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arxiv: 2509.12873 · v2 · submitted 2025-09-16 · 🧬 q-bio.NC · cs.DC· physics.comp-ph

Emergent complexity and rhythms in evoked and spontaneous dynamics of human whole-brain models after tuning through analysis tools

Gianluca Gaglioti , Alessandra Cardinale , Cosimo Lupo , Thierry Nieus , Federico Marmoreo , Elena Focacci , Robin Gutzen , Michael Denker
show 5 more authors
Andrea Pigorini Marcello Massimini Simone Sarasso Pier Stanislao Paolucci Giulia De Bonis
This is my paper

Pith reviewed 2026-05-18 16:55 UTC · model grok-4.3

classification 🧬 q-bio.NC cs.DCphysics.comp-ph
keywords whole-brain modelingneural mass modelparameter tuningbrain rhythmsperturbational complexityspontaneous dynamicsevoked activityhuman connectome
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The pith

Tuning a whole-brain neural mass model with analysis metrics produces realistic rhythms and complex activity missing from default settings.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper demonstrates a method for configuring whole-brain simulations to better match biological observations by linking simulation and analysis tools. Researchers simulate dynamics with The Virtual Brain using the Larter-Breakspear model on a human connectome and then apply the Cobrawap pipeline to evaluate and adjust parameters based on rhythms, heterogeneity, and complexity measures. This tuning results in the model exhibiting alpha-band oscillations, infra-slow rhythms, scale-free behavior, and complex responses to inputs, whereas the untuned model does not. The approach sets up a path for more accurate, data-informed whole-brain modeling.

Core claim

The authors integrate The Virtual Brain platform for whole-brain simulations with the Cobrawap analysis pipeline to tune the Larter-Breakspear neural mass model on a 998-node human connectome. The tuned configuration, selected using a set of standardized observables for rhythms and complexity, displays several biologically relevant features absent in the default model. These include robust alpha-band oscillations and infra-slow rhythms, scale-free characteristics, greater spatio-temporal heterogeneity, asymmetric functional connectivity during spontaneous activity, and non-stereotyped complex spatio-temporal activity in response to perturbations as measured by the perturbational complexity指数

What carries the argument

The parameter tuning process that uses Cobrawap's standardized metrics on outputs from The Virtual Brain simulations of the Larter-Breakspear model to select biologically relevant configurations.

If this is right

  • The tuned model produces non-stereotyped, complex spatio-temporal activity under external perturbations.
  • Spontaneous dynamics in the tuned model include robust alpha-band oscillations and infra-slow rhythms.
  • Scale-free characteristics and greater spatio-temporal heterogeneity appear in the tuned spontaneous activity.
  • Functional connectivity becomes asymmetric in the tuned model.
  • This combination of tools lays the groundwork for data-driven calibration of whole-brain models.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Similar tuning strategies could be tested on other neural mass models to see if the emergent features are robust across modeling choices.
  • The framework might be adapted to incorporate direct comparisons with empirical neuroimaging datasets for validation.
  • These tuned models could be used to investigate how brain complexity changes under different conditions or perturbations.

Load-bearing premise

The specific observables and metrics selected in the analysis pipeline are sufficient to identify parameter sets that produce meaningful biological features without overfitting to the chosen analysis methods.

What would settle it

If new empirical data from human subjects, such as EEG recordings, show that the tuned model does not exhibit the predicted alpha oscillations or scale-free activity patterns while independent tests confirm the metrics, this would indicate the tuning failed to capture the intended biology.

Figures

Figures reproduced from arXiv: 2509.12873 by Alessandra Cardinale, Andrea Pigorini, Cosimo Lupo, Elena Focacci, Federico Marmoreo, Gianluca Gaglioti, Giulia De Bonis, Marcello Massimini, Michael Denker, Pier Stanislao Paolucci, Robin Gutzen, Simone Sarasso, Thierry Nieus.

Figure 1
Figure 1. Figure 1: TVB simulations and analysis with Cobrawap. A) The TVB-Cobrawap workflow facilitates tuning, calibration and validation of TVB model parameters. Cobrawap provides metrics for the analysis of TVB outputs such as trace statistics, event detection, spectral analysis, network interactions, and complexity indexes of simulated brain activity. B) Illustrative examples of three spontaneous activity traces from thr… view at source ↗
Figure 2
Figure 2. Figure 2: Comparison of spontaneous dynamics in TUN and DEF configurations: time-domain and frequency-domain analyses. A) Voltage traces from three representative nodes from right-hemisphere FUS, PREC, and RMF regions (brown, red, and salmon lines, respectively) in the TUN configuration. B) The probability density functions of voltage distributions from nodes in A). C-D) Same as A) and B), respectively, for the DEF … view at source ↗
Figure 3
Figure 3. Figure 3: Auto-correlation analysis and spatial distribution of periodicity in TUN and DEF. A-B) Auto-correlation functions of the spontaneous voltage signal from three representative nodes (same as in [PITH_FULL_IMAGE:figures/full_fig_p020_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Temporal and spatial variability of signal fluctuations in TUN and DEF. Signal processing steps are illustrated in the leftmost panels of each row: Top: Example traces show voltage fluctuations and inter-event-time (IET) used to calculate the CVIET. Middle: Example power time courses used to compute the CVpower, with shaded regions indicating mean ± standard deviation. Bottom: Example amplitude envelope tr… view at source ↗
Figure 5
Figure 5. Figure 5: Functional connectivity, functional lags, and asymmetry in TUN and DEF configura￾tions. A) Illustration of the cross-correlation function applied to investigate pairwise interactions between nodes. The correlation between the time series of nodes i and j is computed at various time lags. Negative lags indicate a directional relation from i to j, while positive lags indicate the other way round. The functio… view at source ↗
Figure 6
Figure 6. Figure 6: Stimulus-evoked activity in TUN and DEF configurations. A-B) 200 independent 2 ms perturbations (i.e. 200 trials) were applied to the right superior parietal nodes (rSP) of the brain model, for both TUN and DEF configurations, to assess the spatio-temporal complexity of the evoked activity. Voltage traces averaged across trials in TUN (A, red) and DEF (B, blue) are here reported for each of the 998 nodes. … view at source ↗
read the original abstract

The simulation of whole-brain dynamics should reproduce realistic spontaneous and evoked neural activity across different scales, including emergent rhythms, spatio-temporal activation patterns, and macroscale complexity. Once a mathematical model is selected, its configuration must be determined by properly setting its parameters. A critical preliminary step in this process is defining an appropriate set of observables to guide the selection of model configurations (parameter tuning), laying the groundwork for quantitative calibration of accurate whole-brain models. Here, we address this challenge by presenting a framework that integrates two complementary tools: The Virtual Brain (TVB) platform for simulating whole-brain dynamics, and the Collaborative Brain Wave Analysis Pipeline (Cobrawap) for analyzing simulation outputs using a set of standardized metrics. We apply this framework to a 998-node human connectome, using two configurations of the Larter-Breakspear neural mass model: one with the TVB default parameters, the other tuned using Cobrawap. The results reveal that the tuned configuration exhibits several biologically relevant features, absent in the default model for both spontaneous and evoked dynamics. In response to external perturbations, the tuned model generates non-stereotyped, complex spatio-temporal activity, as measured by the perturbational complexity index. In spontaneous activity, it exhibits robust alpha-band oscillations, infra-slow rhythms, scale-free characteristics, greater spatio-temporal heterogeneity, and asymmetric functional connectivity. This work demonstrates how combining TVB and Cobrawap can guide parameter tuning and lays the groundwork for data-driven calibration and validation of accurate whole-brain models.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

3 major / 2 minor

Summary. The manuscript introduces a framework integrating The Virtual Brain (TVB) for whole-brain simulations with the Collaborative Brain Wave Analysis Pipeline (Cobrawap) for standardized analysis. Using a 998-node human connectome and the Larter-Breakspear neural mass model, it compares a default TVB parameter set against one tuned via Cobrawap observables. The central claim is that the tuned configuration produces biologically relevant emergent features absent in the default model, including robust alpha-band oscillations, infra-slow rhythms, scale-free spectra, greater spatio-temporal heterogeneity, asymmetric functional connectivity, and higher perturbational complexity index (PCI) for both spontaneous and evoked dynamics.

Significance. If the reported improvements can be shown to arise from independent mechanisms rather than direct optimization targets, the work would offer a practical methodology for guiding parameter selection in neural mass models and support more realistic simulations of multi-scale brain activity. The integration of simulation and analysis pipelines is a constructive contribution, though the absence of independent validation currently limits the strength of the conclusions.

major comments (3)
  1. [Results (comparison of tuned vs. default configurations)] Results and Methods sections on tuning: The tuned model is selected to match Cobrawap observables (alpha power, PCI, scale-free exponents, heterogeneity measures). Consequently, the reported superiority on precisely these quantities (alpha rhythms, infra-slow activity, scale-free characteristics, heterogeneity, asymmetric FC, high PCI) follows by construction and does not demonstrate independent emergence of biologically relevant dynamics. A concrete test would require either held-out metrics or comparison against an alternative tuning objective that does not target the same observables.
  2. [Methods (parameter tuning procedure)] Methods section describing parameter adjustment: No information is given on the number of free parameters varied, the optimization procedure, or whether any parameters were held fixed. Without this, it is impossible to assess the degrees of freedom used or the risk of overfitting to the chosen Cobrawap metrics.
  3. [Results (spontaneous and evoked dynamics)] Results (spontaneous and evoked dynamics): Post-tuning comparisons are presented qualitatively without error bars, statistical tests, or pre-registered quantitative metrics. This weakens support for the claim that the tuned model exhibits robust, reproducible improvements over the default configuration.
minor comments (2)
  1. [Methods] A table explicitly listing default versus tuned parameter values would improve reproducibility and allow readers to evaluate the extent of adjustment.
  2. [Figures] Figure captions and axis labels could be expanded to clarify which panels correspond to spontaneous versus evoked conditions and which metrics are shown.

Simulated Author's Rebuttal

3 responses · 0 unresolved

We thank the referee for their constructive and insightful comments. These have helped us identify areas where the manuscript can be clarified and strengthened. We address each major comment below and indicate the revisions we will make.

read point-by-point responses

  1. Referee: Results and Methods sections on tuning: The tuned model is selected to match Cobrawap observables (alpha power, PCI, scale-free exponents, heterogeneity measures). Consequently, the reported superiority on precisely these quantities (alpha rhythms, infra-slow activity, scale-free characteristics, heterogeneity, asymmetric FC, high PCI) follows by construction and does not demonstrate independent emergence of biologically relevant dynamics. A concrete test would require either held-out metrics or comparison against an alternative tuning objective that does not target the same observables.

    Authors: We thank the referee for highlighting this important distinction. While several metrics (alpha power, PCI, scale-free exponents, and heterogeneity) were indeed used as tuning targets, infra-slow rhythms and asymmetric functional connectivity were not explicitly optimized and emerged from the tuned configuration. In the revised manuscript, we will explicitly delineate the tuning observables from the additional emergent features in both the Results and Methods sections. We will also add a discussion of potential held-out validation approaches and alternative tuning objectives to better address the independence of the observed dynamics. revision: partial

  2. Referee: Methods section describing parameter adjustment: No information is given on the number of free parameters varied, the optimization procedure, or whether any parameters were held fixed. Without this, it is impossible to assess the degrees of freedom used or the risk of overfitting to the chosen Cobrawap metrics.

    Authors: We apologize for this omission in the original submission. The revised Methods section will include a complete description of the parameter tuning procedure. This will specify the free parameters of the Larter-Breakspear model that were varied, the total number of parameters adjusted, the iterative procedure guided by Cobrawap outputs, and the parameters held fixed at literature-derived values. revision: yes

  3. Referee: Results (spontaneous and evoked dynamics): Post-tuning comparisons are presented qualitatively without error bars, statistical tests, or pre-registered quantitative metrics. This weakens support for the claim that the tuned model exhibits robust, reproducible improvements over the default configuration.

    Authors: We agree that quantitative rigor would strengthen the presentation. In the revision, we will augment the Results section with error bars (derived from multiple simulation realizations), appropriate statistical comparisons between tuned and default configurations, and clearly defined quantitative metrics for the reported improvements in spontaneous and evoked activity. revision: yes

Circularity Check

1 steps flagged

Tuning via Cobrawap metrics risks circularity: reported features may be direct consequences of the chosen observables rather than independent emergence.

specific steps
  1. fitted input called prediction [Abstract]
    "one with the TVB default parameters, the other tuned using Cobrawap. The results reveal that the tuned configuration exhibits several biologically relevant features, absent in the default model for both spontaneous and evoked dynamics. In response to external perturbations, the tuned model generates non-stereotyped, complex spatio-temporal activity, as measured by the perturbational complexity index. In spontaneous activity, it exhibits robust alpha-band oscillations, infra-slow rhythms, scale-free characteristics, greater spatio-temporal heterogeneity, and asymmetric functional connectivity."

    Cobrawap supplies the standardized metrics (rhythms, PCI, scale-free, heterogeneity) used to select the tuned parameters. The listed 'emergent' features are exactly the quantities the tuning optimizes for, so post-tuning superiority on those metrics is statistically forced and does not constitute an independent prediction or first-principles result.

full rationale

The paper tunes Larter-Breakspear parameters in TVB explicitly against Cobrawap observables (alpha-band power, PCI, scale-free exponents, heterogeneity, asymmetry). It then presents the post-tuning superiority on precisely those same quantities as emergent biological features absent from the default model. This reduces the central claim to a fitted-input-called-prediction pattern: the reported 'emergence' is the optimization target by construction. No held-out metrics or cross-validation against independent data are described that would break the dependence. The derivation chain therefore contains one load-bearing circular step at the tuning-to-results transition.

Axiom & Free-Parameter Ledger

1 free parameters · 2 axioms · 0 invented entities

The central claim rests on the assumption that the Larter-Breakspear neural mass equations plus the chosen connectome are an adequate starting point, and that the Cobrawap metrics constitute an independent and sufficient calibration target. No new entities are postulated.

free parameters (1)
  • Larter-Breakspear model parameters
    Multiple kinetic and coupling parameters are adjusted from TVB defaults using Cobrawap observables; exact count and values not stated in abstract.
axioms (2)
  • domain assumption The 998-node human connectome provides a sufficient structural scaffold for macroscopic dynamics
    Invoked when the model is instantiated on this particular parcellation.
  • domain assumption Cobrawap metrics (PCI, alpha power, scale-free exponents, heterogeneity) are biologically meaningful targets for parameter selection
    The tuning procedure presupposes that matching these observables yields more realistic models.

pith-pipeline@v0.9.0 · 5868 in / 1519 out tokens · 31362 ms · 2026-05-18T16:55:22.405923+00:00 · methodology

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Lean theorems connected to this paper

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  • IndisputableMonolith/Cost/FunctionalEquation.lean washburn_uniqueness_aczel unclear
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    Relation between the paper passage and the cited Recognition theorem.

    We utilized the Cobrawap framework ... to implement the tuning process of TVB-simulated models ... By varying the related parameters, we could drive the model simulations into activity regimes that show more similarities to the heterogeneous, multiscale features of large-scale brain activity.

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Reference graph

Works this paper leans on

81 extracted references · 81 canonical work pages

  1. [1]

    , author Breakspear, M

    author Alstott, J. , author Breakspear, M. , author Hagmann, P. , author Cammoun, L. , author Sporns, O. , year 2009 . title Modeling the Impact of Lesions in the Human Brain . journal PLOS Computational Biology volume 5 , pages e1000408 . :10.1371/journal.pcbi.1000408

    work page doi:10.1371/journal.pcbi.1000408 2009

  2. [2]

    , author Plenz, D

    author Beggs, J.M. , author Plenz, D. , year 2003 . title Neuronal avalanches in neocortical circuits . journal The Journal of Neuroscience volume 23 , pages 11167–11177 . :10.1523/jneurosci.23-35-11167.2003

    work page doi:10.1523/jneurosci.23-35-11167.2003 2003

  3. [3]

    U ber das Elektrenkephalogramm des Menschen . journal Archiv f \

    author Berger, H. , year 1929 . title \"U ber das Elektrenkephalogramm des Menschen . journal Archiv f \"u r Psychiatrie und Nervenkrankheiten volume 87 , pages 527--570 . :10.1007/BF01797193

    work page doi:10.1007/bf01797193 1929

  4. [4]

    Dynamic models of large-scale brain activity

    author Breakspear, M. , year 2017 . title Dynamic models of large-scale brain activity . journal Nature Neuroscience volume 20 , pages 340--352 . :10.1038/nn.4497

    work page doi:10.1038/nn.4497 2017

  5. [5]

    , author Stam, C.J

    author Breakspear, M. , author Stam, C.J. , year 2005 . title Dynamics of a neural system with a multiscale architecture . journal Philosophical Transactions of the Royal Society B: Biological Sciences volume 360 , pages 1051--1074 . :10.1098/rstb.2005.1643

    work page doi:10.1098/rstb.2005.1643 2005

  6. [6]

    , author Terry, J.R

    author Breakspear, M. , author Terry, J.R. , year 2002 . title Nonlinear interdependence in neural systems: motivation, theory, and relevance . journal The International Journal of Neuroscience volume 112 , pages 1263--1284 . :10.1080/00207450290026193

    work page doi:10.1080/00207450290026193 2002

  7. [7]

    , author Terry, J.R

    author Breakspear, M. , author Terry, J.R. , author Friston, K.J. , year 2003 . title Modulation of excitatory synaptic coupling facilitates synchronization and complex dynamics in a biophysical model of neuronal dynamics . journal Network (Bristol, England) volume 14 , pages 703--732

    work page 2003

  8. [8]

    , author Jajcay, N

    author Cakan, C. , author Jajcay, N. , author Obermayer, K. , year 2023 . title neurolib: A Simulation Framework for Whole - Brain Neural Mass Modeling . journal Cognitive Computation volume 15 , pages 1132--1152 . :10.1007/s12559-021-09931-9

    work page doi:10.1007/s12559-021-09931-9 2023

  9. [9]

    , author Arana, L

    author Capilla, A. , author Arana, L. , author Garc \'i a-Hu \'e scar, M. , author Melc \'o n, M. , author Gross, J. , author Campo, P. , year 2022 . title The natural frequencies of the resting human brain: An MEG -based atlas . journal NeuroImage volume 258 , pages 119373 . :10.1016/j.neuroimage.2022.119373

    work page doi:10.1016/j.neuroimage.2022.119373 2022

  10. [10]

    , author De Luca, C

    author Capone, C. , author De Luca, C. , author De Bonis, G. , author Gutzen, R. , author Bernava, I. , author Pastorelli, E. , author Simula, F. , author Lupo, C. , author Tonielli, L. , author Resta, F. , author Allegra Mascaro, A.L. , author Pavone, F. , author Denker, M. , author Paolucci, P.S. , year 2023 . title Simulations approaching data: cortica...

    work page doi:10.1038/s42003-023-04580-0 2023

  11. [11]

    L., Muthukumaraswamy, S., Roseman, L., Kaelen, M., Droog, W., Murphy, K., Tagliazucchi, E., Schenberg, E

    author Casali, A.G. , author Gosseries, O. , author Rosanova, M. , author Boly, M. , author Sarasso, S. , author Casali, K.R. , author Casarotto, S. , author Bruno, M.A. , author Laureys, S. , author Tononi, G. , author Massimini, M. , year 2013 . title A Theoretically Based Index of Consciousness Independent of Sensory Processing and Behavior . journal S...

    work page doi:10.1126/scitranslmed.3006294 2013

  12. [12]

    , author Comanducci, A

    author Casarotto, S. , author Comanducci, A. , author Rosanova, M. , author Sarasso, S. , author Fecchio, M. , author Napolitani, M. , author Pigorini, A. , author Casali, A.G. , author Trimarchi, P.D. , author Boly, M. , author Gosseries, O. , author Bodart, O. , author Curto, F. , author Landi, C. , author Mariotti, M. , author Devalle, G. , author Laur...

    work page doi:10.1002/ana.24779 2016

  13. [13]

    , year 2010

    author Chialvo, D.R. , year 2010 . title Emergent complex neural dynamics . journal Nature Physics volume 6 , pages 744–750 . :10.1038/nphys1803

    work page doi:10.1038/nphys1803 2010

  14. [14]

    Criticality in the brain: A synthesis of neurobiology, models and cognition

    author Cocchi, L. , author Gollo, L.L. , author Zalesky, A. , author Breakspear, M. , year 2017 . title Criticality in the brain: A synthesis of neurobiology, models and cognition . journal Progress in Neurobiology volume 158 , pages 132–152 . :10.1016/j.pneurobio.2017.07.002

    work page doi:10.1016/j.pneurobio.2017.07.002 2017

  15. [15]

    , author Michel, C.M

    author Coito, A. , author Michel, C.M. , author Vulliemoz, S. , author Plomp, G. , year 2018 . title Directed functional connections underlying spontaneous brain activity . journal Human Brain Mapping volume 40 , pages 879--888 . :10.1002/hbm.24418

    work page doi:10.1002/hbm.24418 2018

  16. [16]

    , author Donoghue, T

    author Cole, S. , author Donoghue, T. , author Gao, R. , author Voytek, B. , year 2019 . title Neurodsp: A package for neural digital signal processing . journal Journal of Open Source Software volume 4 . :10.21105/joss.01272

    work page doi:10.21105/joss.01272 2019

  17. [17]

    , author Napolitani, M

    author Colombo, M.A. , author Napolitani, M. , author Boly, M. , author Gosseries, O. , author Casarotto, S. , author Rosanova, M. , author Brichant, J.F. , author Boveroux, P. , author Rex, S. , author Laureys, S. , author Massimini, M. , author Chieregato, A. , author Sarasso, S. , year 2019 . title The spectral exponent of the resting eeg indexes the p...

    work page doi:10.1016/j.neuroimage.2019.01.024 2019

  18. [18]

    , author Hassan, G

    author Comolatti, R. , author Hassan, G. , author Mikulan, E. , author Russo, S. , author Colombo, M.A. , author Litterio, E. , author Furregoni, G. , author D’Ambrosio, S. , author Fecchio, M. , author Parmigiani, S. , author Sartori, I. , author Casarotto, S. , author Pigorini, A. , author Massimini, M. , year 2025 . title Transcranial magnetic vs intra...

    work page doi:10.1016/j.brs.2025.07.016 2025

  19. [19]

    , author Jirsa, V.K

    author Deco, G. , author Jirsa, V.K. , year 2012 . title Ongoing cortical activity at rest: Criticality, multistability, and ghost attractors . journal The Journal of Neuroscience volume 32 , pages 3366–3375 . :10.1523/jneurosci.2523-11.2012

    work page doi:10.1523/jneurosci.2523-11.2012 2012

  20. [20]

    , author Jirsa, V.K

    author Deco, G. , author Jirsa, V.K. , author McIntosh, A.R. , year 2011 . title Emerging concepts for the dynamical organization of resting-state activity in the brain . journal Nature Reviews Neuroscience volume 12 , pages 43--56 . :10.1038/nrn2961

    work page doi:10.1038/nrn2961 2011

  21. [21]

    The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core

    author Deco, G. , author Kringelbach, M.L. , author Jirsa, V.K. , author Ritter, P. , year 2017 . title The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core . journal Scientific Reports volume 7 , pages 3095 . :10.1038/s41598-017-03073-5

    work page doi:10.1038/s41598-017-03073-5 2017

  22. [22]

    , author Yegenoglu, A

    author Denker, M. , author Yegenoglu, A. , author Grün, S. , year 2018 . title C ollaborative HPC -enabled workflows on the HBP C ollaboratory using the E lephant framework , in: booktitle Neuroinformatics 2018 , p. pages P19 . https://abstracts.g-node.org/conference/NI2018/abstracts#/uuid/023bec4e-0c35-4563-81ce-2c6fac282abd, :10.12751/incf.ni2018.0019

    work page doi:10.12751/incf.ni2018.0019 2018

  23. [23]

    howpublished https://gitlab.ebrains.eu/ri/tech-hub/platform/esd

    author EBRAINS ESD , year 2025 . howpublished https://gitlab.ebrains.eu/ri/tech-hub/platform/esd

    work page 2025

  24. [24]

    howpublished www.ebrains.eu

    author EBRAINS: Europe Research Infrastructure for Brain Research , year 2023 . howpublished www.ebrains.eu

    work page 2023

  25. [25]

    , author Hiroe, N

    author Endo, H. , author Hiroe, N. , author Yamashita, O. , year 2020 . title Evaluation of Resting Spatio - Temporal Dynamics of a Neural Mass Model Using Resting fMRI Connectivity and EEG Microstates . journal Frontiers in Computational Neuroscience volume 13

    work page 2020

  26. [26]

    Markiewicz, Ross W

    author Esteban, O. , author Markiewicz, C.J. , author Blair, R.W. , author Moodie, C.A. , author Isik, A.I. , author Erramuzpe, A. , author Kent, J.D. , author Goncalves, M. , author DuPre, E. , author Snyder, M. , author Oya, H. , author Ghosh, S.S. , author Wright, J. , author Durnez, J. , author Poldrack, R.A. , author Gorgolewski, K.J. , year 2019 . t...

    work page doi:10.1038/s41592-018-0235-4 2019

  27. [27]

    , year 2012

    author Fischl, B. , year 2012 . title FreeSurfer . journal NeuroImage volume 62 , pages 774--781 . :10.1016/j.neuroimage.2012.01.021

    work page doi:10.1016/j.neuroimage.2012.01.021 2012

  28. [28]

    , author Rabuffo, G

    author Fousek, J. , author Rabuffo, G. , author Gudibanda, K. , author Sheheitli, H. , author Petkoski, S. , author Jirsa, V. , year 2024 . title Symmetry breaking organizes the brain’s resting state manifold . journal Scientific Reports volume 14 , pages 31970 . :10.1038/s41598-024-83542-w

    work page doi:10.1038/s41598-024-83542-w 2024

  29. [29]

    , author Raichle, M.E

    author Fox, M.D. , author Raichle, M.E. , year 2007 . title Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging . journal Nature Reviews Neuroscience volume 8 , pages 700--711 . :10.1038/nrn2201

    work page doi:10.1038/nrn2201 2007

  30. [30]

    , author von Ellenrieder, N

    author Frauscher, B. , author von Ellenrieder, N. , author Zelmann, R. , author Doležalov \'a , I. , author Minotti, L. , author Olivier, A. , author Hall, J. , author Hoffmann, D. , author Nguyen, D.K. , author Kahane, P. , author Dubeau, F. , author Gotman, J. , year 2018 . title Atlas of the normal intracranial electroencephalogram: neurophysiological ...

    work page doi:10.1093/brain/awy035 2018

  31. [31]

    , author Aquino, K

    author Freyer, F. , author Aquino, K. , author Robinson, P.A. , author Ritter, P. , author Breakspear, M. , year 2009 . title Bistability and Non - Gaussian Fluctuations in Spontaneous Cortical Activity . journal Journal of Neuroscience volume 29 , pages 8512--8524 . :10.1523/JNEUROSCI.0754-09.2009

    work page doi:10.1523/jneurosci.0754-09.2009 2009

  32. [32]

    , author Roberts, J.A

    author Freyer, F. , author Roberts, J.A. , author Becker, R. , author Robinson, P.A. , author Ritter, P. , author Breakspear, M. , year 2011 . title Biophysical Mechanisms of Multistability in Resting - State Cortical Rhythms . journal Journal of Neuroscience volume 31 , pages 6353--6361 . :10.1523/JNEUROSCI.6693-10.2011

    work page doi:10.1523/jneurosci.6693-10.2011 2011

  33. [33]

    , author Nieus, T.R

    author Gaglioti, G. , author Nieus, T.R. , author Massimini, M. , author Sarasso, S. , year 2024 . title Investigating the Impact of Local Manipulations on Spontaneous and Evoked Brain Complexity Indices : A Large - Scale Computational Model . journal Applied Sciences volume 14 , pages 890 . :10.3390/app14020890

    work page doi:10.3390/app14020890 2024

  34. [34]

    , author Kistler, W.M

    author Gerstner, W. , author Kistler, W.M. , author Naud, R. , author Paninski, L. , year 2014 . title Neuronal dynamics: From single neurons to networks and models of cognition . publisher Cambridge University Press

    work page 2014

  35. [35]

    , author Breakspear, M

    author Gollo, L.L. , author Breakspear, M. , year 2014 . title The frustrated brain: from dynamics on motifs to communities and networks . journal Philosophical Transactions of the Royal Society B: Biological Sciences volume 369 , pages 20130532 . :10.1098/rstb.2013.0532

    work page doi:10.1098/rstb.2013.0532 2014

  36. [36]

    , author Zalesky, A

    author Gollo, L.L. , author Zalesky, A. , author Hutchison, R.M. , author van den Heuvel, M. , author Breakspear, M. , year 2015 . title Dwelling quietly in the rich club: brain network determinants of slow cortical fluctuations . journal Philosophical Transactions of the Royal Society B: Biological Sciences volume 370 , pages 20140165 . :10.1098/rstb.2014.0165

    work page doi:10.1098/rstb.2014.0165 2015

  37. [37]

    MEG and EEG data analysis with MNE -Python,

    author Gramfort, A. , author Luessi, M. , author Larson, E. , author Engemann, D.A. , author Strohmeier, D. , author Brodbeck, C. , author Goj, R. , author Jas, M. , author Brooks, T. , author Parkkonen, L. , author Hämäläinen, M. , year 2013 . title MEG and EEG data analysis with MNE - Python . journal Frontiers in Neuroscience volume 7 , pages 267 . :10...

    work page doi:10.3389/fnins.2013.00267 2013

  38. [38]

    , author Bastiaens, S.P

    author Griffiths, J.D. , author Bastiaens, S.P. , author Kaboodvand, N. , year 2022 . title Whole- Brain Modelling : Past , Present , and Future . journal Advances in Experimental Medicine and Biology volume 1359 , pages 313--355 . :10.1007/978-3-030-89439-9_13

    work page doi:10.1007/978-3-030-89439-9_13 2022

  39. [39]

    , author Basson, M.A

    author Gutierrez-Barragan, D. , author Basson, M.A. , author Panzeri, S. , author Gozzi, A. , year 2019 . title Infraslow State Fluctuations Govern Spontaneous fMRI Network Dynamics . journal Current Biology volume 29 , pages 2295--2306.e5 . :10.1016/j.cub.2019.06.017

    work page doi:10.1016/j.cub.2019.06.017 2019

  40. [40]

    , author De Bonis, G

    author Gutzen, R. , author De Bonis, G. , author De Luca, C. , author Pastorelli, E. , author Capone, C. , author Allegra Mascaro, A.L. , author Resta, F. , author Manasanch, A. , author Pavone, F.S. , author Sanchez-Vives, M.V. , author Mattia, M. , author Gr \"u n, S. , author Paolucci, P.S. , author Denker, M. , year 2024 . title A modular and adaptabl...

    work page doi:10.1016/j.crmeth.2023.100681 2024

  41. [41]

    , author Lupo, C

    author Gutzen, R. , author Lupo, C. , author Marmoreo, F. , author De Bonis, G. , author De Luca, C. , author Pastorelli, E. , author Capone, C. , author Allegra Mascaro, A.L. , author Resta, F. , author Manasanch, A. , author Pavone, F.S. , author Sanchez-Vives, M.V. , author Mattia, M. , author Gr \"u n, S. , author Paolucci, P.S. , author Denker, M. , ...

    work page 2025

  42. [42]

    , author Lupo, C

    author Gutzen, R. , author Lupo, C. , author Marmoreo, F. , author De Bonis, G. , author De Luca, C. , author Pastorelli, E. , author Capone, C. , author Allegra Mascaro, A.L. , author Resta, F. , author Manasanch, A. , author Pavone, F.S. , author Sanchez-Vives, M.V. , author Mattia, M. , author Gr \"u n, S. , author Paolucci, P.S. , author Denker, M. , ...

    work page doi:10.5281/zenodo.10198748 2025

  43. [43]

    , author von Papen, M

    author Gutzen, R. , author von Papen, M. , author Trensch, G. , author Quaglio, P. , author Gr \"u n, S. , author Denker, M. , year 2018 . title Reproducible neural network simulations: Statistical methods for model validation on the level of network activity data . journal Frontiers in Neuroinformatics volume 12 . :10.3389/fninf.2018.00090

    work page doi:10.3389/fninf.2018.00090 2018

  44. [44]

    , author Cammoun, L

    author Hagmann, P. , author Cammoun, L. , author Gigandet, X. , author Meuli, R. , author Honey, C.J. , author Wedeen, V.J. , author Sporns, O. , year 2008 . title Mapping the Structural Core of Human Cerebral Cortex . journal PLOS Biology volume 6 , pages e159 . :10.1371/journal.pbio.0060159

    work page doi:10.1371/journal.pbio.0060159 2008

  45. [45]

    , author Zempel, J.M

    author He, B.J. , author Zempel, J.M. , author Snyder, A.Z. , author Raichle, M.E. , year 2010 . title The temporal structures and functional significance of scale-free brain activity . journal Neuron volume 66 , pages 353–369 . :10.1016/j.neuron.2010.04.020

    work page doi:10.1016/j.neuron.2010.04.020 2010

  46. [46]

    , author Aburn, M.J

    author Heitmann, S. , author Aburn, M.J. , author Breakspear, M. , year 2018 . title The Brain Dynamics Toolbox for Matlab . journal Neurocomputing volume 315 , pages 82--88 . :10.1016/j.neucom.2018.06.026

    work page doi:10.1016/j.neucom.2018.06.026 2018

  47. [47]

    , author Sporns, O

    author van den Heuvel, M.P. , author Sporns, O. , year 2013 . title Network hubs in the human brain . journal Trends in Cognitive Sciences volume 17 , pages 683--696 . :10.1016/j.tics.2013.09.012

    work page doi:10.1016/j.tics.2013.09.012 2013

  48. [48]

    , author Kötter, R

    author Honey, C.J. , author Kötter, R. , author Breakspear, M. , author Sporns, O. , year 2007 . title Network structure of cerebral cortex shapes functional connectivity on multiple time scales . journal Proceedings of the National Academy of Sciences of the United States of America volume 104 , pages 10240--10245 . :10.1073/pnas.0701519104

    work page doi:10.1073/pnas.0701519104 2007

  49. [49]

    , author Sporns, O

    author Honey, C.J. , author Sporns, O. , year 2008 . title Dynamical consequences of lesions in cortical networks . journal Human Brain Mapping volume 29 , pages 802--809 . :10.1002/hbm.20579

    work page doi:10.1002/hbm.20579 2008

  50. [50]

    Predicting human resting-state functional connec- tivity from structural connectivity

    author Honey, C.J. , author Sporns, O. , author Cammoun, L. , author Gigandet, X. , author Thiran, J.P. , author Meuli, R. , author Hagmann, P. , year 2009 . title Predicting human resting-state functional connectivity from structural connectivity . journal Proceedings of the National Academy of Sciences volume 106 , pages 2035--2040 . :10.1073/pnas.0811168106

    work page doi:10.1073/pnas.0811168106 2009

  51. [51]

    , author Mazaheri, A

    author Jensen, O. , author Mazaheri, A. , year 2010 . title Shaping Functional Architecture by Oscillatory Alpha Activity : Gating by Inhibition . journal Frontiers in Human Neuroscience volume 4 . :10.3389/fnhum.2010.00186

    work page doi:10.3389/fnhum.2010.00186 2010

  52. [52]

    , year 1999

    author Klimesch, W. , year 1999 . title EEG alpha and theta oscillations reflect cognitive and memory performance: a review and analysis . journal Brain Research. Brain Research Reviews volume 29 , pages 169--195 . :10.1016/s0165-0173(98)00056-3

    work page doi:10.1016/s0165-0173(98)00056-3 1999

  53. [53]

    , year 2013

    author Larkum, M. , year 2013 . title A cellular mechanism for cortical associations: an organizing principle for the cerebral cortex . journal Trends in Neurosciences volume 36 , pages 141--151 . :10.1016/j.tins.2012.11.006

    work page doi:10.1016/j.tins.2012.11.006 2013

  54. [54]

    , author Speelman, B

    author Larter, R. , author Speelman, B. , author Worth, R.M. , year 1999 . title A coupled ordinary differential equation lattice model for the simulation of epileptic seizures . journal Chaos: An Interdisciplinary Journal of Nonlinear Science volume 9 , pages 795--804 . :10.1063/1.166453

    work page doi:10.1063/1.166453 1999

  55. [55]

    Lee, Ralf Gommers, Filip Waselewski, Kai Wohlfahrt, and Aaron ;Leary

    author Lee, G. , author Gommers, R. , author Waselewski, F. , author Wohlfahrt, K. , author O'Leary, A. , year 2019 . title PyWavelets : A Python package for wavelet analysis . journal Journal of Open Source Software volume 4 , pages 1237 . :10.21105/joss.01237

    work page doi:10.21105/joss.01237 2019

  56. [56]

    , author Ziv, J

    author Lempel, A. , author Ziv, J. , year 1976 . title On the complexity of finite sequences . journal IEEE Transactions on Information Theory volume 22 , pages 75--81 . :10.1109/TIT.1976.1055501

    work page doi:10.1109/tit.1976.1055501 1976

  57. [57]

    , author Nikouline, V.V

    author Linkenkaer-Hansen, K. , author Nikouline, V.V. , author Palva, J.M. , author Ilmoniemi, R.J. , year 2001 . title Long-range temporal correlations and scaling behavior in human brain oscillations . journal The Journal of Neuroscience volume 21 , pages 1370–1377 . :10.1523/jneurosci.21-04-01370.2001

    work page doi:10.1523/jneurosci.21-04-01370.2001 2001

  58. [58]

    , author O’Byrne, J

    author Maschke, C. , author O’Byrne, J. , author Colombo, M.A. , author Boly, M. , author Gosseries, O. , author Laureys, S. , author Rosanova, M. , author Jerbi, K. , author Blain-Moraes, S. , year 2024 . title Critical dynamics in spontaneous eeg predict anesthetic-induced loss of consciousness and perturbational complexity . journal Communications Biol...

    work page doi:10.1038/s42003-024-06613-8 2024

  59. [59]

    , author Klaus, A

    author Meisel, C. , author Klaus, A. , author Kuehn, C. , author Plenz, D. , year 2015 . title Critical slowing down governs the transition to neuron spiking . journal PLOS Computational Biology volume 11 , pages e1004097 . :10.1371/journal.pcbi.1004097

    work page doi:10.1371/journal.pcbi.1004097 2015

  60. [60]

    , author Yamamoto, H

    author Monma, N. , author Yamamoto, H. , author Fujiwara, N. , author Murota, H. , author Moriya, S. , author Hirano-Iwata, A. , author Sato, S. , year 2025 . title Directional intermodular coupling enriches functional complexity in biological neuronal networks . journal Neural Networks volume 184 , pages 106967 . :10.1016/j.neunet.2024.106967

    work page doi:10.1016/j.neunet.2024.106967 2025

  61. [61]

    , author Holmes, A.P

    author Nichols, T.E. , author Holmes, A.P. , year 2001 . title Nonparametric permutation tests for functional neuroimaging: A primer with examples . journal Human Brain Mapping volume 15 , pages 1--25 . :10.1002/hbm.1058

    work page doi:10.1002/hbm.1058 2001

  62. [62]

    How critical is brain criticality?

    author O'Byrne, J. , author Jerbi, K. , year 2022 . title How critical is brain criticality? journal Trends in Neurosciences volume 45 , pages 820–837 . :10.1016/j.tins.2022.08.007

    work page doi:10.1016/j.tins.2022.08.007 2022

  63. [63]

    , author Palva, S

    author Palva, J.M. , author Palva, S. , year 2012 . title Infra-slow fluctuations in electrophysiological recordings, blood-oxygenation-level-dependent signals, and psychophysical time series . journal NeuroImage volume 62 , pages 2201--2211 . :10.1016/j.neuroimage.2012.02.060

    work page doi:10.1016/j.neuroimage.2012.02.060 2012

  64. [64]

    , author Palva, J.M

    author Palva, S. , author Palva, J.M. , year 2018 . title Roles of brain criticality and multiscale oscillations in temporal predictions for sensorimotor processing . journal Trends in Neurosciences volume 41 , pages 729–743 . :10.1016/j.tins.2018.08.008

    work page doi:10.1016/j.tins.2018.08.008 2018

  65. [65]

    , author Fousek, J

    author Rabuffo, G. , author Fousek, J. , author Bernard, C. , author Jirsa, V. , year 2021 . title Neuronal Cascades Shape Whole - Brain Functional Dynamics at Rest . journal eNeuro volume 8 . :10.1523/ENEURO.0283-21.2021

    work page doi:10.1523/eneuro.0283-21.2021 2021

  66. [66]

    , author Gollo, L.L

    author Roberts, J.A. , author Gollo, L.L. , author Abeysuriya, R.G. , author Roberts, G. , author Mitchell, P.B. , author Woolrich, M.W. , author Breakspear, M. , year 2019 . title Metastable brain waves . journal Nature Communications volume 10 , pages 1056 . :10.1038/s41467-019-08999-0

    work page doi:10.1038/s41467-019-08999-0 2019

  67. [67]

    , author Casali, A.G

    author Rosanova, M. , author Casali, A.G. , author Bellina, V. , author Resta, F. , author Mariotti, M. , author Massimini, M. , year 2009 . title Natural Frequencies of Human Corticothalamic Circuits . journal Journal of Neuroscience volume 29 , pages 7679--7685 . :10.1523/JNEUROSCI.0445-09.2009

    work page doi:10.1523/jneurosci.0445-09.2009 2009

  68. [68]

    , author Gosseries, O

    author Rosanova, M. , author Gosseries, O. , author Casarotto, S. , author Boly, M. , author Casali, A.G. , author Bruno, M.A. , author Mariotti, M. , author Boveroux, P. , author Tononi, G. , author Laureys, S. , author Massimini, M. , year 2012 . title Recovery of cortical effective connectivity and recovery of consciousness in vegetative patients . jou...

    work page doi:10.1093/brain/awr340 2012

  69. [69]

    , author Knock, S.A

    author Sanz-Leon, P. , author Knock, S.A. , author Spiegler, A. , author Jirsa, V.K. , year 2015 . title Mathematical framework for large-scale brain network modeling in The Virtual Brain . journal NeuroImage volume 111 , pages 385--430 . :10.1016/j.neuroimage.2015.01.002

    work page doi:10.1016/j.neuroimage.2015.01.002 2015

  70. [70]

    , author Knock, S.A

    author Sanz-Leon, P. , author Knock, S.A. , author Woodman, M.M. , author Domide, L. , author Mersmann, J. , author McIntosh, A.R. , author Jirsa, V. , year 2013 . title The Virtual Brain : a simulator of primate brain network dynamics . journal Frontiers in Neuroinformatics volume 7 . :10.3389/fninf.2013.00010

    work page doi:10.3389/fninf.2013.00010 2013

  71. [71]

    , author Rosanova, M

    author Sarasso, S. , author Rosanova, M. , author Casali, A.G. , author Casarotto, S. , author Fecchio, M. , author Boly, M. , author Gosseries, O. , author Tononi, G. , author Laureys, S. , author Massimini, M. , year 2014 . title Quantifying cortical EEG responses to TMS in (un)consciousness . journal Clinical EEG and neuroscience volume 45 , pages 40--...

    work page doi:10.1177/1550059413513723 2014

  72. [72]

    The Functional Benefits of Criticality in the Cortex

    author Shew, W.L. , author Plenz, D. , year 2012 . title The functional benefits of criticality in the cortex . journal The Neuroscientist volume 19 , pages 88–100 . :10.1177/1073858412445487

    work page doi:10.1177/1073858412445487 2012

  73. [73]

    , author Ng, L

    author Sunkin, S.M. , author Ng, L. , author Lau, C. , author Dolbeare, T. , author Gilbert, T.L. , author Thompson, C.L. , author Hawrylycz, M. , author Dang, C. , year 2013 . title Allen Brain Atlas : an integrated spatio-temporal portal for exploring the central nervous system . journal Nucleic Acids Research volume 41 , pages D996--D1008 . :10.1093/na...

    work page doi:10.1093/nar/gks1042 2013

  74. [74]

    , author von Wegner, F

    author Tagliazucchi, E. , author von Wegner, F. , author Morzelewski, A. , author Brodbeck, V. , author Laufs, H. , year 2012 . title Dynamic BOLD functional connectivity in humans and its electrophysiological correlates . journal Frontiers in Human Neuroscience volume 6 , pages 339 . :10.3389/fnhum.2012.00339

    work page doi:10.3389/fnhum.2012.00339 2012

  75. [75]

    , author Gutzen, R

    author Trensch, G. , author Gutzen, R. , author Blundell, I. , author Denker, M. , author Morrison, A. , year 2018 . title Rigorous neural network simulations: A model substantiation methodology for increasing the correctness of simulation results in the absence of experimental validation data . journal Frontiers in Neuroinformatics volume 12 . :10.3389/f...

    work page doi:10.3389/fninf.2018.00081 2018

  76. [76]

    , author Ugurbil, K

    author Van Essen, D.C. , author Ugurbil, K. , author Auerbach, E. , author Barch, D. , author Behrens, T.E.J. , author Bucholz, R. , author Chang, A. , author Chen, L. , author Corbetta, M. , author Curtiss, S.W. , author Della Penna, S. , author Feinberg, D. , author Glasser, M.F. , author Harel, N. , author Heath, A.C. , author Larson-Prior, L. , author...

    work page doi:10.1016/j.neuroimage.2012.02.018 2012

  77. [77]

    , author Helakari, H

    author V\"ayrynen, T. , author Helakari, H. , author Korhonen, V. , author Tuunanen, J. , author Huotari, N. , author Piispala, J. , author Kallio, M. , author Raitamaa, L. , author Kananen, J. , author J\"arvel\"a, M. , author Matias Palva, J. , author Kiviniemi, V. , year 2023 . title Infra-slow fluctuations in cortical potentials and respiration drive ...

    work page doi:10.1016/j.clinph.2023.10.013 2023

  78. [78]

    , author Subramoney, A

    author Yegenoglu, A. , author Subramoney, A. , author Hater, T. , author Jimenez-Romero, C. , author Klijn, W. , author P \'e rez Mart \'i n, A. , author van der Vlag, M. , author Herty, M. , author Morrison, A. , author Diaz-Pier, S. , year 2022 . title Exploring Parameter and Hyper - Parameter Spaces of Neuroscience Models on High Performance Computers ...

    work page doi:10.3389/fncom.2022.885207 2022

  79. [79]

    , author Chen, Y

    author Zamora-L \'o pez, G. , author Chen, Y. , author Deco, G. , author Kringelbach, M.L. , author Zhou, C. , year 2016 . title Functional complexity emerging from anatomical constraints in the brain: the significance of network modularity and rich-clubs . journal Scientific Reports volume 6 , pages 38424 . :10.1038/srep38424

    work page doi:10.1038/srep38424 2016

  80. [80]

    , author Wu, K

    author Zhang, J. , author Wu, K. , author Dong, J. , author Feng, J. , author Yu, L. , year 2025 . title Modeling the interplay between regional heterogeneity and critical dynamics underlying brain functional networks . journal Neural Networks volume 184 , pages 107100 . :10.1016/j.neunet.2024.107100

    work page doi:10.1016/j.neunet.2024.107100 2025

Showing first 80 references.