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NeuroImage

Elsevier BV

Preprints posted in the last 30 days, ranked by how well they match NeuroImage's content profile, based on 813 papers previously published here. The average preprint has a 0.42% match score for this journal, so anything above that is already an above-average fit.

1
Rapid cortical mapping with cross-participant encoding models

Tang, J.; Huth, A. G.

2026-03-27 neuroscience 10.64898/2026.03.26.714320 medRxiv
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Voxelwise encoding models trained on functional MRI data can produce detailed maps of cortical organization. However, voxelwise encoding models must be trained on many hours of brain responses from each participant, limiting clinical applications. In this study, we introduce a cross-participant modeling framework for rapid cortical mapping. In this framework, voxelwise encoding models are trained on many hours of brain responses from previously scanned reference participants, and then transferred to a new participant by aligning brain responses using a small set of stimuli. We evaluated cross-participant encoding models on linguistic semantic mapping, non-linguistic semantic mapping, and auditory mapping. In each case we found that cross-participant encoding models had more accurate selectivity estimates and prediction performance than within-participant encoding models trained on the same amount of data from the new participant. We also found that cross-participant encoding models improved with the amount of data from each reference participant and the number of reference participants. These results demonstrate that cross-participant modeling can substantially reduce the amount of data required for accurate cortical mapping, which may facilitate new clinical applications of functional neuroimaging.

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The Incremental Cluster Threshold-Free Cluster Enhancement Algorithm for Functional Connectivity Analysis

Cravo, F.; Rodriguez, R.; Nieto-Castanon, A.; Noble, S.

2026-04-09 neuroscience 10.64898/2026.04.06.716826 medRxiv
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Threshold-free cluster enhancement (TFCE) is one of the most used statistical inference methods in neuroimaging, but its computational cost limits some of its applications. The current implementations recompute clusters at each threshold step, creating computation costs that poorly scale with precision increases. Furthermore, as larger samples and reduced noise increase maximum t-statistics, computational burden grows correspondingly. As the field moves towards finer parcellations, the number of FC edges grows quadratically with the number of ROIs, making TFCE computationally infeasible at the scales increasingly demanded by the field. We present Incremental Cluster TFCE (IC-TFCE), an algorithm that produces numerically equivalent results to standard TFCE while decoupling runtime from discretization precision. The IC-TFCE builds clusters incrementally from previous threshold steps rather than recomputing them, stores TFCE results on a region of interest (ROI) based structure instead of a functional connectivity (FC) edge structure for improved speed, and can be applied to voxel data through a novel graph transformation described and validated herein. This algorithm achieves a measured 3-93x speedup for FC TFCE depending on the precision parameter $dh$, making TFCE analyses with fine parcellations of 1000 or more ROIs computationally tractable for the first time. Finally, we validate correctness through mathematical proof and numerical comparison. The efficiency provided by IC-TFCE allowed a large-scale empirical power analysis across $dh$ values to guide practitioners in parameter selection for their analyses.

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Bridging Higher-Order Information Theory and Neuroimaging: A Voxel-Wise O-Information Framework

Camino-Pontes, B.; Jimenez-Marin, A.; Tellaetxe-Elorriaga, I.; Erramuzpe Aliaga, A.; Diez, I.; Bonifazi, P.; Gatica, M.; Rosas, F. E.; Marinazzo, D.; Stramaglia, S.; Cortes, J.

2026-04-08 neuroscience 10.64898/2026.04.06.716652 medRxiv
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The brains functional organization has been extensively studied through pairwise connectivity analyses. While these approaches have provided important insights into brain network organization, they fall short in capturing the complexity of high-order functional interactions (HOI). Particularly relevant is the investigation of redundancy and synergy patterns -not addressable with pairwise interactions-, revealing fundamental mechanisms of brain integration and information processing across various cognitive functions and clinical conditions. Conventional neuroimaging software packages are primarily designed for classical (general linear model-like) analyses but lack native support for HOI metrics. To address this gap, this study introduces a novel framework that bridges high-order information theory with conventional neuroimaging analysis pipelines and is subsequently applied to resting-state functional MRI to demonstrate its practical utility. By representing HOI into voxel-level metrics, our approach allows standard neuroimaging analyses to probe complex multivariate dependencies. Moreover, voxel-level group-comparison analyses show age differences linked with reduced redundancy in default mode network interactions. These findings advance our understanding of the complex relationship between multivariate functional interactions, voxel-level neuroimaging, and behavior, highlighting novel analytic strategies to study high-order information processing underlying cognitive function and its alterations in pathological conditions.

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Bridging the gap with invasive imaging: promises and challenges of a new generation of ultrahigh resolution fMRI

Knudsen, L.; Lazarova, Y.; Moeller, S.; Nothnagel, N.; Faes, L. K.; Yacoub, E.; Ugurbil, K.; Vizioli, L.

2026-04-14 neuroscience 10.64898/2026.04.10.717824 medRxiv
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The human neocortex is organized into six laminae forming the structural basis for feedforward and feedback connections across the brain, yet their functional contributions have remained largely inaccessible for non-invasive imaging methods. Leveraging the ultrahigh field of a 10.5 Tesla scanner, we acquired anatomical and functional MRI data at 0.37mm ([~]0.05 {micro}L) and 0.35mm ([~]0.04 {micro}L) isotropic resolution, respectively, approaching the scale of individual cortical layers in humans. Using the Stria of Gennari as an in-vivo anatomical landmark, we extend our previous finding that feedforward visual activation in layer IV of the primary visual cortex during visual stimulation was resolved in laminar BOLD profiles. These laminar features were reproducible across sessions and were not clearly visible with more typical 0.8 mm resolutions at 7T, underscoring the benefits of further increases in magnetic field strength and resolution. This imaging domain, however, comes with increasing challenges of distortion, alignment, and cortical depth estimation, which must be addressed and mitigated to realize its benefits. In this paper we discuss the promises and challenges of this new regime of high resolutions. Our findings showcase the potential of ultrahigh field, ultrahigh resolution human fMRI to bridge the gap with invasive imaging of cortical layers.

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Reproducibility of Diffusion, Shape, and Connectivity Metrics Across Scanners: Implications for Multi-Site Tractography

Anand, S.; Yeh, F.-c.; Venkadesh, S.

2026-04-20 neuroscience 10.64898/2026.04.15.718542 medRxiv
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Multi-site diffusion MRI studies face scanner-induced variability that can obscure biological signal. Harmonization methods such as ComBat have been developed to address this, but have been evaluated primarily on diffusion scalar metrics. Whether scanner reproducibility differs across fundamentally distinct tract-derived representations has not been systematically compared. Here, we compared the reproducibility of three metric families (diffusion, shape, and connectivity) across 36 association tracts using the MASiVar dataset (5 subjects, 4 scanners, 27 sessions). We assessed intraclass correlation coefficients (ICC) and multivariate subject discrimination at baseline, under dimensionality reduction, and after ComBat harmonization. At baseline, shape metrics showed the highest reproducibility (median ICC 0.69), followed by connectivity (0.49) and diffusion (0.34). Shape and connectivity achieved comparable subject discrimination (both 1.75), significantly exceeding diffusion (1.23). ComBat harmonization improved all families but harmonized diffusion (0.58) remained below unharmonized shape (0.69), indicating that metric family selection remains consequential even after harmonization. Under low-dimensional representation, connectivity showed the largest gains (ICC 0.86, subject discrimination 3.0), exceeding other families at any dimensionality. Analysis of principal component loadings identified a small number of cortical regions per tract (median 6) that capture 95% of the reproducible connectivity signal, providing a per-tract reference for selecting the most informative regions in future multi-site studies. These findings indicate that the choice of which tract-derived metrics to analyze in multi-site studies deserves at least as much consideration as how to harmonize them.

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Latent Gaussian Process Modeling for Dynamic PET Data: A Hierarchical Extension of the Simplified Reference Tissue Model

Vegelius, J.

2026-04-16 neuroscience 10.64898/2026.04.11.717906 medRxiv
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Dynamic positron emission tomography (PET) provides a powerful tool for studying in vivo neurochemical processes, including transient neurotransmitter release. However, widely used models such as the simplified reference tissue model (SRTM) assume time-invariant kinetic parameters, limiting their ability to capture dynamic changes in binding. Existing extensions introduce time-varying effects through parametric response functions or basis expansions, but are often constrained by restrictive functional assumptions, computational complexity, or limited uncertainty quantification. We propose a latent Gaussian process extension of SRTM (LGPE-SRTM), in which the apparent efflux parameter is modeled as a smooth, time-varying function within a hierarchical framework. By applying a first-order implicit discretization of the governing differential equation, the model admits a representation that is linear in all kinetic parameters in the mean structure, while nonlinearity is confined to a parameter-dependent covariance. This yields a conditionally linear mixed-effects model with structured covariance, enabling efficient likelihood-based inference. The proposed approach integrates mechanistic modeling, nonparametric flexibility, and hierarchical inference in a unified and computationally scalable framework. By representing functional effects on a shared temporal domain, all core computations reduce to operations on low-dimensional matrices whose size is independent of the number of subjects. This enables robust population-level inference on timevarying neurotransmitter dynamics without imposing restrictive parametric forms. The method is demonstrated on both simulated and empirical PET data, where it accurately recovers transient effects, provides well-calibrated uncertainty, and distinguishes constant from time-varying dynamics.

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Robust MR-AIV: A Systematic Study of Robustness Improvement and Sensitivity Analysis of MR-AIV

Vaezi, M.; Diego Toscano, J.; Guo, Y.; Stefan Gomolka, R.; Em. Karniadakis, G.; H. Kelley, D.; A. S. Boster, K.

2026-04-17 neuroscience 10.64898/2026.04.14.718498 medRxiv
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AO_SCPLOWBSTRACTC_SCPLOWCerebrospinal and interstitial fluid transport play a central role in brain metabolic waste clearance, yet non-invasive quantification of deep-brain flow dynamics remains challenging. Magnetic Resonance Artificial Intelligence Velocimetry (MR-AIV) is a physics-informed neural network framework that infers three-dimensional velocity, pressure, and permeability fields from dynamic contrastenhanced MRI by embedding porous-media flow physics into the learning process. Here, we present a methodological refinement and systematic evaluation of MR-AIV. We introduce a universal, anatomically informed, region-of-interest-based permeability initialization that improves anatomical alignment and physical consistency across subjects. We quantify the sensitivity of inferred fields to key modelling choices, including initialization strategies, permeability bounds, diffusivity assumptions, signal-concentration relationships, and measurement noise. Across these conditions, MR-AIV yields stable velocity and permeability estimates with preserved spatial structure. Together, these results establish practical guidelines and identify stable operating regimes for reliable deployment of MR-AIV. By improving robustness and reproducibility, this work strengthens MR-AIV as a minimally invasive approach for mapping brain-wide porous fluid transport and supports its application to studies of neurological health and disease.

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Encoder-based Curvature-Aware Regularization for estimating asymmetric fiber orientation distribution functions in diffusion MRI

Taherkhani, M.; Pizzolato, M.; Morup, M.; Dyrby, T. B.

2026-04-02 neuroscience 10.64898/2026.03.31.715534 medRxiv
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Diffusion-weighted magnetic resonance imaging (dMRI) is used to study white matter microstructure and to delineate pathways by estimating fiber orientation distributions (FODs). Symmetric FODs represent the conventional model assuming antipodal symmetry in water diffusion. However, in complex regions with bending, branching or fanning fibers, this assumption is not guaranteed. To better capture such underlying fibers geometries, asymmetric FODs (A-FODs), derived from neighboring FODs, have been introduced. Here, we propose an Encoder-based Curvature-Aware Regularization (EnCAR) method for estimating A-FODs. Incorporating curvature features into the regularization weight applied to neighboring voxels improves reconstruction of A-FODs. A self-supervised Transformer network, combined with a Spherical Harmonics Semantic Encoder, learns region-specific regularization parameters from this local neighborhood to capture the diversity of fiber geometries across the brain. The EnCAR method was verified on the DiSCo challenge phantom, and applied to in vivo multi-shell Human data. The model estimated sharp, high-angular-resolution A-FODs that were well aligned with local fiber pathway. Compared with established FOD and A-FOD methods, it performed on par in regions dominated by symmetric FODs and outperformed them in complex asymmetric regions. Quantitative evaluation using the Asymmetry Index (ASI) and Model Discrepancy Index (MDI) confirmed improved consistency with the underlying diffusion signals. By ensuring smooth directional transitions, this work enhances the visibility of continuous fiber segments.

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System identification and surrogate data analyses imply approximate Gaussianity and non-stationarity of resting-brain dynamics

Matsui, T.; Li, R.; Masaoka, K.; Jimura, K.

2026-03-28 neuroscience 10.64898/2026.03.25.714361 medRxiv
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Compared with model-based and phenomenological descriptions of the spatiotemporal dynamics of resting-brain activity, statistical characterizations of resting-state fMRI (rs-fMRI) data remain relatively underexplored. Some sophisticated analysis techniques, such as Mapper-based topological data analysis (TDA) and innovation-driven coactivation pattern analysis (iCAP), can distinguish real data from phase-randomized (PR) surrogates, suggesting that rs-fMRI data are not as simple as stationary Gaussian processes. However, the exact statistical properties that distinguish real rs-fMRI data from PR surrogates have not yet been determined. In this study, we conducted system identification analysis and surrogate data analysis to specify key statistical properties that allow TDA and iCAP to discriminate real rs-fMRI data from PR surrogates. We first analyzed rs-fMRI data concatenated across scans using autoregressive (AR) modeling and found that the scan-concatenated rs-fMRI data were weakly non-Gaussian. However, non-Gaussianity alone was insufficient to reproduce realistic TDA and iCAP results because of non-stationarity across scans. AR modeling of single-scan data revealed that rs-fMRI data were statistically indistinguishable from a Gaussian distribution within a single scan, although TDA and iCAP results still differed between the real data and PR surrogates. A new surrogate dataset designed to preserve non-stationarity successfully reproduced realistic TDA and iCAP results, suggesting that TDA and iCAP likely capture the non-stationarity of rs-fMRI data to distinguish it from PR surrogates. Together, these results indicate approximate Gaussianity and non-stationarity in rs-fMRI data, providing a data-driven and statistical characterization of resting-state brain activity that can serve as a quantitative reference for whole brain simulations and generative models.

10
Global Signal Removal (GSR) as graph spatial filtering

Arab, F.; Sipes, B. S.; Nagarajan, S. S.; Raj, A.

2026-04-09 neuroscience 10.64898/2026.04.06.716832 medRxiv
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Global Signal Removal (GSR) is a widely applied step in functional magnetic resonance imaging (fMRI) preprocessing. Although GSR conventionally denotes Global Signal Regression, we use Global Signal Removal to encompass a broader family of spatial filtering operations. GSR in general remains controversial due to concerns about introducing spurious anticorrelations and removing neurally meaningful signals. In this paper, we provide a precise geometric characterization by formalizing GSR as graph spatial filtering. We demonstrate that the most common form of GSR, Regression-GSR, equates to a rank-1 deflation of the covariance matrix (i.e. functional connectivity) by the degree vector. Empirically, the degree vector is dominated by the first principal component of the functional connectivity matrix (correlation = 0.88 {+/-} 0.12 in resting-state HCP data), making Regression-GSR an approximation to first eigenmode removal. This view of GSR as a spatial projection framework allows us to develop a family of GSR variants, each expressible in a unified spatial filter: Naive-GSR removes the uniform vector, PCA-GSR precisely removes the first eigenvector, and SC-GSR, a new variant we introduce that removes the first harmonic of the structural connectivity matrix. A key distinction emerges: while Naive, PCA, and SC-GSR are orthogonal projections, Regression-GSR is an oblique projection that computes regional weights proportional to the degree vector but removes a spatially uniform signal. All GSR variants induce numerical singularity in the covariance matrix, but they differ in their effects on task-state separability, which we examine empirically. In summary, we reframe GSR as a family of graph spatial filters that enable interpretability of its effects, with systematically varying effects on network connectivity across variants.

11
Towards patient-specific biomechanical human brain models

Tueni, N.; Rauh, B.; Hinrichsen, J.; Rampp, S.; Doerfler, A.; Budday, S.

2026-04-17 neuroscience 10.64898/2026.04.16.718870 medRxiv
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Reliable characterization of spatial variations in brain tissue stiffness is essential for predictive biomechanical modeling, yet most current methods rely on coarse regional parameter assignments based on invasive mechanical testing. In this study, we propose a new approach to obtain subject-specific mechanical properties at voxel resolution from in vivo diffusion tensor magnetic resonance imaging (DTI) based on a linear regression between the fractional anisotropy (FA) from DTI and experimentally measured stiffness values. To assess how such heterogeneity in mechanical properties influences simulated brain deformation, we construct a finite element model based on two material parameterizations of the same human brain: one employing nine anatomically defined regions, each with uniform material parameters, and another in which the shear modulus is assigned voxel-wise on the corresponding FA value. Applying this FA-stiffness mapping yields a smoothly varying mechanical property distribution that better captures local microstructural differences not represented by region-wise parameterizations. Both parameterizations are subjected to an identical atrophy-driven loading scenario. They exhibit comparable overall volume loss, but diverge in regional behavior. The voxel-resolved parameterization predicts more pronounced ventricular expansion and differs in the displacement and stretch distributions, indicating that variability in stiffness can alter local predicted responses even when global outcomes appear similar. This work presents a pipeline for estimating individualized mechanical properties directly from imaging protocols that are routinely performed on patients, with important implications for brain biomechanics. While the approach depends on a simplified linear FA-stiffness relation and assumes isotropic constitutive behavior, it provides a framework for integrating imaging-based microstructure into subject-specific simulations. Future validation against in vivo or experimental deformation data is needed to determine the fidelity and clinical utility of FA-derived stiffness fields.

12
Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference for diffusion MRI in the human brain

Wanjau, E.; Chourrout, M.; Maffei, C.; Balbastre, Y.; Keenlyside, A.; Brunet, J.; Sharma, A.; Huang, S. Y.; Tafforeau, P.; Fischl, B.; Yendiki, A.; Lee, P. D.; Walsh, C.

2026-04-06 neuroscience 10.64898/2026.04.02.715729 medRxiv
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Diffusion MRI (dMRI) allows us to image the human connectome non-invasively, yet it provides indirect estimates of axonal orientations based on the diffusion of water molecules in millimeter-scale voxels, hence struggling to resolve complex micrometer-scale fiber geometries. Invasive methods for imaging axonal orientations ex vivo, e.g. histology, are destructive and limited to small volumes, creating a critical need for a non-destructive modality for imaging microscopic fiber orientations in 3D. Here, we use Hierarchical Phase-Contrast Tomography (HiP-CT) to characterize white matter architecture at the microscale. Applying structure-tensor analysis to HiP-CT data, we compute fiber Orientation Distribution Functions and perform tractography analogous to dMRI. Across multiple brain regions, HiP-CT derived fiber architecture shows strong correspondence with that derived from dMRI while revealing substantially greater microstructural complexity. Despite its label-free nature, we demonstrate that vascular structures minimally confound HiP-CT orientation estimates. These results establish HiP-CT as a reference microscopic modality that can complement dMRI in multi-scale studies of white-matter organization.

13
Bi-cross-validation: a data-driven method to evaluate dynamic functional connectivity models in fMRI

Wei, Y.; Smith, S. M.; Gohil, C.; Huang, R.; Griffin, B.; Cho, S.; Adaszewski, S.; Fraessle, S.; Woolrich, M. W.; Farahibozorg, S.-R.

2026-04-06 neuroscience 10.64898/2026.04.02.716067 medRxiv
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Dynamic functional connectivity (dFC) models have become increasingly popular over the past decade for characterising time-varying interactions between brain regions. However, assessing and comparing dFC models remains challenging. Here, we introduce bi-cross-validation as a general framework for evaluating dFC models and selecting key hyperparameters, such as the number of states. By jointly partitioning the data across subjects and brain regions, bi-cross-validation enables out-of-sample evaluation without re-estimating latent states on the same data used for testing, thereby avoiding circularity. Using simulated data with known ground-truth dynamics, we show that bi-cross-validation favours models that accurately capture the underlying state structure. Applying the framework to real resting-state fMRI data, we demonstrate that bi-cross-validation naturally balances goodness-of-fit against model complexity, with performance improving and then declining as model complexity increases. Finally, we use bi-cross-validation to directly compare static and dynamic FC models, showing that dynamic models underperform static models at low spatial dimensionality, but outperform static models at sufficiently high dimensionality. Together, these results establish bi-cross-validation as a principled tool for dFC model selection, evaluation, and comparison.

14
Psilocybin acutely reduces low-frequency BOLD power and frequency-specific connectivity

Olsen, A. S.; Larsen, K.; McCulloch, D. E.-W.; Ganz, M.; Madsen, M. K.; Ozenne, B.; Knudsen, G. M.; Rehman, N. u.; Fisher, P. M.

2026-04-13 neuroscience 10.64898/2026.04.09.717379 medRxiv
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Psilocybin and other serotonergic drugs acutely alter human brain function and large-scale connectivity as measured with BOLD fMRI, but whether these effects are frequency-specific remains unknown. We applied multitaper spectral and cross-spectral analyses to resting-state fMRI data from 28 healthy volunteers scanned multiple times acutely following oral psilocybin administration (0.2 - 0.3 mg/kg), together with plasma psilocin measurements, to estimate psilocin associations with temporal frequency-specific activity and connectivity. Psilocybin produced a selective reduction in low-frequency spectral power (0.01 - 0.06Hz) and an increase in spectral entropy, with the strongest effects in transmodal networks. We also observed a reduction in low-frequency connectivity energy explained by the unimodal/transmodal axis. These findings demonstrate that psilocin induces spatially distributed, frequency-dependent alterations, suggesting that broadband fMRI analyses may obscure low-frequency dynamics. Frequency-resolved approaches may offer greater sensitivity for characterizing psychedelic effects on brain activity.

15
Estimating Visual Receptive Fields from EEG

Huang, C.; Shi, N.; Wang, Y.; Gao, X.

2026-04-15 neuroscience 10.64898/2026.04.13.718144 medRxiv
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The visual receptive field (RF) characterizes the spatiotemporal properties of the visual pathway and serves as a fundamental unit for information encoding. While RFs have been extensively studied across various neural modalities, such as functional Magnetic Resonance Imaging (fMRI), Electrocorticography (ECoG), and Magnetoencephalography (MEG), their investigation via Electroencephalography (EEG) remains limited. In this study, we introduce a stimulation paradigm that combines white noise image sequences with a letter detection task to elicit central visual field EEG responses. Using the aligned/shuffled reverse correlation, we estimate RFs across different resolutions and demonstrate that the resulting RFs exhibit rich spatiotemporal characteristics. To validate the reliability of the estimated RFs, we constructed a visual EEG reconstruction model, which achieved good performance in a classification task. The same RF estimation method was subsequently applied to high-density EEG recordings to investigate the information gain afforded by high-density configurations in visual space. This work fills a gap in the study of visual RFs regarding the EEG modality and may inform the paradigm design of visual brain-computer interfaces.

16
Assessment of Coupled Phase Oscillators-Based Modeling in Swine Brain Connectome

Ahmed, I.; Laballe, M. H.; Taber, M. F.; Sneed, S. E.; Kaiser, E. E.; West, F. D.; Wu, T.; Zhao, Q.

2026-04-01 neuroscience 10.64898/2026.03.27.713751 medRxiv
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Linking structural connectivity (SC) to functional connectivity (FC) through mechanistic models remains challenging in network neuroscience. In this study, empirical data of diffusion magnetic resonance imaging (dMRI) and resting-state functional MRI (rs-fMRI) were used to reconstruct SC and FC of a swine connectome. We evaluated a structurally constrained Kuramoto phase-oscillator framework to reproduce resting-state FC and then assessed the models sensitivity to traumatic brain injury (TBI) and its longitudinal progression post-TBI. A joint tuning procedure was implemented to calibrate data-informed natural frequencies and global coupling strength. The tuned Kuramoto model was then used to evolve oscillator phases constrained by the SC, followed by a Balloon-Windkessel hemodynamic model. The optimized model produced significant edge-wise correspondence between averaged simulated FC and the empirical FC (r = 0.61, p < 0.001). Graph-theoretical analysis across network densities (30-50%) showed strong agreement for global efficiency, characteristic path length, and clustering coefficient, while modularity and small-worldness exhibited deviations. Longitudinal analysis of the swine TBI dataset revealed modest reductions in structure-function coupling over time but no significant differences across injury severities. These results demonstrate that optimized Kuramoto models can reproduce key functional network features while preserving inter-subject variability.

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Harmonising Structural Brain MRI from Multiple Sites with Limited Sample Sizes

Bhalerao, G. V.; Markiewicz, P.; Turnbull, J.; Thomas, D. L.; De Vita, E.; Parkes, L.; Thompson, G.; MacKewn, J.; Krokos, G.; Wimberley, C.; Hallett, W.; Su, L.; Malhotra, P.; Hoggard, N.; Taylor, J.-P.; Brooks, D.; Ritchie, C.; Wardlaw, J.; Matthews, P.; Aigbirho, F.; O'Brien, J.; Hammers, A.; Herholz, K.; Barkhof, F.; Miller, K.; Matthews, J.; Smith, S.; Griffanti, L.

2026-04-22 radiology and imaging 10.64898/2026.04.21.26351106 medRxiv
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Harmonisation is widely used to mitigate site- and scanner-related batch variability in multisite neuroimaging studies and is particularly critical in longitudinal clinical trials, where detection of subtle biological or treatment-related changes depends on reliable measurement across scanners and timepoints. However, the effectiveness of harmonisation in small, heterogeneous clinical datasets remains insufficiently understood, particularly in relation to subject-level variability and consistency across acquisition settings, and its impact on both removal of technical variability and preservation of biological variation in pooled multisite analyses. We systematically evaluated a range of image-based and statistical harmonisation methods using a clinically realistic multisite, multiscanner structural T1-weighted (T1w) MRI test-retest dataset comprising three controlled acquisition scenarios: repeatability, intra-scanner reproducibility and inter-scanner reproducibility. Methods were applied under different batch specifications (site, scanner, or both) and performance was assessed within each scenario and in pooled data using a multi-metric framework capturing both technical and biological variability in volumetric imaging-derived phenotypes (IDPs) relevant to aging and dementia research. Across IDPs, before harmonisation variability was lowest in the repeatability scenario (median variability=0.6 to 2.7%, rank consistency {rho} [&ge;]0.9), with modest increases under intra-scanner reproducibility (0.5 to 3.2%, {rho}=0.5 to 1.0) and substantially greater variability under inter-scanner reproducibility conditions (1.7 to 19.2%, {rho} =-0.1 to 0.9). These results offer important information to consider for multisite study design, including sample size calculation in clinical trials. Harmonisation performance was strongly context dependent, with clearer benefits emerged in inter-scanner scenarios where both variability reduction and improvements in subject-level consistency were observed. In pooled data, approaches that explicitly modelled site as batch and accounted for repeated-measure structure showed greater consistency across IDPs in batch effect mitigation and more accurately reflected underlying biological variation. Our evaluation metrics enabled disentangling the removal of global batch effect while highlighting residual variability at the phenotype-specific or multivariate levels. These findings demonstrate that harmonisation cannot be treated as a one-size-fits-all solution and must be interpreted relative to the acquisition context, dataset structure, and downstream analytic goals. Multi-metric evaluation under realistic clinical constraints is essential to support reliable and translatable neuroimaging inference by ensuring appropriate correction of batch effects while preserving longitudinal biological signals and sensitivity to clinically meaningful change in multisite studies.

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Time-resolved hemodynamic responses to sentence-level speech perception, production, and self-monitoring

Leong, T. I.; Li, A.; Ang, J. H.; Reynolds, B. L.; Leong, C. T.; Choi, C. U.; Sereno, M. I.; Li, D.; Lei, V. L. C.; Huang, R.-S.

2026-04-14 neuroscience 10.64898/2026.04.13.715885 medRxiv
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Functional magnetic resonance imaging (fMRI) has been widely utilized to explore the neural mechanisms underlying speech processing. However, the intertwining of perception and production that exists in real-world scenarios remains underexplored due to challenges such as gradient noise and head motion artifacts from speaking. Previous research has often employed sparse-sampling designs, pausing image acquisition intermittently to present auditory stimuli or record overt speech. While this approach mitigates some challenges, it cannot capture continuous brain activity during speech processing and does not separate the mixed hemodynamic responses to external and self-generated speech occurring in succession. We overcame these limitations and continuously scanned thirty-one participants as they listened to and recited English sentences. Through independent component analysis (ICA), we decomposed each functional scan into spatially independent components (ICs), identifying task-related ICs in the superior temporal cortex, inferior frontal gyrus, and orofacial sensorimotor cortex. These ICs demonstrated time-resolved hemodynamic responses corresponding to distinct stages of speech perception, planning, and production. A linear subtraction between the IC time courses from the listening-reciting (perception-to-production) and listening (perception-only) tasks further revealed a secondary hemodynamic response to self-generated speech in the superior temporal cortex. Furthermore, we established precise temporal relationships between overt speech output and the peak, rise, and fall of hemodynamic responses for each independent component. Together, we present a methodological framework that can inform future fMRI studies on naturalistic tasks involving the perception of external auditory stimuli and monitoring of self-generated sounds.

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Highly replicable multisite patterns of adolescent white matter maturation

Meisler, S. L.; Cieslak, M.; Bagautdinova, J.; Hendrickson, T. J.; Pandhi, T.; Chen, A. A.; Hillman, N.; Radhakrishnan, H.; Salo, T.; Feczko, E.; Weldon, K. B.; McCollum, r.; Fayzullobekova, B.; Moore, L. A.; Sisk, L.; Davatzikos, C.; Huang, H.; Avelar-Pereira, B.; Caffarra, S.; Chang, K.; Cook, P. A.; Flook, E. A.; Gomez, T.; Grotheer, M.; Hagen, M. P.; Huque, Z. M.; Karipidis, I. I.; Keller, A. S.; Kruper, J.; Luo, A. C.; Macedo, B.; Mehta, K.; Mitchell, J. L.; Pines, A. R.; Pritschet, L.; Rauland, A.; Roy, E.; Sevchik, B. L.; Shafiei, G.; Singleton, S. P.; Stone, H. L.; Sun, K. Y.; Sydnor,

2026-04-19 neuroscience 10.64898/2026.04.18.719321 medRxiv
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The Adolescent Brain Cognitive Development (ABCD) Study is the largest U.S.-based neuroimaging initiative of adolescent brain maturation. Diffusion MRI (dMRI) provides unique insights into white matter organization, yet applying advanced processing pipelines and managing technical variability across scanning environments remains challenging at scale. To address these issues, we present ABCD-BIDS Community Collection (ABCC) release 3.1.0, including a curated resource of more than 24,000 fully processed ABCD dMRI datasets. ABCC provides fully processed images, nuanced image quality metrics, advanced microstructural measures, and person-specific bundle tractography. Evaluating these rich data revealed that measures of diffusion restriction and non-Gaussianity--in particular the intracellular volume fraction from NODDI and return-to-origin probability from MAP-MRI--were highly sensitive to neurodevelopment and robust to variation in image quality. Additionally, harmonization of microstructural features markedly improved the cross-vendor generalizability of developmental effects. Together, ABCC accelerates reproducible, rigorous research on adolescent white matter development.

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Fractional Anisotropy as a Surrogate Marker of Brain Mechanics

Rampp, S.; Budday, S.; Reiter, N.; Tueni, N.; Hinrichsen, J.; Braeuer, L.; Paulsen, F.; Schnell, O.; Fle, G.; Laun, F. B.; Doerfler, A.

2026-04-13 neuroscience 10.64898/2026.04.13.717439 medRxiv
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Understanding the mechanical properties of brain tissue may provide crucial insights into brain development, injury, disease and surgical planning. Conventionally, these properties are measured ex vivo or in vivo during surgical procedures, while non-invasive in vivo alternatives are sparse. This study investigates whether fractional anisotropy (FA) derived from diffusion-weighted magnetic resonance imaging can serve as a surrogate marker for brain tissue stiffness in healthy human brains. MRI data were collected from three body donor brains, 28 healthy adults, and a publicly available independent dataset of 26 adults. FA values were compared with mechanical properties from ex vivo mechanical testing of brain tissue. Statistical analysis revealed a strong negative correlation between FA and the mechanical response for small strains expressed as shear modulus of a one-term hyperelastic Ogden model, indicating that higher FA values are associated with lower tissue stiffness. The nonlinearity parameter alpha exhibited a qualitatively similar, but considerably weaker correlation with FA. These findings were consistent across datasets. The findings suggest that FA can be a robust, non-invasive marker for estimating mechanical properties of brain tissue, with potential applications in clinical diagnosis and computational modeling of brain mechanics and the study of brain development. Further research is needed to clarify the relationship in lesional tissues and to optimize clinical utility.