w. VIPP-SR first trains a view-independent patched generator (VIP-GAN) to learn local T1c-to-T2w anatomical correspondence from high-resolution axial slices. The trained generator is then applied to axial, coronal, and sagittal views of the T1c volume to generate three orthogonal T2w estimates. Shape-preserving patching and deepest-skip removal reduce view-specific shortcuts, thereby constraining the generator to learn patch-local representations and enabling the zero-shot inter-plane transfer. Central to VIPP-SR, a projection-based optimization then enforces anatomical consistency across the three view-specific volumes, fusing them by balancing inter-plane self-consistency against per-view data fidelity. The generator is trained on BraTS-MET and evaluated on both the held-out BraTS-MET testing set and the BraTS-GLI cohort without retraining, assessing the cross-cohort generalizability. The results validate that VIPP-SR improves downstream segmentation over the real anisotropic T2w baseline, raising mean-label Dice from 0.330 to 0.465 on BraTS-MET and, zero-shot, from 0.473 to 0.563 on BraTS-GLI and ablation studies identify inter-plane self-consistency as the main source of the gain.

Brain magnetic resonance imaging (MRI) is central to neuroscience and clinical assessment, but models are commonly developed for individual diseases, populations or imaging protocols. Foundation models promise more general representations, yet they are usually pretrained once and can lose earlier capabilities when updated with new data. Here we show that Alcmaeon, a three-dimensional brain MRI foundation model pretrained without manual labels on more than 425,000 volumes and derived imaging maps, can be expanded sequentially across clinical domains. Alcmaeon combines volumetric encoding and latent diffusion generation with Graph-Blueprint Pruning (GBP), which protects network modules important to earlier domains while leaving the remaining capacity trainable. Across expansion from healthy ageing and neurodegeneration to developmental, psychiatric and tumour imaging, GBP showed less forgetting than sequential adaptation and elastic weight consolidation across voxel-level reconstruction measures, with its largest advantage after adaptation to tumour imaging. The blueprints provided an inspectable record of how model capacity was protected and reused. Representations from different model levels supported image synthesis, disease classification, survival modelling and postoperative prediction, although no single representation was optimal for every task. These findings provide a route towards brain MRI foundation models that can grow with emerging data while retaining earlier capabilities.

Headache is the most common neurological disorder in children and substantially affects quality of life. We investigated whether resting-state functional MRI (rs-fMRI) can support pediatric headache classification using machine learning. We encoded rs-fMRI data using NeuroSTORM, a recent foundation model, and fine-tuned it to distinguish healthy controls from children with headache and subsequently classify headache subtypes. We compared NeuroSTORM with a standard neuroscience approach using functional-connectivity (FC) matrices derived from brain activity as predictors. Using 189 rs-fMRI scans from 110 individuals collected across two visits (prevalence of any headache: 74%), NeuroSTORM achieved an area under the receiver operating characteristic curve (AUROC) of 0.82 (95% CI, 0.82-0.82) and an area under the precision-recall curve (AUPRC) of 0.93 (95% CI, 0.93-0.94) for discriminating headache from non-headache. In contrast, models trained on FC matrices showed lower performance (AUROC, 0.67 [95% CI, 0.67-0.67]; AUPRC, 0.85 [95% CI, 0.85-0.85]). In multiclass classification of healthy controls, chronic migraine, and non-chronic headaches (e.g., post-viral headache, new daily persistent headache, post-traumatic headache), NeuroSTORM achieved a macro-AUROC of 0.69 (95% CI, 0.68-0.69). Results suggest that the approach can distinguish chronic migraine but has difficulty differentiating other headache subtypes from chronic migraine. Overall, under limited-data conditions, NeuroSTORM appears to capture latent rs-fMRI representations that transfer to headache-related tasks without relying on FC features. These findings provide proof of concept for fMRI-based prediction of pediatric headache and highlight potential future utility for subtype identification and individualized treatment strategies.

Fetal brain biometry is essential for quantitative assessment of brain development, supporting gestational age estimation, developmental monitoring, and detection of abnormalities. In clinical practice, measurements are manually performed, making them time-consuming and prone to variability. While automated approaches have been proposed, reproducible methods remain limited, particularly those providing anatomically interpretable landmark localization. We present a fully automated deep learning-based framework for reliable and reproducible brain biometry from 3D super-resolution-reconstructed fetal brain MRI. The proposed four-step pipeline derives biometric parameters by jointly estimating linear measurements and their corresponding anatomical landmarks. A 3D convolutional neural network is trained to regress landmark coordinates from brain segmentation label maps, followed by measurement-specific geometric optimization to refine landmark positions and compute measurements. The pipeline is evaluated on two publicly available fetal MRI datasets comprising 150 volumes (gestational age range: 20-37 weeks) acquired across different scanners and protocols, assessing five key biometric measurements across varying acquisition settings and providing a comprehensive evaluation of both measurement accuracy and landmark localization using quantitative metrics and visual assessment. Compared with the only available automated pipeline, the proposed method achieves comparable or improved accuracy for most measurements. In conclusion, we introduce a straightforward pipeline for reliable biometry estimations, with efficiency, interpretability and scalability that support integration into clinical workflows.

Vision-language models (VLMs), including medical specialists, are increasingly proposed for medical imaging, yet their stated confidence is rarely evaluated separately from correctness. We use brain MRI as a controlled, high-stakes testbed for a broader failure mode in frontier multimodal systems: models can appear competent while lacking reliable self-knowledge. We present an automatically graded behavioral audit and pilot study of six instruction-tuned VLMs (five general-purpose and one medical specialist) on 4,102 images (4,032 axial/coronal/sagittal MRI slices from 250 subjects plus 70 non-brain/noise controls), with labels derived from public metadata and released expert segmentation masks rather than new human annotation. Across models, answer coverage is near-complete, but verbalized-confidence calibration is poor: ECE ranges from 0.27 to 0.40, mean confidence on incorrect answers ranges from 0.82 to 0.97, and 33-46% of answered items are high-confidence errors. The most accurate model is also the most confident on its errors, while a base/specialist family contrast suggests that medical adaptation improves tumor-presence detection without improving confidence reliability. Open-ended diagnostics further show that hallucination and abstention vary separately from multiple-choice accuracy. These findings argue that medical-image VLM evaluation should report verbalized-confidence reliability, confident error, hallucination, and abstention alongside accuracy.

Decoding visual experience from non-invasive brain activity is central to neuroscience and brain-computer interfaces. Functional magnetic resonance imaging (fMRI) offers fine spatial detail, but its slow hemodynamics and burdensome acquisition limit temporally resolved decoding. Electroencephalography (EEG) and magnetoencephalography (MEG) provide millisecond resolution, making image retrieval compelling: identify the viewed image from one neural response and a fixed candidate bank. Contrastive alignment to pretrained visual representations enables zero-shot retrieval from EEG and MEG, but most systems collapse heterogeneous visual supervision into a single embedding before ranking. This early consolidation imposes one similarity geometry on every candidate order and removes encoder-specific disagreements from the final ranking. We propose CORTIVA, a candidate-score fusion framework that preserves this complementary evidence. Three decoding routes are aligned to heterogeneous visual targets, score the same indexed candidates independently, and combine only their temperature-scaled score vectors before ranking. On the 200-way THINGS-EEG2 benchmark, CORTIVA reaches 73.5% Top-1 and 95.3% Top-5 across ten participants, exceeding the strongest reported baseline by 10.3 and 5.4 percentage points. With a modality-specific neural encoder, the same fusion principle reaches 42.4% Top-1 on THINGS-MEG. Matched route-removal retraining and four weight controls demonstrate that CORTIVA's gain arises from integrating complementary route scores and persists with uniform weighting, without requiring a specialized weighting rule. Independent DINOv2 analyses further reproduce the local error neighborhoods and posterior neural-visual correspondence. These results establish candidate-score fusion as a simple and testable alternative to embedding-level consolidation for neural image retrieval.

Numerous unsupervised domain adaptation (UDA) algori-thms exist, but for clinical practice, selecting the best-suited one along with proper hyperparameters often remains unclear, as the unlabeled deployment (target) domain prevents direct evaluation. We propose a label-free criterion that jointly selects the algorithm and hyperparameters for UDA. Given a pool of candidate models from multiple algorithms trained with different hyperparameters, our approach scores each candidate against an agreement reference, and selects the one with the highest score. The agreement reference is constructed in two levels without using target labels. First, we leverage multiple label-free selection signals, using each to nominate a model within every algorithm. Second, the nominated models are aggregated across algorithms to form a reference prediction for each unlabeled target sample. The candidate whose predictions agree most with this reference is then selected for deployment. Experimental results on four brain MRI and four chest X-ray datasets across seven clinically relevant transfer scenarios show that our method achieves better selection performance than other methods and remains effective across different algorithm pools. Our approach takes a step towards practical, label-free algorithm selection for clinical deployment of UDA.

Functional magnetic resonance imaging (fMRI) is a widely used technique for studying the brain. Recent methods that utilize graph neural networks (GNNs) for analysis of brain functional connectivity have shown great potential for the classification of brain disorders, such as Alzheimer's disease (AD). However, these methods often assume a preset number of functional modules across all subjects, which overlooks inter-subject variability. In addition, the discovered modules are rarely used to directly guide the learned connectivity patterns. Here, to address these issues, we propose a Meta Probabilistic Pooling GNN (MPP-GNN). We frame the model's task as a coupled, bilevel optimization that performs adaptive graph partitioning hierarchically to discover subject-specific modules and then uses the discovered brain modules as an explicit prior to guide edge refinement and representation learning. We validate MPP-GNN on two public datasets for AD classification, achieving the highest AUC in comparison to established baselines for both datasets. Furthermore, our analysis demonstrates that MPP-GNN shows significant alignment with the canonical functional-network organization defined by the Yeo brain atlas and reveals a network-level dedifferentiation pattern for AD.

Real-time closed-loop neurofeedback based on functional magnetic resonance imaging (fMRI) has led to important scientific and clinical advances. However, the sophistication of the analysis methods used in real-time fMRI lags behind the state-of-the-art in fMRI decoding, largely due to computational factors: Most advanced decoding pipelines do not fit within the envelope of real-time processing, where the analysis needs to be conducted in a matter of seconds and without leveraging data acquired later in the session. Here, we present a real-time compatible adaptation of a computationally intensive state-of-the-art pipeline for reconstructing perceived natural images (MindEye2), and we demonstrate that reliable fine-grained decoding is still achievable in this setting. Using RT-Cloud, an open-source, scalable cloud-based platform, we performed a real-time scan where we decoded single-trial visual perception within seconds after an image was shown to the participant. Finally, we use simulated analyses to document the factors driving changes in performance from offline to real-time analysis. This work serves as a proof-of-concept that it is feasible to deploy these powerful fMRI decoding pipelines in real-time analysis, paving the way for their use in brain-computer interfaces for scientific discovery and clinical treatment.

Functional magnetic resonance imaging (fMRI)-based visual decoding aims to recover visual information from measured brain activity, commonly by mapping fMRI responses into latent visual features for downstream decoding tasks. Most existing methods learn mappings from fMRI responses to visual features extracted by artificial neural networks (ANNs), yet it remains unclear whether ANN-derived features provide suitable targets for brain decoding. In this study, we investigate spiking neural network (SNN)-derived visual features as alternative targets for fMRI-based visual decoding. We compare an ANN baseline with four SNN variants from the same architectural family, which differ in their spiking dynamics. To isolate the effect of the target features, all models use the same L2-regularized linear fMRI-to-feature decoder, while only the feature vectors used as regression targets are varied. Compared with the ANN baseline, SNN-derived features exhibit stronger alignment with fMRI responses and improve visual semantic decoding performance. For instance, on the GoD dataset, SNN-derived features reduce feature-prediction error from 0.7707 to 0.0282 and improve top-1 semantic decoding accuracy from 0.1800 to 0.4400. Ablation results further indicate that both spiking neural dynamics and temporal simulation steps contribute to the observed advantage. These findings support SNN-derived features as effective brain-decodable visual representations and highlight target feature design as an important component of fMRI-based visual decoding.

Kernel regression with tensor trains and Hadamard overparameterization (KReTTaH) is introduced as a training-data-free, interpretable, and nonparametric framework for multi-way data imputation. The imputation problem is reformulated as regression in reproducing kernel Hilbert spaces (RKHS), where the tensor regression coefficients are explicitly constrained to lie on fixed-rank tensor-train (TT) manifolds and structured via Hadamard overparameterization to promote sparsity and high representational efficiency. Rather than relying on costly cross-validation, KReTTaH jointly optimizes the TT coefficient tensors and the kernel covariance matrices within a Riemannian product-manifold framework -- the former on fixed-rank TT manifolds, the latter on the manifold of positive-definite matrices -- thereby enabling automated kernel-hyperparameter selection. Numerical tests on two challenging applications -- imputation of high-dimensional functional magnetic resonance imaging (fMRI) data and recovery of missing edge flows in dynamic graphs -- demonstrate that KReTTaH consistently outperforms state-of-the-art tensor-, Bayesian-, and neural-network-based baselines in terms of modeling accuracy.

Foundation models provide powerful representations for brain MRI analysis, but their predictions remain difficult to interpret in anatomically meaningful terms. Clinical assessment of brain MRI is commonly organized around anatomically defined structures and regional abnormalities, whereas conventional explanation methods typically produce voxel- or patch-level importance maps that do not explicitly quantify the contributions of individual brain regions. To address this mismatch, we propose RegionFM, an interpretable framework that integrates anatomical segmentation with brain MRI foundation-model embeddings. RegionFM first divides each MRI scan into anatomical regions and constructs a separate MRI volume for each region. A frozen foundation model then encodes each region into an embedding, and a region-additive logistic model combines these embeddings such that every anatomical region contributes an explicit scalar term to the final prediction. This formulation supports both subject-level and cohort-level analyses of regional contributions. We evaluate RegionFM on cognitive-impairment classification using embeddings from multiple pretrained brain MRI foundation models. The results show that RegionFM maintains performance comparable to less interpretable fine-tuning approaches while providing anatomically grounded explanations. Randomized embedding ablations yield near-chance performance, indicating that the predictions rely on meaningful structure captured by the foundation-model embeddings rather than simple feature statistics. Overall, RegionFM better aligns model explanations with anatomy-based clinical reasoning while maintaining competitive predictive performance.

Decoding continuous language from fMRI signals remains a core challenge in non-invasive brain-computer interface research. We present two complementary investigations. First, we improve the Huth et al. ridge regression encoding pipeline through expanded voxel selection (10K->15K), substitution of GPT-2 medium for GPT-1 as the beam-search proposal model, and GPU-accelerated bootstrap training, achieving mean METEOR = 0.149 and BLEU-1 = 0.200 across three held-out narratives for subject UTS03 -- an 11% relative METEOR gain over our replication baseline. Second, we introduce fMRIFlamingo, which maps BOLD activity to a frozen Llama-3.2-1B with trainable gated cross-attention layers via a learned brain tokenizer and a Perceiver Resampler. Despite achieving 42.86% Top-1 accuracy on a 1-in-100 ranking task, well above chance, a blind control ablation with zeroed fMRI inputs yields near-identical scores, revealing that apparent decoding success is driven primarily by the frozen language prior rather than by neural input. These results demonstrate that high-capacity language models do not inherently improve fMRI decoding and can actively obscure failures without rigorous blind-control evaluation.

Decoding brain activity is useful for characterizing brain processes and understanding the functional architecture underlying cognition. However, the inter-individual variability in brain response patterns limits the development of decoders that generalize across individuals. A solution to this challenge is functional alignment: aligning functional data across individuals before training population-level decoders. The core issue is to strike the balance between aligning functional features and preserving the anatomical structure, while maintaining computational efficiency. We introduce a new functional alignment method for fMRI, SpectralOT, that embeds cortical geometry into Laplace-Beltrami eigenmodes along functional data to regularize the alignment.

While generative models enable encoding of complex neuroimaging data for feature generation and reconstruction, developing optimal architectural frameworks with appropriate encoding and latent space processes is crucial for studying structural and functional properties of the brain. We design a multimodal generative framework for structural and functional magnetic resonance imaging (MRI) features through systematic evaluation of encoding strategies, latent multimodal fusion, and generative model selection. Using structural gray matter volume (GMV) and static functional network connectivity (sFNC) features from a large neuroimaging dataset, we analyze generative frameworks involving variational autoencoders (VAEs), transformers, generative adversarial networks (GANs), and diffusion models. Architectures that employ modality-aware graph encoding of functional connectivity into a lower-dimensional latent space outperform vectorized encoders or direct data space approaches. The proposed multimodal graph VAE (gMMVAE) surpasses alternative generative variants across multiple metrics for generation fidelity, reconstruction quality, efficiency, and latent space discriminability, highlighting its potential for robust multimodal neuroimaging analysis.

Brain decoding aims to uncover neural mechanisms by inferring stimulus-related representations from brain signals. In fMRI studies, this is typically achieved by mapping fMRI responses to the latent representations of computational models. Recently, CLIP has become a popular choice for brain decoding due to its rich vision--language embedding space. However, aligning fMRI signals with CLIP representations remains challenging. As CLIP is not explicitly optimized for neural alignment, its representations may capture statistically predictive cues that are only partially reflected in brain activity, limiting decoding performance. In this paper, we investigate whether adversarially robust representations improve neural decoding with CLIP. Adversarial training suppresses non-robust features and promotes more stable, perceptually structured representations, which may better align with brain activity. We evaluate this by fixing the fMRI decoder and varying only the target representation (standard CLIP vs. robust variants) on fMRI-image retrieval and zero-shot classification tasks across NSD and GOD datasets. Empirical results show that this simple change consistently improves task performance and yields stronger alignment across multiple metrics. Attribution analysis further reveals consistently low agreement between standard CLIP and its robust variants, suggesting that adversarial robustness reorganizes feature importance in the visual representation. These findings suggest that the choice of target representation influences neural decoding performance and that adversarial robustness may serve as a useful criterion for brain decoding.

Pathologic complete response and tumor shrinkage measure whether breast cancer responds to neoadjuvant therapy, but not whether that response was structurally favorable, persistent, or hidden beneath volume loss. We built an outcome-blind longitudinal DCE-MRI manifold from I-SPY2 trajectories to test whether pretreatment imaging carries a structural response phenotype missed by conventional descriptors. The dominant axis of response geometry was not recoverable from the full clinical and genomic stack -- age, receptor subtype, MammaPrint, PAM50, treatment arm, and tumor burden -- but became strongly recoverable once baseline structural entropy was added. A constrained representation mapping recovered the same axes as unconstrained decomposition, establishing the structure as intrinsic rather than a post-hoc interpretation. The phenotype persisted through therapy, and as treatment proceeded the volumetric signal faded while entropy stayed separated -- a crossover from burden to structural persistence. Among complete responders, structurally disordered tumors could shrink more early yet remain structurally disordered, a volumetric deception invisible to endpoint labels. External analyses in UCSF, I-SPY1, and Duke established recurrence relevance under representation-dependent boundaries, and a representation-family commensurability assessment showed why feature-name matching is insufficient: the same label can fail, transport, or entangle with extraction geometry. Pretreatment MRI therefore exposes a structural response phenotype that endpoint-based language leaves invisible -- including, among complete responders, a pretreatment imaging signal of structurally distinct response states that awaits prospective validation.

Jointly learning to segment and classify medical images demands cross-task synergy, yet encoder-sharing architectures limit decoder reconstruction to task-private representations, permanently discarding the boundary cues and semantic priors each branch could supply to the other. This work introduces BTI-Net, which establishes bidirectional communication at every decoder level through two parallel pathways via Task Interaction Modules (TIM). Spatial boundary context is gated into the classification branch, while global semantic priors multiplicatively modulate the decoder, with refined features propagating progressively from coarse semantics to fine boundary detail across all four decoder resolutions. Since cross-task interaction is not equally reliable for every input, Uncertainty Proxy Attention (UPA) gates each TIM output per instance and per level using three signals that capture cross-task alignment, scene complexity, and prediction confidence, without external annotations or additional inference passes. Experiments on three medical benchmarks spanning ultrasound, dermoscopy, and brain MRI demonstrate consistent improvements in segmentation IoU and classification accuracy over both encoder-sharing and decoder-interaction baselines. Ablation confirms adaptive gating contributes +2.36 IoU over fixed bidirectional interaction, and classification accuracy improves by up to +2.26 points over the strongest multi-task baseline. UPA's uncertainty proxies serve as reliable single-pass task-failure signals without the overhead of stochastic sampling. Code: https://github.com/C-loud-Nine/BTI-Net_MTL

Introduction: Objective neuroimaging biomarkers may improve Parkinson's disease motor assessment by capturing brain variation not directly observable from clinical examination. We used interpretable machine learning to predict current motor severity, measured by MDS-UPDRS Part III, from QSM and multiband multi-echo resting-state fMRI-derived ReHo features. Methods: Regional QSM and ReHo features were extracted from 28 participants, including 24 individuals with Parkinson's disease and 4 controls. Thirteen feature-set experiments evaluated imaging-only, clinical-only, imaging-plus-clinical, full, reduced, and multimodal inputs. Support vector regression, Elastic Net, Random Forest, and XGBoost models were trained using nested cross-validation. Performance was assessed using pooled held-out R^2, RMSE, MAE, Pearson correlation, permutation testing, and the proportion of participants predicted within +/-5 MDS-UPDRS Part III points. Results: Imaging-only models carried meaningful predictive signal, whereas the clinical-only model performed weakly. Full fMRI, full QSM, and clinical variables provided the strongest global fit, explaining 45.4% of variance in motor severity. Selected QSM plus clinical variables produced the most clinically close predictions, with 75.0% of participants predicted within +/-5 points and the lowest MAE among top-performing models. SHAP highlighted cerebellar, thalamic, striatal, insular, and motor cortical features. Conclusion: QSM and multiband multi-echo fMRI-derived ReHo capture distinct, interpretable dimensions of Parkinson's disease motor severity. These findings show that structural and functional imaging contribute differently depending on the clinical prediction goal.

We study a quantum autoencoder (QAE) for compression-driven anomaly detection in brain MRI data. The approach leverages angle encoding to map image patches into quantum states, followed by a variational encoder-decoder architecture trained to discard information via auxiliary trash qubits. Anomaly scores reflect the degree to which inputs resist compression relative to normal data, with higher scores corresponding to deviations from the learned normal manifold. Evaluated on publicly available brain MRI DICOM datasets, the method achieves a slice-level ROC-AUC of approximately 0.95 and a patch-level ROC-AUC of approximately 0.813, outperforming classical autoencoder and PCA baselines. Analysis of the learned parameters reveals a pronounced encoder-decoder asymmetry, where effective anomaly detection arises from structured information compression within the encoder rather than increased parameter magnitude or decoder expressivity. This results in a controlled compression-reconstruction trade-off with a clear operating regime that supports principled threshold selection. Qualitative evaluation further shows that the QAE produces spatially localized anomaly heatmaps aligned with tumorous regions. The results, supported by promising baseline performances, demonstrate that quantum autoencoders provide an interpretable and controllable mechanism for anomaly detection based on incompressibility with respect to a learned latent representation. This work highlights the potential of quantum autoencoders as a principled tool for studying compression dynamics in quantum machine learning, with promising implications for decision support in medical imaging workflows.

Functional magnetic resonance imaging (fMRI) utilizes echo-planar imaging (EPI) to capture blood-oxygen-level-dependent (BOLD) signals with high temporal resolution. However, EPI is inherently sensitive to magnetic field inhomogeneities, resulting in susceptibility-induced geometric distortions along the phase-encoding (PE) direction. To correct these distortions, conventional approaches rely on additional calibration scans, such as field maps or reverse PE acquisitions, which are not always available in practice. To overcome this limitation, we propose SACRED, a calibration scan-free susceptibility distortion correction framework that corrects geometric distortions via image translation-based registration using only a routinely acquired anatomical T1-weighted (T1w) image and a unidirectional PE BOLD image. SACRED employs an invertible neural network as the image translation backbone to bridge the contrast gap between BOLD and T1w images while enforcing structural consistency through a modality independent neighborhood descriptor. This design enables the use of a mono-contrast similarity objective to train the registration network in an unsupervised manner without requiring distortion-corrected BOLD images. In addition, we incorporate test-time adaptation (TTA) to further enhance performance on out-of-distribution (OOD) data at inference time. SACRED was evaluated on one in-distribution (ID) dataset and two OOD datasets, and was compared with representative fMRI distortion correction methods. The results demonstrate that SACRED significantly outperforms competing methods on both ID and OOD datasets, exhibiting robustness to scanner and population shifts, partly enabled by TTA. The code will be made publicly available upon acceptance.

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.

Medical image classification is often constrained by limited labeled data, motivating generative augmentation; recently, quantum generative models have been proposed for this purpose, frequently reporting accuracy gains. However, such claims are typically based on single training runs, do not match the parameter budgets of the quantum and classical generators, and do not characterize the data regime in which any benefit appears. We present a controlled benchmark that isolates the contribution of a quantum generator to brain-MRI augmentation. Images are encoded into a KL-regularized latent space in which a conditional Wasserstein GAN with gradient penalty is trained using either a variational quantum generator or a classical generator of near-identical parameter count (1648 vs. 1632). Synthetic samples are decoded and used to augment a pretrained classifier across labeled data fractions from 5% to 100%, evaluated over eight random seeds with paired significance testing (with multiple-comparison correction) and with intraset diversity and latent-distribution analyses. Across all fractions, no augmentation variant significantly outperforms real-data-only training, and the quantum and classical generators are statistically indistinguishable. Any low-data benefit behaves as regularization rather than faithful data expansion:synthetic samples are off distribution and severely mode collapsed precisely where data is scarce, and the quantum generator is no more diverse thanits classical counterpart. We release the protocol as a testbed for rigorous evaluation of quantum generative augmentation in medical imaging.

Decoding inner speech from non-invasive brain signals remains a fundamental challenge due to the absence of overt linguistic output, limited training data, and large inter-subject variability. Existing brain-to-text approaches often rely on task-specific decoder fine-tuning, which restricts scalability and complicates adaptation to new participants. We propose MindAlign, a decoupled two-stage brain-to-language framework that enables open-ended text generation from fMRI signals without modifying the underlying language model. The first stage learns a subject-specific neural-semantic alignment that maps fMRI activity into a shared multimodal semantic space, extracting a latent semantic sketch of the internally generated sentence. The second stage integrates this sketch with visual context to prompt a frozen multimodal language model for free-form generation. Experiments on fMRI data collected during silent image description demonstrate that the proposed approach consistently outperforms fMRI-only and random baselines. We further show that the learned semantic-to-language projection can generalize across subjects, enabling effective decoding when paired with subject-specific neural alignment. These results indicate that neural signals modulate semantic content beyond image-driven priors, supporting a scalable and modular direction for brain-to-text decoding.

Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces, such as fMRI data on brain graphs, as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce topological flow matching, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a drop-in replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

We design a new unconstrained coordinate system where a $p\times p$ symmetric positive definite (SPD) matrix $Θ$ is represented by a reverse telescoping map $Θ(x)=\rm{RT}(x)$, with $x=(v,d,r)\in\mathbb{R}\times\mathbb{R}^{(p-1)}\times\mathbb{R}^{p(p-1)/2}$, representing respectively the log volume or log determinant; and the shape, as encoded by log relative diagonal scales and partial covariances among the nodes. This construction results in important properties not available in other charts, e.g., matrix logarithm, such as Jacobian depending on only the log-determinant. A useful feature of our construction is $x$ contains a lossless symbolic representation of both the matrix and its inverse. Many important computations involving a matrix and its inverse can be performed in $O(p^2)$ in the transformed domain, while it is the rendering of results in matrix forms (on demand) that must incur an $O(p^3)$ cost. Moreover, two unit-determinant matrices in the transformed domain can be joined by a straight line with pathwise unit determinant. For generative modeling, this allows designing a split volume-shape flow model trained by conditional flow matching for transporting the shape over the unit-determinant path, with a separate one-dimensional flow for transporting the volume or the determinant. The forbidding SPD constraint, tamed thus into a powerful guiding force, leads to the surprising insight that it is in some sense easier to design a volume-normalized shape flow for SPD compared to the unconstrained $\mathbb{R}^{p\times p}$, with no intrinsic notion of volume to aid normalization, unlike the determinant of SPD matrices. We apply our construction for up to $p=200$ in generative modeling of SPD matrices on a difficult synthetic bimodal target, and in generating brain connectivity networks by models trained on fMRI data; as well as in intrinsic diffusion on the SPD manifold.

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.

Large and demographically balanced datasets are essential for reliable neuroimaging biomarkers. Full-resolution 3D brain MRI synthesis can support data augmentation in this setting, but existing approaches either incur prohibitive computational cost at volumetric scale or rely on lossy latent compression that may compromise anatomical detail. As a result, practical 3D generative augmentation often requires specialized compute infrastructure. We propose WaveDiT, a conditional flow matching framework operating in the coefficient space of a 3D Haar Discrete Wavelet Transform. The model combines factorized spatio-depth attention with band-wise heteroscedastic uncertainty modeling derived from higher-order wavelet statistics. Predicted log-variance is integrated directly into both the flow objective and conditioning pathway, enabling adaptive precision consistent with the heavy-tailed and input-dependent variance structure of anatomical detail. This formulation supports full-resolution 3D synthesis under practical memory and time constraints on a single modern GPU. Evaluation on a multi-site cohort demonstrates improved alignment between generated and real MRI distributions, together with enhanced downstream brain age prediction and region-level anatomical agreement relative to diffusion, latent, and wavelet-based baselines. Code is available at https://github.com/sisinflab/WaveDiT

MRI preprocessing defines the input distribution seen by brain MRI foundation models, yet it is usually treated as routine data cleaning rather than a modeling choice. We ask how much preprocessing is worth its computational cost for self-supervised 3D MRI pretraining. Keeping the corpus, 3D ViT backbone, masking protocol, and downstream evaluations fixed, we compare a graded P0-P7 preprocessing spectrum for masked autoencoding (MAE) and joint-embedding predictive learning (JEPA) on 20,000 heterogeneous brain MRI volumes, then transfer the encoders to IDH prediction, MCI classification, brain age regression, and GLI/PED tumor segmentation. The results do not support a simple "more is better" rule. P0/P1 are numerically unstable, making P2 the lowest-cost feasible level; beyond P2, choosing the best feasible preprocessing level improves aggregate utility by only 3.4 percentage points for MAE and 1.8 percentage points for JEPA, with most paired gains statistically unresolved. Stronger preprocessing is beneficial only in selected regimes: IDH improves modestly, AGE and GLI/PED are often near or best at P2, and MCI shows the clearest empirical P7 gain. Cross-level MCI transfer further shows that much of the P7 advantage can be recovered by applying stronger preprocessing downstream, without requiring P7 throughout pretraining. These findings recast MRI preprocessing as a downstream-aware cost-utility decision rather than a default escalation pipeline. Code is available at https://github.com/PangJiangShuan/PreBrain.

Objectives: Automatic data extraction from free-text radiology reports enables large-scale research, but few studies assessed the performance of large language models (LLMs) on Dutch neuroradiology reports. Methods: We analyzed 947 brain MRI reports from a tertiary memory clinic (2016-2021), authored by consultant neuroradiologists. Trained medical students annotated thirty variables; 100 reports were double-annotated to assess inter-rater reliability. We evaluated the performance of the open-weight LLM LLaMA 3.1 using different languages (Dutch vs. English translation) and few-shot prompting with different example selection strategies. Performance was evaluated using balanced accuracy for categorical variables, accuracy and mean absolute error for counts, and text similarity for free-text. Metrics were computed across 10 random splits of the 947 reports. Results: LLaMA 3.1 demonstrated high zero-shot performance for visual rating scores (mean [95%-CI]): Medial Temporal Atrophy: 90% [77-100%] on the left and 96% [94-99%] on the right, Global Cortical Atrophy: 87% [83-91%], and Fazekas: 94% [93-96%]. Microbleed mentions were detected with 93% accuracy [92-95%] and infarct mentions with 82% [80-84%]. Text similarity for lesion location reached 0.95 [0.95-0.96]. Performance was lower for numerical variables: 80% [78-82%] for the number of microbleeds and 66% [63-68%] for infarcts. English translation yielded comparable results. Few-shot prompting improved performance for numerical variables, achieving 92% [90-93%] for microbleeds and 81% [77-85%] for infarcts using structural similarity-based selection. Conclusion: LLaMA 3.1 shows strong potential for extracting data from Dutch neuroradiology reports. Few-shot prompting enhances performance for numerical variables, whereas challenges remain for location-specific variables.

Brain decoding is limited by the availability of labeled neural data, and remains challenging in low-data regimes. To address this issue, we investigate whether and when brain decoding can be boosted by augmenting small fMRI datasets with synthetic data generated by a pretrained model of fMRI responses to stimuli. We use TRIBE v2, a large encoding model pretrained on more than 1000 hours of fMRI responses to video, audio and language. For each dataset, we evaluate systematic grids that show how the performance of image decoders varies with the amount of synthetic data used for training. Our results, based on two datasets (the 7T fMRI Natural Scenes Dataset and 3T fMRI BOLD5000), show up to 68% improvement in Top-10 image-retrieval accuracy compared to decoders trained only on real data. Importantly, the proportion of augmented data required to reach a given image decoding performance needs to be adjusted depending on the data source. Surprisingly, image decoders trained exclusively on synthetic fMRI can perform above chance in some settings, suggesting that TRIBE v2 can support zero-shot brain-to-image decoding. Together, these results show how large-scale models of the fMRI responses to sight, sound and language may provide a foundation to improve the data efficiency for image decoding.

Diffusion MRI (dMRI) tractography is the only noninvasive approach for mapping white-matter pathways in the living human brain. It represents each brain as a tractogram: a large, unordered set of three-dimensional streamlines that includes information about both local streamline geometry and whole-brain anatomical organization. This structure makes tractograms a natural but challenging target for representation learning. Existing methods treat streamline classification and subject-level prediction as separate problems: streamline classifiers focus on geometric patterns, whereas subject-level prediction often depends on hand-crafted features. As a result, current methods do not learn reusable representations that connect streamline anatomy with whole-brain inter-subject variation. Here we introduce TractFM, a tractogram foundation model that learns reusable representations directly from whole-brain streamline sets. TractFM combines a local streamline encoder with a permutation-equivariant tractogram encoder, allowing all streamlines from a subject to be contextualized jointly in a single forward pass. Pretraining on dense anatomical tract parcellation, i.e., assigning anatomical labels to individual streamlines, yields two complementary representations: contextualized streamline-level embeddings for tract parcellation and compact subject-level descriptors for downstream prediction of subject phenotypes. Across three tractography algorithms and five dMRI datasets, TractFM transfers to both streamline-level and subject-level tasks. Its frozen representations achieve accurate tract parcellation and predict age and sex across independent datasets. These results show that whole-brain geometric context, learned once, can generalize across tractography pipelines, datasets, and prediction tasks.

Understanding the relationship between deep visual representations and the human visual system is a fundamental challenge in computational neuroscience. While modern vision models achieve strong performance in image recognition, their correspondence with the hierarchical organization of the human visual cortex remains an open question. In this study, we propose CHASMBrain, a novel hierarchical two-stage framework for image-to-fMRI encoding. Our architecture leverages a dual-stream Mamba design to explicitly separate and process global semantic tokens and local spatial patches, motivated by the functional organization of the visual cortex. A coarse-to-fine strategy is employed: Stage 1 predicts denoised ROI-level activations, while Stage 2 refines these coarse responses into full voxel-level predictions using a Mamba-VAE. Experiments on the Natural Scenes Dataset (NSD) demonstrate that our method achieves a Pearson correlation of 0.429 and an MSE of 0.261, outperforming all evaluated baselines including ridge regression and DINOv2 linear probes. Beyond predictive performance, causal branch-ablation experiments reveal an asymmetric specialization: the patch stream is specifically locked to early visual cortex (retinotopic regions), while the CLS stream contributes broader semantic context to higher-order areas -- a correspondence that holds causally, not merely correlationally. Cross-subject transfer experiments further show that the learned backbone generalizes across individuals with minimal per-subject adaptation, suggesting the model captures a shared, subject-agnostic visual representation.

Brain foundation models (BFMs) are self-supervised Transformers pretrained on fMRI data. We posit that these models should capture each subject's cognitive performance from their fMRI signal. Yet across three state-of-the-art BFMs and every readout we test, they predict cognition worse than a linear regression from the $\sim$80K parameters of the functional connectivity matrix (FC). The gap widens with scale: BrainLM's 650M model predicts cognition worse than its 111M. We attribute this to a \textbf{variance allocation problem}: BFM pretraining captures the variance components that dominate fMRI but not the higher-order structure that predicts cognition. Our per-cumulant analysis of the reconstructed signal shows that the second-order covariance is partially preserved, while the third-order co-skewness tensor is largely destroyed. To recover what BFMs lose, we design a linear pipeline that projects the fMRI signal into the subspace that best preserves its co-skewness and computes FC there. This \textbf{exceeds raw FC and every pretrained BFM} on every dataset and parcellation we test, outperforming prior state-of-the-art under controlled evaluation \textbf{with no pretraining and no GPU}. We \textbf{recover the raw-FC ceiling on BrainLM's forward pass} by finetuning with a loss targeted at this same subspace. This shows that the bottleneck is the pretraining objective, not the architecture or the model size.

Recent progress in task-optimized neural networks has established encoding models as a powerful tool for predicting brain responses to naturalistic stimuli, yet most existing approaches rely on unimodal representations. The emergence of omni-modal foundation models and rich multimodal neural datasets enables encoding models that jointly integrate visual, auditory, and linguistic information across subjects. We introduce MIRAGE, a brain encoding framework for predicting whole-brain fMRI responses to naturalistic audiovisual stimuli. MIRAGE achieves state-of-the-art performance via a native multimodal backbone and adaptive feature gating across layers. These representations are then combined with a transformer-based brain encoder and a subject-specific linear head over the cortical parcels. Controlled comparisons show that natively multimodal features consistently outperform post-hoc aggregation of independent unimodal features, across architectural levels and backbones. Beyond predictive accuracy, the learned attention weights are directly inspectable to interpret the modality-specific gating profile over the backbone, and each modality traces a distinct anatomical pattern across cortex. Together, these results propose adaptive layer-wise aggregation of natively multimodal features as a generalizable, interpretable, and accurate approach for whole-brain encoding.

Functional Magnetic Resonance Imaging (fMRI) provides non-invasive access to dynamic brain activity by measuring blood oxygen level-dependent (BOLD) signals over time. However, the resource-intensive nature of fMRI acquisition limits the availability of high-fidelity samples required for data-driven brain analysis models. While modern generative models can synthesize fMRI data, they often remain challenging in replicating their inherent non-stationarity, intricate spatiotemporal dynamics, and physiological variations of raw BOLD signals. To address these challenges, we propose Dual-Spectral Flow Matching (DSFM), a novel fMRI generative framework that cascades dual frequency representation of BOLD signals with spectral flow matching. Specifically, our framework first converts BOLD signals into a wavelet decomposition map via a discrete wavelet transform (DWT) to capture globalized transient and multi-scale variations, and projects into the discrete cosine transform (DCT) space across brain regions and time to exploit localized energy compaction of low-frequency dominant BOLD coefficients. Subsequently, a spectral flow matching model is trained to generate class-conditioned cosine-frequency representation. The generated samples are reconstructed through inverse DCT and inverse DWT operations to recover physiologically plausible time-domain BOLD signals. This dual-transform approach imposes structured frequency priors and preserves key physiological brain dynamics. Ultimately, we demonstrate the efficacy of our approach through improved downstream fMRI-based brain network classification. The code is available at https://github.com/htew0001/DSFM.git .

Decoding visual content from fMRI signals recorded while a person views images, and specifically answering questions about the seen images, is a long-standing challenge. While significant progress has been made in recent years in visual question answering (VQA) from fMRI, performance remains limited. Moreover, although recent models can make increasingly accurate predictions, they have rarely been used as tools for understanding the structure of visual representations in the brain. We present Brain-IT-VQA, a framework for visual question answering from fMRI. Building on the Brain Interaction Transformer (Brain-IT), our method decodes language tokens from brain activity and integrates them with a language model to answer visual questions. Our model substantially outperforms previous fMRI-based captioning and VQA approaches. We further introduce NSD-VQA, a new dataset and benchmark for visual question answering from fMRI. Unlike existing image-fMRI VQA datasets, which typically provide only a few broad and weakly controlled questions per image, NSD-VQA provides on average 20 question-answer pairs per image across 20 controlled question categories that disentangle multiple levels of visual understanding. This enables more reliable and interpretable evaluation despite limited fMRI test data. Together, Brain-IT-VQA and NSD-VQA provide both a strong predictive framework and a tool for studying brain representations. Using this benchmark, we quantify which forms of visual and semantic information can be reliably decoded from fMRI responses to natural images. We further analyze the contributions of different brain regions across question types.

Functional magnetic resonance imaging (fMRI) is a powerful tool for investigating human brain function. However, the high cost of data acquisition and the inherent subjectivity of psychiatric rating scales often lead to datasets with small sample sizes and variable label quality, especially when targeting a specific neurological condition. Combined with the inherently high dimensionality of fMRI data, these limitations substantially increase the risk of model overfitting. Recent years have seen growing interest in developing fMRI foundation models by combining multiple datasets; however, the computational resources needed for pretraining and fine-tuning are often prohibitive. We show that a lightweight self-supervised framework yields representations that generalize across diverse downstream tasks, outperforming fully supervised baselines and approaching the performance of large-scale models. We introduce BrainSimSiam, a data-efficient self-supervised representation learning framework that leverages positive-only data pairs to learn robust and generalizable features. We demonstrate that the learned representations achieve strong performance across multiple downstream classification and regression tasks, highlighting the potential of BrainSimSiam for data-limited neuroimaging applications.

Task-based fMRI provides a direct readout of task-evoked neural dynamics, but it is expensive and difficult to acquire at scale, motivating rest-to-task synthesis from widely available resting-state fMRI (rsfMRI). We propose FM-fMRI, an event-conditioned flow-matching model that learns a continuous-time conditional vector field to generate task ROI time series from a subject's rsfMRI and the task event information. The formulation enables fast ODE-based sampling and flexible conditioning over heterogeneous event schedules. Rather than optimizing for pointwise reconstruction, we evaluated generated signals using complementary criteria that probe temporal and spectral structure, subject and group-level connectome consistency, and distributional alignment. On the public Human Connectome Project and internal BioPoint autism cohort, FM-fMRI achieves the strongest spectral and connectivity agreement and improved distribution-level matching over conditional diffusion, generative adversarial networks (GANs), and variational autoencoders (VAEs) baselines. Furthermore, we augment the BioPoint cohort by synthesizing task-fMRI ROI time series with our method, improving downstream autism classification and demonstrating practical utility in data-limited clinical settings. The code will be available on GitHub.

Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a Selective ROI Spherical Tokenizer (SRST) for efficient geometric encoding, and a Structure-Guided Mixture of Experts (SG-MoE) that explicitly models individual anatomy using cortical features. On the Natural Scenes Dataset, NeurIPS establishes a new state-of-the-art for surface decoders and achieves performance comparable to strong 1D baselines. This is achieved with unprecedented efficiency, as the model converges dramatically faster (10 vs. 600 epochs). This efficiency enables rapid adaptation to new subjects using only 20% of data and ensures robust scalability as the training cohort is expanded. Ablations provide causal evidence that these gains are driven by the model's use of cortical features, not by memorizing subject IDs. By leveraging anatomical priors, NeurIPS provides a principled and scalable path toward robust, generalizable brain decoding.

Diagnosing Major Depressive Disorder (MDD) from functional magnetic resonance imaging (fMRI) using functional connectivity (FC) analysis requires large amounts of labeled data that are scarce in clinical settings. Existing augmentation methods synthesize FC matrices, which compress fMRI recordings into static pairwise summaries and discard temporal information. We propose fMRI-Diffusion, a framework that synthesizes region-of-interest (ROI)-level fMRI time series rather than FC matrices. A Temporal Transformer serves as the denoising network within a denoising diffusion probabilistic model, treating each time point as a token to capture temporal dependencies through self-attention. A supervised pretraining strategy initializes the Transformer with task-relevant representations before diffusion training, and FC matrices are derived from the synthesized time series for classification. Experiments on the REST-meta-MDD dataset show that augmenting training data with synthetic time series consistently improves diagnostic accuracy across ten classifiers, six parcellation atlases, and three acquisition sites. The method outperforms five recent FC-based synthesis approaches, with accuracy gains of up to 3.7 percentage points over the strongest baseline. Ablation studies confirm the contributions of both the Transformer-based denoiser and the pretraining strategy. Distributional fidelity metrics remain below 0.06 across all conditions, indicating close agreement between real and synthetic distributions. These findings suggest that synthesizing fMRI time series before FC computation preserves temporal information lost in matrix-level augmentation and provides a practical strategy for MDD diagnosis under limited data.

Generative augmentation is often proposed as a remedy for small medical-image datasets, but synthetic images are only useful when they improve downstream task performance. "Augmentation" here means synthetic supplementation: GAN-generated samples added to the real training pool, not geometric or photometric transforms of existing images. Twelve class-plane StyleGAN2-ADA generators were trained on constrained BRISC 2025 partitions to test whether their output, with or without InceptionV3 feature-space filtering, improves held-out tumour classification across three classifier families: a random forest (RF) on InceptionV3 features, a compact two-headed convolutional neural network (CNN), and MobileViTV2, a mobile hybrid convolutional-transformer. Each was evaluated at 1:1 and 1:2 real-to-synthetic ratios. An independent GPT-5.5 blind test placed gated real-versus-synthetic discrimination at 57.73% (95% CI: 54.48--60.92%) on the model-legible subset -- modestly above chance. The RF classifier did not benefit from the synthetic MRIs. The CNN showed consistent mean gains that did not survive Holm correction. MobileViTV2 showed the clearest benefit: filtered 1:1 augmentation improved tumour classification accuracy by 1.02% absolute (95% CI: 0.54--1.54%; Holm-corrected p = 0.0104). A secondary efficiency analysis found that every augmented CNN condition selected its checkpoint 42--64% earlier than baseline, while compute-matched MobileViTV2 runs reached selection after 50--67% fewer real-data epochs. Overall, augmentation utility was found to be architecture- and ratio-dependent, not guaranteed by visual fidelity alone.

Magnetic resonance imaging (MRI) is highly susceptible to patient motion due to its relatively long acquisition times and the fact that data are acquired sequentially in k-space. Even small patient movements introduce phase inconsistencies across measurements, leading to severe artifacts such as blurring, ghosting, and geometric distortions that can compromise diagnostic quality. Retrospective motion compensation remains challenging, particularly in accelerated acquisitions, due to the ill-posed nature of the joint reconstruction and motion estimation problem. In this work, we propose a unified Bayesian framework for motion-compensated 3D MRI that jointly estimates the anatomical image, rigid-body motion parameters, and coil sensitivity maps directly from motion-corrupted k-space data. Our approach integrates pretrained 3D complex-valued score-based diffusion models as expressive anatomical image priors within a physics-based forward model. Inference is performed by alternating diffusion posterior image updates with efficient proximal optimization steps for motion and coil sensitivity estimation, enabling fully unsupervised reconstruction without the need for paired motion-free training data. Experiments on simulated and real-motion brain MRI datasets demonstrate that the proposed method achieves improved image quality and motion robustness compared to state-of-the-art classical and learning-based motion correction techniques, particularly in the presence of severe motion and high acceleration.

Dictionary learning is a powerful tool for creating interpretable representations. When applied to functional magnetic resonance imaging (fMRI) data, the resulting patterns of brain activity can be used for various downstream tasks, such as brain state classification or population-level analysis. However, a major challenge is the variability in brain geometry across individuals. This is usually addressed by projecting each individual brain geometry onto a common template, which removes subject-specific information. In this work, we introduce a novel approach to dictionary learning on fMRI data that explicitly accounts for this variability. We use the optimal transport-based Fused Gromov-Wasserstein (FGW) distance to compare graphs with different geometries and features. To address the challenge of computing multiple FGW distances for large graphs such as those arising from fMRI data, we rely on amortized optimization to learn a neural network that predicts an approximation of the optimal transport plans, which substantially reduces the computational cost. Additionally, we learn dictionary atoms that depend on the FGW trade-off parameter, which controls the balance between feature alignment and structural consistency. Numerical experiments on the HCP dataset demonstrate that the proposed approach captures different levels of geometric variability in the data and provides representations that preserve essential information.

The Strong Platonic Representation Hypothesis suggests that representational convergence in artificial neural networks can be harnessed constructively: embeddings can be translated across models through a universal latent space without paired data. We ask whether an analogous geometry can be recovered across human brains. Using fMRI data from the Natural Scenes Dataset, we propose a self-supervised encoder that learns subject-specific embeddings from brain data alone by exploiting repeated stimulus presentations. We show that these independently learned spaces can be translated across subjects using unsupervised orthogonal rotations, without paired cross-subject samples or intermediate model representations. Synchronizing pairwise rotations into a single shared latent space further improves cross-subject retrieval, indicating that subject-specific spaces are mutually compatible with a common coordinate system. These results provide evidence for a shared neural geometry in the human visual cortex: subject-specific fMRI representations are approximately isometric across individuals and can be translated through purely geometric transformations.

Functional MRI data exhibit high-dimensional spatiotemporal structure, making both prediction and decoding challenging. In this work, we investigate neural integral-operator-based models for encoding and decoding tasks in fMRI, with particular emphasis on the role of nonlocal spatiotemporal context. We implement a latent neural integral operator framework that performs fixed point iterations in an auxiliary space from which classification and stimuli prediction is performed via a decoder. We evaluate our model on two open-source fMRI datasets. Our experiments examine both decoding of stimuli from fMRI recordings and encoding of fMRI dynamics from stimulus representations. A main focus is the effect of spatiotemporal context: we systematically compare short and long temporal windows, as well as the use of visual cortex vs whole brain recordings, and analyze their influence on performance and latent-space geometry. Across tasks and datasets, larger temporal windows generally improve results and produce more structured learned representations. In decoding experiments, the learned latent space often provides clearer class separation than the raw data. In encoding experiments, although absolute performance remains moderate due to the difficulty of the task, longer temporal windows still yield consistent gains. These findings suggest that neural integral operators provide a promising framework for modeling fMRI dynamics and that broader spatiotemporal context can be beneficial for both prediction and representation learning. More broadly, the results indicate that exploiting distributed nonlocal structure in brain dynamics requires model architectures specifically designed to capture such dependencies.

Visual image reconstruction from functional Magnetic Resonance Imaging (fMRI) is a fundamental task in brain decoding, providing a crucial pathway for understanding human perceptual mechanisms and developing advanced brain-computer interfaces (BCIs). However, most current methods simply flatten fMRI signals from localized visual cortices into one-dimensional (1D) vectors, mapping them directly into latent spaces such as that of Contrastive Language-Image Pre-training (CLIP). This paradigm not only disrupts the inherent network topology of the brain-leading to limited neuroscientific interpretability-but also overlooks the synergistic contributions of other distributed functional networks in processing high-level visual semantics. To address these limitations, we propose FPED, a Functional-Network Prior-Guided Mixture of Experts (MoE) framework for interpretable brain decoding. FPED explicitly models different functional brain networks as specialized experts and employs adaptive routing to capture their complementary contributions to visual semantic understanding. Unlike conventional homogeneous decoding paradigms, our framework incorporates neurobiologically grounded priors to enable structured and interpretable network-level representation learning. Experimental results demonstrate that FPED achieves highly competitive semantic reconstruction performance with only 0.68B parameters. The learned routing dynamics reveal biologically meaningful correspondence between functional brain networks and modality-specific semantic processing, providing transparent neuroscientific interpretability. This suggests that brain network-aware expert modeling is a promising direction for bridging neural decoding and biologically inspired artificial intelligence.

Neuroscientists have recently turned to intracranial brain recording methods, like electrocorticography (ECoG), for human experiments because of the fine spatial and temporal resolution that they afford. Models trained on this data, however, are fundamentally restricted by the patient populations that can receive the implants necessary for recording. We propose using non-invasive fMRI to bridge the gap in training data. Using spoken language representations fine-tuned on fMRI, we build encoding models of ECoG. These representations showed improved prediction performance in ECoG, even though the temporal resolution of fMRI is two orders of magnitude worse. Prediction improved in frequency bands well beyond what is directly measured in fMRI. Next, to test the procedure's generalization ability, we fine-tuned models on fMRI responses that were temporally downsampled by a factor of 2. Despite the loss in resolution, these models were able to predict fMRI and ECoG responses at levels comparable to the original fMRI-tuned models. Finally, we showed that ECoG performance steadily scales with the amount of fMRI-tuning data. Our results show that "slow" data like fMRI can be a valuable resource for building better models of "fast" brain data like ECoG. In the future, integrating across multiple recording methods may further improve performance in other applications, like decoding.