The Virtual Brain

Last modified by abonard on 2025/04/10 15:18

Beginner

GUI tutorials – Getting Started

Level: beginner  Type: user documentation

This tutorial presents the basic steps to upload a project, and share data with other users and/or link data to other TVB projects. After this tutorial you should be able to import a new dataset, create, import, export and delete a project and share your data with among your projects or with a colleague

My first simulation with The Virtual Brain

Level: beginner  Type: video tutorial

This presentation by Paul Triebkorn is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging. brain simulation. personalised brain models, TVB use cases, etc.

Population Models in The Virtual Brain (TVB) and the Phase Plane

Level: beginner  Type: video tutorial

This presentation by Dr. Michael Schirner is part of the TVB Node 10 series, a 4 day workshop dedicated to learning about The Virtual Brain, brain imaging. brain simulation. personalised brain models, TVB use cases, etc.

GUI tutorials – Building Your Own Brain Network Model

Level: beginner  Type: user documentation

This tutorial presents the basic anatomy of a brain network model at the region level using The Virtual Brain’s (TVB’s) graphical interface. You are not expected to launch all the simulations.

We will be using the Default Project that should be imported when you start TVB. We’ll only go through the necessary steps required to reproduce some simulations. You can always start over, click along and/or try to change parameters.

Advanced

The Bayesian Virtual Epileptic Patient (BVEP)

Level: advanced  Type: video tutorial

Meysam Hashemi in his tutorial touches upon bayesian model inversion, BVEP workflow, Jupyter notebook examples, Python & Stan interfaces, PyMC3 example and comparing Stan & PyMC3 accuracy.

GUI tutorials – Modeling Epilepsy

Level: advanced  Type: -

The main goal of this tutorial is to provide a clear understanding of how we can reproduce clinically relevant senarios such as the modelisation of propagation of an epileptic seizure in the human brain, electrical stimulation of a brain region that can trigger a seizure, or surgical resection of brain regions.

We will be using the ModelingEpilepsy project. We’ll only go through the necessary steps required to reproduce these simulations, along with the relevant outline. You can always start over, click along and/or try to change parameters. We will use the default subject connectivity matrix and surface.

GUI tutorials – Resting State Networks

Level: advanced  Type: user documentation

This tutorial will demonstrate a brain network model approach to the human resting state and its network structure, with the goals of understanding how to parametrize a neural mass model, place it in a network context, identify and explore the relevant parameter space, perform extended simulations in the realistic region of parameter space and finally analyze the resulting simulated fMRI BOLD signals to reproduce experimental results published in the resting state literature.

Integrated workflows: Image processing pipeline

Level: advanced  Type: video tutorial

Michael Schirner in this tutorial is going over the TVB processing pipelines with KG annotated outputs, the Software architecture, the Pipeline APIs, the Software maturity, integration, testing, versioning & deployment as well as the MINDS format, the Computing and Security requirements.

TVB to NEST multi-scale simulation

Level: advanced  Type: video tutorial

Dionysios Perdikis in this tutorial is going over the software structure, default workflow, EBRAINS collaboratory usage, Use cases, Modifications to the TVB simulator, Benchmarking, Parameters exploration and future works.

Scripting tutorials – Modeling Epilepsy

Level: advanced  Type: interactive tutorial

In this tutorial we will be exploring the epileptor model, look into region based simulation of a temporal lobe seizure and start modeling surgical resection, and triggering a seizure by stimulation.

Hands-On: Modeling stroke brain

Level: advanced  Type: video tutorial

Paul Triebkorn will guide you through manipulation of the connectomes, parameter space exploration and functional connectivity analysis.

Modeling brain dynamics in brain tumor patients using The Virtual Brain

Level: advanced  Type: video tutorial

Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage).

Import Virtual Brain ready data into TVB and create a brain model

Level: advanced  Type: video tutorial

Patrik Bey covers in this lesson how to import Virtual Brain ready data into TVB and how to create brain models in TVB.

TVB Clinical Applications - Stroke Recovery & Dementia

Level: advanced  Type: video tutorial

Randy McIntosh in this tutorial first gives a general introduction to stroke and later covers topics on the TVB simulation workflow for stroke patients, structural reconstruction: “Virtual Brain Transplant”, parameter space exploration and fitting, general introduction to dementia, the TVB simulation workflow for patients with dementia, pre-processing issues related to atrophy, two-stage modeling: sub- and full-brain network model and cognition predictor: model parameters vs. metrics of neuroimaging data.

Scripting tutorials – Evoked Responses in the Visual Cortex

Level: advanced  Type: interactive tutorial

We will show you how to set up a connectivity and its attributes, set up a model, choose an integration scheme (noise or not?), build a stimulus, create a simulator instance and finally how to create a run function to perform the simulation.

Scripting tutorials – Region simulation tutorial

Level: advanced  Type: interactive tutorial

Here you will learn how to use a script implementing the basic region imulation.

Simulating The Virtual Mouse Brain (TVMB)

Level: advanced  Type: video tutorial

Step-by-step guide to simulating The Virtual Mouse Brain.

Surface-based simulations and deep brain stimulations

Level: advanced  Type: video tutorial

Jil Meier covers in this tutorial surface-based simulations as well as deep brain simulations answering  what they are, when to use them and how?

Human Brain Project (HBP) TVB-NEST co-simulation

Level: advanced  Type: video tutorial

Learn how to use the TVB-NEST toolbox co-simulation in the HBP collab.

Scripting tutorials – Surface simulation tutorial

Level: advanced  Type: interactive tutorial

In addition to the components discussed for a region simulation here we introduce one new major component, that is:

Cortex, the primary component of which is a mesh surface defining a 2d representation of the convoluted cortical surface embedded in 3d space. This object includes a range of ancillary information and methods required for using it in simulations.

We will also introduce two new Monitors that make more sense in the context of surface simulations

Scripting tutorials – Exploring a neural mass model

Level: advanced  Type: interactive tutorial

In this tutorial we will look into creating an interactive phase-plane, specifying stochastic integration and finally learn how to simulate and visualise these models.

Scripting tutorials – Resting State Networks

Level: advanced  Type: interactive tutorial

We will demonstrate some starting points for modeling resting state networks in TVB, using the default data set.

Brain stimulation in The Virtual Brain

Level: advanced  Type: video tutorial

Topics covered in this lesson by Andreas Spiegler:
Introduction to stimulation paradigm and stimulation techniques
How to model brain stimulation with TVB
Region-based stimulus
Surface-based stimulus
Examples of stimulated network dynamics using
Human brain model
Mouse brain model
Example of Transcranial Direct-Current Stimulation (tDCS)

Modelling Epilepsy with The Virtual Brain

Level: advanced  Type: video tutorial

Julie Courtiol is covering in this tutorial the fundamentals of epilepsy and closes in on the question on how to build a virtual epileptic patient? The lessons is followed with a hands-on-guide through the iPython notebook and with creating your own epilepsy simulations with TVB.