This lesson introduces the practical usage of The Virtual Brain (TVB) in its graphical user interface and via python scripts. In the graphical user interface, you are guided through its data repository, simulator, phase plane exploration tool, connectivity editor, stimulus generator, and the provided analyses. The implemented iPython notebooks of TVB are presented, and since they are public, can be used for further exploration of TVB. 

This hands-on tutorial focuses on a brief introduction to the GUI of TVB. You will visualize a structural connectome and use it for simulation. The local neural mass model will be explored through the phase plane viewer and a parameter space exploration will be performed to observe different dynamics of the large-scale brain model.

Simulate your own stimulation with the TVB graphical user interface. This hands-on shows you how to configure a stimulus for a specific brain region and apply it to the simulation. Afterwards the results are visualized with the TVB 3D viewer.

Explore how to setup an epileptic seizure simulation with the TVB graphical user interface. This lesson will show you how to program the epileptor model in the brain network to simulate a epileptic seizure originating in the hippocampus. It will also show how to upload and view mouse connectivity data, as well as give a short introduction to the python script interface of TVB.

Manipulate the default connectome provided with TVB to see how structural lesions effect brain dynamics. In this hands-on session you will insert lesions into the connectome within the TVB graphical user interface (GUI). Afterwards, the modified connectome will be used for simulations and the resulting activity will be analysed using functional connectivity.

Brain network reconstruction from empirical data is of key importance to generate personalized virtual brain models. This lecture will introduce the basic concepts of preprocessing structural, functional and diffusion weighted neuroimages. It highlights the latest methods and pipelines to extract structural as well as functional connectomes according to a multimodal parcellation.

Learn how to simulate strokes with the simulation platform, The Virtual Brain. We will go through two papers: Functional Mechanisms of Recovery after Stroke: Modeling with The Virtual Brain and The Virtual Brain: Modeling Biological Correlates of Recovery After Chronic Stroke, and apply the same processes with our own structural connectivity dataset in The Virtual Brain.

In this lesson you will learn how to simulate seizure events and epilepsy in The Virtual Brain. We will look at the paper On the Nature of Seizure Dynamics, which describes a new local model called the Epileptor, and apply this same model in The Virtual Brain. This is part 1 of 2 in a series explaining how to use the Epileptor. In this part, we focus on setting up the parameters.

In this lecture we will focus on a paper called The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread. We will have a closer look at the equations of the epileptor model and particular the epileptogenicity index, which controls the excitability of each brain region. Subsequently, we will begin to setup the epileptogenic zone in our own brain network model with TVB.

After introducing the local epileptor model in the previous two videos, we will now use it in a large-scale brain simulation. We again focus on the paper The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread. Two simulations with different epileptogenicity across the network are visualized to show the difference in seizure spread across the cortex.

This lecture gives an overview on the article Individual brain structure and modelling predict seizure propagation, in which 15 subjects with epilepsy were modelled to predict individual epileptogenic zones. With the TVB GUI we will model seizure spread and the effect of lesioning the connectome. The impact of cutting edges in the network on seizure spreading will be visualized.

This lecture presents the Graphical (GUI) and Command Line (CLI) User Interface of TVB. Alongside with the speakers, explore and interact with all means necessary to generate, manipulate and visualize connectivity and network dynamics.

This lecture presents two recent clinical case studies using TVB: stroke recovery and dementia (due to Alzheimer’s Disease (AD)). Using a multi-scale neurophysiological model based on empirical multi-modal neuroimaging data, we show how local and global biophysical parameters characterize changes in individualized patient-specific brain dynamics, predict recovery of motor function for stroke patients, and correlate with individual differences in cognition for AD patients.

This tutorial demonstrates how to use the image processing pipeline with the HBP collab.

This tutorial provides instruction on how to use the TVB-NEST toolbox co-simulation in HBP collab.

In this tutorial, you will learn how to use TVB-NEST toolbox on your local computer.

This tutorial provides instruction on how to perform multi-scale simulation of Alzheimer's disease on The Virtual Brain Simulation Platform.

This presentation accompanies the paper entitled: An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data (see link below to download publication). 

This lesson consists of a supplementary video for the publication: Inferring multi-scale neural mechanisms with brain network modelling.

Research Resource Identifiers (RRIDs) are ID numbers assigned to help researchers cite key resources (e.g., antibodies, model organisms, and software projects) in biomedical literature to improve the transparency of research methods.