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NeuroImage

Elsevier BV

All preprints, 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. Older preprints may already have been published elsewhere.

1
Establishing the Validity of Compressed Sensing Diffusion Spectrum Imaging

Radhakrishnan, H.; Zhao, C.; Sydnor, V. J.; Baller, E. B.; Cook, P. A.; Fair, D.; Giesbrecht, B.; Larsen, B.; Murtha, K.; Roalf, D. R.; Rush-Goebel, S.; Shinohara, R.; Shou, H.; Tisdall, M. D.; Vettel, J.; Grafton, S.; Cieslak, M.; Satterthwaite, T.

2023-02-23 neuroscience 10.1101/2023.02.22.529546 medRxiv
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Diffusion Spectrum Imaging (DSI) using dense Cartesian sampling of q-space has been shown to provide important advantages for modeling complex white matter architecture. However, its adoption has been limited by the lengthy acquisition time required. Sparser sampling of q-space combined with compressed sensing (CS) reconstruction techniques has been proposed as a way to reduce the scan time of DSI acquisitions. However prior studies have mainly evaluated CS-DSI in post-mortem or non-human data. At present, the capacity for CS-DSI to provide accurate and reliable measures of white matter anatomy and microstructure in the living human brain remains unclear. We evaluated the accuracy and inter-scan reliability of 6 different CS-DSI schemes that provided up to 80% reductions in scan time compared to a full DSI scheme. We capitalized on a dataset of twenty-six participants who were scanned over eight independent sessions using a full DSI scheme. From this full DSI scheme, we subsampled images to create a range of CS-DSI images. This allowed us to compare the accuracy and inter-scan reliability of derived measures of white matter structure (bundle segmentation, voxel-wise scalar maps) produced by the CS-DSI and the full DSI schemes. We found that CS-DSI estimates of both bundle segmentations and voxel-wise scalars were nearly as accurate and reliable as those generated by the full DSI scheme. Moreover, we found that the accuracy and reliability of CS-DSI was higher in white matter bundles that were more reliably segmented by the full DSI scheme. As a final step, we replicated the accuracy of CS-DSI in a prospectively acquired dataset (n=20, scanned once). Together, these results illustrate the utility of CS-DSI for reliably delineating in vivo white matter architecture in a fraction of the scan time, underscoring its promise for both clinical and research applications.

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Empirical evaluation of fused EEG-MEG source reconstruction. Application to auditory mismatch generators

lecaignard, f.; Bertrand, O.; Caclin, A.; Mattout, J.

2019-09-12 neuroscience 10.1101/765966 medRxiv
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Since their introduction in the late eighties, Bayesian approaches for neuroimaging have opened the way to new powerful and quantitative analysis of brain data. Here, we apply this statistical framework to evaluate empirically the gain of fused EEG-MEG source reconstruction, compared to unimodal (EEG or MEG) one. Combining EEG and MEG information for source reconstruction has been consistently evidenced to enhance localization performances using simulated data. However, given considerable efforts to conduct simultaneous recordings, empirical evaluation becomes necessary to quantify the real information gain. And this is obviously not straightforward due to the ill-posedness of the inverse problem. Here, we consider Bayesian model comparison to quantify the ability of EEG, MEG and fused (EEG/MEG) inversions of individual data to resolve spatial source models. These models consisted in group-level cortical distributions inferred from real EEG, MEG and EEG/MEG brain responses. We applied this comparative evaluation to the timely issue of the generators of auditory mismatch responses evoked by unexpected sounds. These included the well-known Mismatch Negativity (MMN) but also earlier deviance responses. As expected, fused localization was evidenced to outperform unimodal inversions with larger model separability. The present methodology confirms with real data the theoretical interest of simultaneous EEG/MEG recordings and fused inversion to highly inform (spatially and temporally) source modeling. Precisely, a bilateral fronto-temporal network could be identified for both the MMN and early deviance response. Interestingly, multimodal inversions succeeded in revealing spatio-temporal details of the functional organization within the supratemporal plane that have not been reported so far, nor were visible here with unimodal inversions. The present refined auditory network could serve as priors for auditory modeling studies.

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Cluster-permutation statistical analysis for high-dimensional brain-wide functional connectivity mapping

Sanchez Bornot, J. M.; Lopez, M. E.; Bruna, R.; Maestu, F.; Youssofzadeh, V.; Yang, S.; Prasad, G.; McClean, P.; Wong-Lin, K.

2019-11-21 neuroscience 10.1101/849554 medRxiv
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Brain functional connectivity (FC) analyses based on magnetoencephalographic (MEG) signals have yet to exploit the intrinsic high-dimensional information. Typically, these analyses are constrained to regions of interest to avoid the curse of dimensionality, which leads to conservative hypothesis testing. We removed such constraint by extending cluster-permutation statistics for high-dimensional MEG-FC analyses. We demonstrated the feasibility of this approach by identifying MEG-FC resting-state changes in mild cognitive impairment (MCI), a prodromal stage of Alzheimers disease. We found dense clusters of increased connectivity strength in MCI compared to healthy controls (hypersynchronization), in delta (1-4 Hz) and higher-theta (6-8 Hz) bands oscillations. These clusters mainly consisted of interactions between occipitofrontal and occipitotemporal regions in the left hemisphere and could potentially be used as neuromarkers of early progression in Alzheimers disease. Our novel approach can be used to generate high-resolution statistical FC maps for neuroimaging studies in general.

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Along-tract quantification of resting-state BOLD hemodynamic response functions in white matter

Schilling, K.; Li, M.; Rheault, F.; Ding, Z.; Anderson, A. W.; Kang, H.; Landman, B. A.; Gore, J. C.

2022-06-12 neuroscience 10.1101/2022.06.09.495555 medRxiv
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Detailed knowledge of the BOLD hemodynamic response function (HRF) is crucial for accurate analysis and interpretation of functional MRI data. Considerable efforts have been made to characterize the HRF in gray matter (GM) but much less is known about BOLD effects in white matter (WM). However, recent reports have demonstrated reliable detection and analyses of WM BOLD signals after stimulation and in a resting state. WM and GM differ in energy requirements and blood flow, so neurovascular couplings may well be different. We aimed to derive a comprehensive characterization of the HRF in WM across a population, including accurate measurements of its shape and its variation along and between WM pathways, using resting-state fMRI acquisitions. Our results show that the HRF is significantly different between WM and GM. Features of the HRF, such as a prominent initial dip, show strong relationships with features of the tissue microstructure derived from diffusion imaging, and these relationships differ between WM and GM, consistent with BOLD signal fluctuations reflecting different energy demands and differences in neurovascular coupling between tissues of different composition. We also show that the HRF varies significantly along WM pathways, and is different between different WM pathways. Thus, much like in GM, changes in flow and/or oxygenation are different for different parts of the WM. These features of the HRF in WM are especially relevant for interpretation of the biophysical basis of BOLD effects in WM.

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Localization of Spatially Extended Brain Sources by Flexible Alternating Projections (FLEX-AP)

Hecker, L.; Giri, A.; Pantazis, D.; Adler, A.

2023-11-08 neuroscience 10.1101/2023.11.03.565461 medRxiv
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Magnetoencephalography (MEG) and electroencephalography (EEG) are widely employed techniques for the in-vivo measurement of neural activity with exceptional temporal resolution. Modeling the neural sources underlying these signals is of high interest for both neuroscience research and pathology. The method of Alternating Projection (AP) was recently shown to outperform the well-established recursively applied and projected multiple signal classification (RAP-MUSIC) algorithm. In this work, we further enhanced AP to allow for source extent estimation, a novel approach termed flexible extent AP (FLEX-AP). We found that FLEX-AP achieves significantly lower errors for spatially coherent sources compared to AP, RAP-MUSIC, and the corresponding extension, FLEX-RAP-MUSIC. We also found an advantage for discrete dipoles under forward modeling errors encountered in real-world scenarios. Together, our results indicate that the FLEX-AP method can unify dipole fitting and distributed source imaging into a single algorithm with promising accuracy.

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Benchmarking Orientation Distribution Function Estimation Methods for Tractometry in Single-Shell Diffusion Magnetic Resonance Imaging - An Evaluation of Test-Retest Reliability and Predictive Capability

Rauland, A.; Meisler, S. L.; Alexander-Bloch, A. F.; Bagautdinova, J.; Baller, E. B.; Gur, R. E.; Gur, R. C.; Luo, A. C.; Moore, T. M.; Popovych, O. V.; Reetz, K.; Roalf, D. R.; Shinohara, R. T.; Sotardi, S.; Sydnor, V. J.; Vossough, A.; Eickhoff, S. B.; Cieslak, M.; Satterthwaite, T. D.

2025-09-07 neuroscience 10.1101/2025.09.02.673635 medRxiv
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Deriving white matter (WM) bundles in-vivo has thus far mainly been applied in research settings, leveraging high angular resolution, multi-shell diffusion MRI (dMRI) acquisitions that enable advanced reconstruction methods. However, these advanced acquisitions are both time-consuming and costly to acquire. The ability to reconstruct WM bundles in the massive amounts of existing single-shelled, lower angular resolution data from legacy research studies and healthcare systems would offer much broader clinical applications and population-level generalizability. While legacy scans may offer a valuable, large-scale complement to contemporary research datasets, the reliability of white matter bundles derived from these scans remains unclear. Here, we leverage a large research dataset where each 64-direction dMRI scan was acquired as two independent 32-direction runs per subject. To investigate how recently developed bundle segmentation methods generalize to this data, we evaluated the test-retest reliability of the two 32-direction scans, of WM bundle extraction across three orientation distribution function (ODF) reconstruction methods: generalized q-sampling imaging (GQI), constrained spherical deconvolution (CSD), and single-shell three-tissue CSD (SS3T). We found that the majority of WM bundles could be reliably extracted from dMRI scans that were acquired using the 32-direction, single-shell acquisition scheme. The mean dice coefficient of reconstructed WM bundles was consistently higher within-subject than between-subject for all WM bundles and ODF reconstruction methods, illustrating preservation of person-specific anatomy. Further, when using features of the bundles to predict complex reasoning assessed using a computerized cognitive battery, we observed stable prediction accuracies (r: 0.15-0.36) across the test-retest data. Among the three ODF reconstruction methods, SS3T had a good balance between sensitivity and specificity in external validation, a high intra-class correlation of extracted features, more plausible bundles, and strong predictive performance. More broadly, these results demonstrate that bundle segmentation can achieve robust performance even on lower angular resolution, single-shell dMRI, with particular advantages for ODF methods optimized for single-shell data. This highlights the considerable potential for dMRI collected in healthcare settings and legacy research datasets to accelerate and expand the scope of WM research.

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Beyond BOLD: Evidence for diffusion fMRI contrast in the human brain distinct from neurovascular response

Olszowy, W.; Diao, Y.; Jelescu, I. O.

2021-06-30 neuroscience 10.1101/2021.05.16.444253 medRxiv
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Functional Magnetic Resonance Imaging (fMRI) is an essential method to measure brain activity non-invasively. While fMRI almost systematically relies on the blood oxygenation level-dependent (BOLD) contrast, there is an increasing interest in alternative methods that would not rely on neurovascular coupling. A promising but controversial such alternative is diffusion fMRI (dfMRI), which relies instead on dynamic fluctuations in apparent diffusion coefficient (ADC) due to microstructural changes underlying neuronal activity, i.e. neuromorphological coupling. However, it is unclear whether genuine dfMRI contrast, distinct from BOLD contamination, can be detected in the human brain in physiological conditions. Here, we present the first dfMRI study in humans attempting to minimize BOLD contamination sources and comparing functional responses at two field strengths (3T and 7T). Our study benefits from unprecedented high spatio-temporal resolution, harnesses novel denoising strategies and examines characteristics of not only task but also resting-state dfMRI. We report task-induced decrease in ADC with temporal and spatial features distinct from the BOLD response and yielding more specific activation maps. Furthermore, we report dfMRI resting-state functional connectivity which, compared to its BOLD counterpart, is essentially free from physiological artifacts and preserves positive correlations but preferentially suppresses anti-correlations, which are likely of vascular origin. A careful acquisition and processing design thus enable the detection of genuine dfMRI contrast on clinical MRI systems. As opposed to BOLD, diffusion functional contrast could be particularly well suited for low-field MRI.

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Functional covariance modes reveal aligned fetal and neonatal brain functional connectomes.

Karolis, V. R.; O'Muircheartaigh, J.; McAlonan, G.; Arichi, T.

2025-07-24 neuroscience 10.1101/2025.07.20.665719 medRxiv
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Multiple lines of evidence suggest that that spatially distributed functional networks in the brain may first start emerging before birth. Reliably demonstrating this in utero using fMRI remains a very challenging problem due to a variety of MRI-adverse factors, including distant coil positioning and motion-induced magnetic field perturbations. Here, we introduce a novel approach to functional network analysis, called seed-based functional covariance modes (FCMs), which leverages inter-subject variability in connectivity between seed regions and the rest of the brain to infer whole-brain network configurations. We first applied the FCMs approach to neonatal data to benchmark it against group-level independent component factorisation - a standard in fMRI network analysis - and found a high degree of concordance between the results produced by the two methods. We then applied it to the fetal data, where the standard approach has consistently failed to reveal spatially distributed networks. For the first time, and despite fundamental differences in signal characteristics between fetal and neonatal data, we detected network-like patterns with high spatial correspondence to neonatal functional networks. In particular, the FCMs approach efficiently recovered interhemispheric connections, a landmark feature of neonatal functional networks. Systematic organisation of interhemispheric fetal networks was observed; they tended to cluster along the brain midline but also were present in lateral sensorimotor and temporal areas as well as cortical limbic territories in ventral orbitofrontal cortex and temporal pole. By aligning fetal and neonatal connectomes, this study represents a crucial step towards supporting the biological veracity of observations made using fetal fMRI. Meanwhile, the concordance between FCMs and independent component factorisation in neonates prompts a re-evaluation of how inter-individual variability contributes to network structure inference in methods that ostensibly emphasise shared correlation patterns across subjects.

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Bottom-up control of leakage in spectral electrophysiological source imaging via structured sparse bayesian learning

Gonzalez-Moreira, E.; Paz-Linares, D.; Areces-Gonzalez, A.; Wang, Y.; Li, M.; Harmony, T.; Valdes-Sosa, P. A.

2020-02-26 neuroscience 10.1101/2020.02.25.964684 medRxiv
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Brain electrical activity in different spectral bands has been associated with diverse mechanisms underlying Brain function. Deeper reconnoitering of these mechanisms entails mapping in grayordinates (Gray Matter coordinates), the spectral features of electrophysiological Brain signals. Such mapping is possible through MEG/EEG signals, due to their wide Brain coverage and excellent temporal resolution in reflecting neural-electrical-activity. This process-coined Electrophysiological Source Imaging (ESI)-can only produce approximated images of Brain activity, which are severely distorted by leakage: a pervasive effect in almost any imaging technique. It has been proposed that leakage control to tolerable levels can be achived through using priors or regularization within ESI, but their implementation commonly yields meager statistical guaranties. We introduce bottom-up control of leakage: defined as maximum Bayesian evidence search braced with priors precisely on the spectral responses. This is feasible due to an instance of Bayesian learning of complex valued data: spectral Structured Sparse Bayesian Learning (sSSBL). "Spectral" refers to specific spatial topologies that are reflected by the MEG/EEG spectra. We also present a new validation benchmark based on the concurrency between high density MEG and its associated pseudo-EEG of lower density. This reveals that prevealing methods like eLORETA and LCMV can fall short of expectations whereas sSSBL exibits an exellent performance. A final qualitative assesment reveals that sSSBL can outline brain lessions using just low density EEG, according to the T2 MRI shine through of the affected areas.

10
Automatic Reconstruction of Cerebellar Cortex from Standard MRI Using Diffeomorphic Registration of a High-Resolution Template (ARCUS)

Samuelsson, J. G.; Rosen, B.; Hamalainen, M. S.

2020-12-02 neuroscience 10.1101/2020.11.30.405522 medRxiv
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As cumulating evidence points to a wider range of functional tasks and neurological conditions that involve the cerebellum than previously known, the interest for examining the cerebellum with non-invasive neuroimaging techniques is growing. However, the standard methods of computational neuroanatomy for segmenting and reconstructing the cerebral cortex work poorly for the cerebellar cortex at the resolutions attainable with contemporary MRI technology because of its extremely intricate folding, making detailed and topologically correct reconstructions of the geometry of the cerebellar cortical surface unfeasible. Recently, a detailed surface reconstruction of the human cerebellar cortex was achieved from an ex-vivo specimen. These novel anatomical data enable a new reconstruction technique where this detailed surface reconstruction is morphed to subject space based on standard in-vivo MRI data. The result is an approximate reconstruction of the cerebellar cortex that requires only standard-resolution MRI data and can be used e.g., in functional neuroimaging, for integrating topographic population data or for visualizing topographic data on flattened surface patches.

11
Predicting Sex from Resting-State fMRI Across Multiple Independent Acquired Datasets

AL Zoubi, O.; Misaki, M.; Tsuchiyagaito, A.; Zotev, V.; White, E.; T1000 Investigators, ; Paulus, M. P.; Bodurka, J.

2020-08-23 neuroscience 10.1101/2020.08.20.259945 medRxiv
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Sex is an important biological variable often used in analyzing and describing the functional organization of the brain during cognitive and behavioral tasks. Several prior studies have shown that blood-oxygen-level-dependent (BOLD) functional MRI (fMRI) functional connectivity (FC) can be used to differentiate sex among individuals. Herein, we demonstrate that sex can be further classified with high accuracy using the intrinsic BOLD signal fluctuations from resting-state fMRI (rs-fMRI). We adopted the amplitude of low-frequency fluctuation (ALFF), and the fraction of ALFF (fALFF) features from the automated anatomical atlas (AAL) and Powers functional atlas as an input to different machine learning (ML) methods. Using datasets from five independently acquired subject cohorts and with eight fMRI scanning sessions, we comprehensively assessed unbiased performance using nested-cross validation for within-sample and across sample accuracies. The results demonstrated high prediction accuracies for the Human Connectome Project (HCP) dataset (area under cure (AUC) > 0.89). The yielded accuracies suggest that sex difference is embodied and well-pronounced in the low-frequency BOLD signal fluctuation. The performance degrades with the heterogeneity of the cohort and suggests that other factors.e.g. psychiatric disorders and demographics influences the BOLD signal and may interact with the classification of sex. In addition, the results revealed high learning generalizability with the HCP scan, but not across different datasets. The intraclass correlation coefficient (ICC) across HCP scans showed moderate-to-good reliability based on atlas selection (ICC = 0.65 [0.63-0.67] and ICC= 0.78 [0.76-0.80].). We also assessed the effect of scan duration on the predictability of sex and showed that sex differences could be detected even with a short rs-fMRI scan (e.g., 2 minutes). Moreover, we provided statistical maps of the brain regions differentially recruited by or predicting sex using Shapely values and determined an overlap with previous reports of brain response due to sex differences. Altogether, our analysis suggests that sex differences are well-pronounced in rs-fMRI and should be considered seriously in any study design, analysis, or interpretation.

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In vivo super-resolution track-density imaging for thalamic nuclei identification

Basile, G. A.; Bertino, S.; Bramanti, A.; Anastasi, G. P.; Milardi, D.; Cacciola, A.

2021-01-04 neuroscience 10.1101/2021.01.03.425122 medRxiv
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The development of novel techniques for the in vivo, non-invasive visualization and identification of thalamic nuclei has represented a major challenge for human neuroimaging research in the last decades. Thalamic nuclei have important implications in various key aspects of brain physiology and many of them show selective alterations in various neurologic and psychiatric disorders. In addition, both surgical stimulation and ablation of specific thalamic nuclei have been proven to be useful for the treatment of different neuropsychiatric diseases. The present work aimed at describing a novel protocol for histologically-guided delineation of thalamic nuclei based on short-tracks track-density imaging (stTDI), which is an advanced imaging technique that exploits high angular resolution diffusion tractography to obtain super-resolved white matter maps with high anatomical information. We tested this protocol on i) six healthy individual 3T MRI scans from the Human Connectome Project database, and on ii) a group population template reconstructed by averaging 100 unrelated healthy subjects scans from the same repository. We demonstrated that this approach can identify up to 13 distinct thalamic nuclei bilaterally with very high reliability (intraclass correlation coefficient: 0.996, 95% CI: 0.993-0.998; total accumulated overlap: 0.43) and that both subject-based and group-level thalamic parcellation show a fair share of similarity to a recent standard-space histological thalamic atlas. Finally, we showed that stTDI-derived thalamic maps can be successfully employed to study thalamic structural and functional connectivity, and may have potential implications both for basic and translational research, as well as for pre-surgical planning purposes.

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Identifying components that vary in space and time from resting-state functional MRI

Scott, G.; Leech, R.

2021-07-02 neuroscience 10.1101/2021.07.01.450675 medRxiv
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A widespread assumption of fMRI-derived large-scale intrinsic connectivity networks (ICNs) is that they are spatially static over time. However, the assumption of spatial stationarity of ICNs has been challenged by a range of techniques that allow for time-varying connectivity between brain regions and demonstration that canonical networks like the default model network (DMN) can be fractionated according to time-varying connectivity relationships of their subcomponents. Previously, we developed a simple spatiotemporal ICA (stICA) technique to allow the discovery of patterns of spatiotemporal evolution in task fMRI data in a way that avoided the traditional constraint of spatial stationarity on brain networks, and we validated the approach in fMRI of task-to-rest transitions. Here, we apply our stICA technique to resting-state fMRI datasets to explore whether spatiotemporally evolving components of brain activity can be identified in the absence of an overt behavioural task. We found that stICA components could generally be described in terms of graded onsets and offsets of ICNs that had been calculated based on techniques that assumed spatial stationarity. Our results suggest that, to a reasonable approximation, stable ICNs can be taken to be building blocks of the spatiotemporal patterns measured with resting-state fMRI.

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Joint cmICA: auto-linking of structural and functional connectivity

Wu, L.; Calhoun, V.

2022-09-14 neuroscience 10.1101/2022.09.12.507415 medRxiv
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The study of human brain connectivity, including structural connectivity (SC) and functional connectivity (FC), provides insights into the neurophysiological mechanism of brain function and its relationship to human behavior and cognition. Both types of connectivity measurements provide crucial yet complementary information. However, integrating these two modalities into a single framework remains a challenge, because of the differences in their quantitative interdependencies as well as their anatomical representations due to distinctive imaging mechanisms. In this study, we introduced a new method, joint cmICA (connectivity matrix ICA), which provides a data-driven parcellation and automated-linking of SC and FC information simultaneously using a joint analysis of functional MRI and diffusion-weighted MRI data. We showed that these two connectivity modalities produce common cortical segregation, though with various degrees of (dis)similarity. Moreover, we show conjoint functional connectivity networks and structural white matter tracts that directly link these cortical parcellations/sources, within one analysis. Overall, data driven joint cmICA provides a new approach for integrating or fusing structural connectivity and functional connectivity systematically and conveniently, and provides an effective tool for connectivity-based multimodal data fusion in brain.

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A thalamic perspective of (un)consciousness in pharmacological and pathological states in humans

Szocs, D.; Lyu, D.; Luppi, A. I.; Coppola, P.; Woodrow, R.; Williams, G. B.; Allanson, J.; Pickard, J. D.; Owen, A. M.; Naci, L.; Menon, D. K.; Stamatakis, E. A.

2024-05-31 neuroscience 10.1101/2024.05.30.596600 medRxiv
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Currently, there is substantial ongoing discussion around the functional role of the thalamus in consciousness. What is missing in the literature, however, is a systematic investigation of the relevance of specific thalamic nuclei in pharmacologically and pathologically altered states of consciousness in humans. Using functional neuroimaging in both healthy anaesthetised volunteers and patients with disorders of consciousness (DOC), we sought to identify which specific thalamic subregions in both cohorts may be differentially significant for loss of consciousness. Our findings revealed that the pulvinar (Pu) and ventral-latero-ventral (VLV) nuclei, in anaesthesia, and the VLV, in DOC, had distinct functional connectivity patterns related to the default mode and somatomotor networks. Remarkably, among all nuclei, the Pu was found to have the strongest functional connectivity change with anaesthetic-induced loss of consciousness, while in DOC patients, we found the VLV revealed the strongest connectivity change in comparison with healthy controls. Furthermore, we provide evidence that this neural connectivity biomarker in patients also mirrors the changes observed at the behavioural level, which could have clinical implications for targeted deep brain stimulation in therapy for DOC.

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Multivariate Time-Lagged Multidimensional Pattern Connectivity (mvTL-MDPC) for EEG/MEG Functional Connectivity Analysis

Rahimi, S.; Jackson, R. L.; Hauk, O.

2024-01-22 neuroscience 10.1101/2024.01.20.576221 medRxiv
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Multidimensional connectivity methods are critical to reveal the full pattern of complex interactions between brain regions over time. However, to date only bivariate multidimensional methods are available for time-resolved EEG/MEG data, which may overestimate connectivity due to the confounding effects of spurious and indirect dependencies. Here, we introduce a novel functional connectivity method which is both multivariate and multidimensional, Multivariate Time-lagged Multidimensional Pattern Connectivity (mvTL-MDPC), to address this issue in time-resolved EEG/MEG applications. This novel method extends its bivariate counterpart TL-MDPC to estimate how well patterns in an ROI 1 at time point t1 can be linearly predicted from patterns of an ROI 2 at time point t2 while partialling out the multivariate contributions from other brain regions. We compared the performance of mvTL-MDPC and TL-MDPC on simulated data designed to test their ability to identify true direct connections, using the Euclidean distance to the ground truth to measure goodness-of-fit. These simulations demonstrate that mvTL-MDPC produces more reliable and accurate results than the bivariate method. We therefore applied this method to an existing EEG/MEG dataset contrasting words presented in more or less demanding semantic tasks, to identify the dynamic brain network underlying controlled semantic cognition. As expected, mvTL-MDPC was more selective than TL-MDPC, identifying fewer connections, likely due to a reduction in the detection of spurious or indirect connections. Dynamic connections were identified between bilateral anterior temporal lobes, posterior temporal cortex and inferior frontal gyrus, in line with recent neuroscientific models of semantic cognition.

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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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Diffuse optical reconstructions of NIRS data using Maximum Entropy on the Mean

Cai, Z.; Machado, A.; Chowdhury, R. A.; Spilkin, A.; Vincent, T.; Aydin, U.; Pellegrino, G.; Lina, J.-M.; Grova, C.

2021-02-23 neuroscience 10.1101/2021.02.22.432263 medRxiv
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Functional near-infrared spectroscopy (fNIRS) measures the hemoglobin concentration changes associated with neuronal activity. Diffuse optical tomography (DOT) consists of reconstructing the optical density changes measured from scalp channels to the oxy-/deoxy-hemoglobin (i.e., HbO/HbR) concentration changes within the cortical regions. In the present study, we adapted a nonlinear source localization method developed and validated in the context of Electro- and Magneto-Encephalography (EEG/MEG): the Maximum Entropy on the Mean (MEM), to solve the inverse problem of DOT reconstruction. We first introduced depth weighting strategy within the MEM framework for DOT reconstruction to avoid biasing the reconstruction results of DOT towards superficial regions. We also proposed a new initialization of the MEM model improving the temporal accuracy of the original MEM framework. To evaluate MEM performance and compare with widely used depth weighted Minimum Norm Estimate (MNE) inverse solution, we applied a realistic simulation scheme which contained 4000 simulations generated by 250 different seeds at different locations and 4 spatial extents ranging from 3 to 40cm2 along the cortical surface. Our results showed that overall MEM provided more accurate DOT reconstructions than MNE. Moreover, we found that MEM was remained particularly robust in low signal-to-noise ratio (SNR) conditions. The proposed method was further illustrated by comparing to functional Magnetic Resonance Imaging (fMRI) activation maps, on real data involving finger tapping tasks with two different montages. The results showed that MEM provided more accurate HbO and HbR reconstructions in spatial agreement with the main fMRI cluster, when compared to MNE. HighlightsO_LIWe introduced a new fNIRS reconstruction method - Maximum Entropy on the Mean. C_LIO_LIWe implemented depth weighting strategy within the MEM framework. C_LIO_LIWe improved the temporal accuracy of the original MEM reconstruction. C_LIO_LIPerformances of MEM and MNE were evaluated with realistic simulations and real data. C_LIO_LIMEM provided more accurate and robust reconstructions than MNE. C_LI

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Connecting the Dots: Approaching a Standardized Nomenclature for Molecular Connectivity Combining Data and Literature

Reed, M. B.; Cocchi, L.; Knudsen, G. M.; Sander, C.; Gryglewski, G.; Chen, J.; Volpi, T.; Fisher, P.; Khattar, N.; Silberbauer, L. R.; Murgas, M.; Godbersen, G. M.; Nics, L.; Walter, M.; Hacker, M.; Hammers, A.; Ogden, T. R.; Mann, J. J.; Biswal, B.; Rosen, B.; Carson, R.; Price, J.; Lanzenberger, R.; Hahn, A.

2024-05-10 neuroscience 10.1101/2024.05.10.593490 medRxiv
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PET-based connectivity computation is a molecular approach that complements fMRI-derived functional connectivity. However, the diversity of methodologies and terms employed in PET connectivity analysis has resulted in ambiguities and confounded interpretations, highlighting the need for a standardized nomenclature. Drawing parallels from other imaging modalities, we propose "molecular connectivity" as an umbrella term to characterize statistical dependencies between PET signals across brain regions at the individual level (within-subject). Like fMRI resting-state functional connectivity, "molecular connectivity" leverages temporal associations in the PET signal to derive brain network associations. Another within-subject approach evaluates regional similarities of tracer kinetics, which are unique in PET imaging, thus referred to as "kinetic connectivity". On the other hand, "molecular covariance" denotes group-level computations of covariance matrices across-subject. Further specification of the terminology can be achieved by including the employed radioligand, such as "metabolic connectivity/covariance" for [18F]FDG as well as "tau/amyloid covariance" for [18F]flutemetamol / [18F]flortaucipir. To augment these distinctions, high-temporal resolution functional [18F]FDG PET scans from 17 healthy participants were analysed with common techniques of molecular connectivity and covariance, allowing for a data-driven support of the above terminology. Our findings demonstrate that temporal band-pass filtering yields structured network organization, whereas other techniques like 3rd order polynomial fitting, spatio-temporal filtering and baseline normalization require further methodological refinement for high-temporal resolution data. Conversely, molecular covariance from across-subject data provided a simple means to estimate brain region interactions through regularized or sparse inverse covariance estimation. A standardized nomenclature in PET-based connectivity research can reduce ambiguity, enhance reproducibility, and facilitate interpretability across radiotracers and imaging modalities. Via a data-driven approach, this work provides a transparent framework for categorizing and comparing PET-derived connectivity and covariance metrics, laying the foundation for future investigations in the field.

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A novel 4D fMRI clustering technique to examine event-related spatiotemporal dynamics of face processing in naturalistic stimuli

Ekstrand, C.

2023-06-15 neuroscience 10.1101/2023.06.15.545143 medRxiv
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Cortical function is complex, nuanced, and involves information processing in a multimodal and dynamic world. However, previous functional magnetic resonance imaging (fMRI) research has generally characterized static activation differences between strictly controlled proxies of real-world stimuli that do not encapsulate the complexity of everyday multimodal experiences. Of primary importance to the field of neuroimaging is the development of techniques that distill complex spatiotemporal information into simple, behaviorally relevant representations of neural activation. Herein, we present a novel 4D spatiotemporal clustering method to examine dynamic neural activity associated with events (specifically the onset of human faces in audiovisual movies). Results from this study showed that 4D spatiotemporal clustering can extract clusters of fMRI activation over time that closely resemble the known spatiotemporal pattern of human face processing without the need to model a hemodynamic response function. Overall, this technique provides a new and exciting window into dynamic functional processing across both space and time using fMRI that has wide applications across the field of neuroscience.