User’s Guide

This document provides the most basic tutorial to get the new user started working with TheVirtualBrain. As TheVirtualBrain is updated from time to time, please check for updates on our web site: http://www.thevirtualbrain.org.

• Overview of TheVirtualBrain
• Installing the Application
  • TheVirtualBrain’s interfaces
  • Launching the application
    • Launching the GUI
    • Launching scripting interfaces
  • Configuring TVB
  • Users of TVB (registration and default account)
  • Uninstalling TVB
  • Upgrading the Application
  • Removing user data
  • Finding TVB Demo Data
  • Supported operating systems
  • Application requirements
• Configuring TVB
  • Configuring a headless TVB
  • Setting up a client/server configuration
  • Installing PosgreSQL on Windows
• Web User Interface of TheVirtualBrain
  • User
    • TVB Settings
    • Login
    • Register
    • User Profile
  • Project
    • List of All Projects
    • Basic Properties
    • Image Archive
    • Operations
    • Data Structure
  • Simulator
    • Simulation History
    • Configure a Simulation
      • The Phase plane page
      • Region-based simulations
      • Surface-based simulations
      • Parameter Space Exploration
    • Display Simulation Results
    • Simple Visualizers
      • Brain Activity Visualizer
      • Time Series Visualizer (svg/d3)
      • Animated Time Series Visualizer
      • Dual Brain Activity Visualizer
      • Volume Visualizer
      • Connectivity Measure Visualizer
      • Topographic Visualizer
      • Surface Visualizer
      • Sensor Visualizer
      • Local Connectivity Visualizer
      • Annotations Visualizer
    • Group Display
      • Discrete PSE Visualizer
      • Isocline PSE Visualizer
    • Analyzers + Visualizers
      • Covariance Visualizer
      • Cross Coherence Visualizer
      • Complex Coherence Visualizer
      • Cross Correlation Visualizer
      • Pearson Coefficients Visualizer
      • Fourier Spectrum Visualizer
      • Principal Component Visualizer
      • Independent Component Visualizer
      • Wavelet Spectrogram Visualizer
      • Matrix Visualizer
      • Connectivity Edge Bundle Visualizer
      • Pearson Edge Bundle Visualizer
  • Analyze
    • Cross-correlation of nodes
    • Fourier Spectral Analysis
    • TimeSeries Metrics
    • Cross coherence of nodes
    • Complex coherence of nodes
    • Temporal covariance of nodes
    • Principal Component Analysis (PCA)
    • Independent Component Analysis (ICA)
    • Continuous Wavelet Transform (CWT)
    • Brain Connectivity Toolbox Analyzers
    • Functional Connectivity Dynamics metric
  • Stimulus
    • Region level stimulus
    • Surface level stimulus
  • Connectivity
    • Long Range Connectivity
      • Connectivity Matrix Editor
      • Viewers
      • Connectivity 3D Edges
      • Connectivity 2D Viewer
      • Visualizing Connectivity Measures
      • Space-Time
    • Local Connectivity
    • Allen Connectome Downloader
    • Siibra Connectivity Creator
• Console Interfaces of TheVirtualBrain
  • TVB Profiles
  • Ipython notebook shell
  • Terminal shell
• A Description of a Complete Dataset
  • General Considerations
  • Parcellation Mask
  • Connectivity and path length data
  • Cortical Mesh
  • Region Mapping
  • Head model
  • The TVB demonstration dataset
  • Other datasets
    • Hagmann
    • The Human Connectome Project
• TheVirtualBrain Data Formats
  • Exchange Projects
    • Export Project
      • File Format
    • Import Project
      • File Format
  • Export Data
    • File Format
  • Import Data
    • Import Data in TheVirtualBrain Format
      • File Format
    • Import Volume Time Series from NIFTI-1 Format
      • File Format
    • Import Sensors
      • File Format
    • Import Connectivity from ZIP
      • File Format
    • Import Surface from ZIP
      • File Format
    • Import Surface from wavefront obj
      • File Format
    • Import Surface and TimeSeries from GIFTI
      • File Format
    • Import Region Mapping
      • File Format
    • Import Projection Matrix
      • File Format

Copyright notice

Note

TheVirtualBrain is a brain-simulation software. See also http://www.thevirtualbrain.org

© 2012-2024, Baycrest Centre for Geriatric Care (“Baycrest”) and others

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

CITATION

When using The Virtual Brain for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

If you’re using The Virtual Brain v2.2 or higher, please cite additionally this paper:

M. Schirner, L. Domide, D. Perdikis, P. Triebkorn, L. Stefanovski, R. Pai, P. Popa, B. Valean, J. Palmer, C. Langford, A. Blickensdörfer, M. van der Vlag, S. Diaz-Pier, A. Peyser, W. Klijn, D. Pleiter, A. Nahm, O. Schmid, M. Woodman, L. Zehl, J. Fousek, S. Petkoski, L. Kusch, M. Hashemi, D. Marinazzo, J.-F. Mangin, A. Flöel, S. Akintoye, B. C. Stahl, M. Cepic, E. Johnson, G. Deco, A. R. McIntosh, C. C. Hilgetag, M. Morgan, B. Schuller, A. Upton, C. McMurtrie, T. Dickscheid, J. G. Bjaalie, K. Amunts, J. Mersmann, V. Jirsa, P. Ritter (2022) Brain simulation as a cloud service: The Virtual Brain on EBRAINS NeuroImage 2022, doi.org/10.1016/j.neuroimage.2022.118973