The Virtual Brain

Last modified by jessicamitchell on 2023/09/11 11:44

Available tutorials:

Building Your Own Brain Network Model

Level: beginner

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.

Getting Started

Level: beginner

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

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

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.

Brain stimulation in The Virtual Brain

Level: advanced

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)

Clinical Applications - Stroke Recovery & Dementia

Level: advanced

Topics covered in this lesson by Randy McIntosh:
General introduction to stroke
TVB simulation workflow for stroke patients
Structural reconstruction: “Virtual Brain Transplant”
Parameter space exploration and fitting
General introduction to dementia
TVB simulation workflow for patients with dementia
Pre-processing issues related to atrophy
Two-stage modeling: sub- and full-brain network model
Cognition predictor: model parameters vs. metrics of neuroimaging data

Evoked Responses in the Visual Cortex

Level: advanced

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, Create a run function to perform the simulation

Exploring a model

Level: advanced

Create An Interactive Phase-Plane, Specifying Stochastic Integration,
Simulate and Visualize

Hands-On: Modeling stroke brain

Level: advanced

Topics covered in this lesson by Paul Triebkorn:
Manipulation of the connectome
Parameter space exploration
Functional connectivity analysis

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

Level: advanced

How to use the TVB-NEST toolbox co-simulation in HBP collab

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

Level: advanced

Topics covered in this lesson by Patrik Bey:
Importing Virtual Brain ready data into TVB
Creating brain models in TVB

Integrated workflows: Image processing pipeline

Level: advanced

Topics covered in this lesson by Michael Schirner:
TVB processing pipelines with KG annotated outputs
Software architecture
Pipeline APIs
Software maturity, integration, testing, versioning & deployment
MINDS format
Computing requirements
Security requirements

Modeling brain dynamics in brain tumor patients using The Virtual Brain

Level: advanced

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

Modeling Epilepsy

Level: advanced

Exploring the Epileptor model, Region based simulation of a temporal lobe seizure, Modeling surgical resection, Triggering a seizure by stimulation

Modelling Epilepsy with The Virtual Brain

Level: advanced

Topics covered in this lesson by Julie Courtiol:
Fundamentals of epilepsy
How to build a virtual epileptic patient?
Hand-on-guide through the iPython notebook
Creating your own epilepsy simulations with TVB

Region simulation tutorial

Level: advanced

A script implementing the basic region imulation.

Resting State Networks

Level: advanced

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

Simulating The Virtual Mouse Brain (TVMB)

Level: advanced

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

Surface simulation tutorial

Level: advanced

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