The Virtual Brain is an open-source, multi-scale, multi-modal brain simulation platform. In this lesson, you get introduced to brain simulation in general and to The Virtual brain in particular. Prof. Ritter will present the newest approaches for clinical applications of The Virtual brain - that is, for stroke, epilepsy, brain tumors and Alzheimer’s disease - and show how brain simulation can imp

This lecture briefly introduces The Virtual Brain (TVB), a multi-scale, multi-modal neuroinformatics platform for full brain network simulations using biologically realistic connectivity, as well as its potential neuroscience applications: for example with epilepsy.

Topics covered in this lesson by Petra Ritter

• Introduction to TVB
• Motivations and achievements of TVB
• Presentation

The practical usage of The Virtual brain in its graphical user interface and via python scripts is introduced. 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

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.

Topics covered in this lesson by Paula Popa & Mihai Andrei

• Setting up the Graphical User Interface (GUI)
• Workflow of TVB and its major activities:

This hands-on 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.

Topics covered in this lesson by Paul Triebkorn

• TVB graphical u

This tutorial on how to simulate using TVB 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Paul Triebkorn

• Step by step guide to performing a simulation with TVB

The concept of neural masses, an application of mean field theory, is introduced as a possible surrogate for electrophysiological signals in brain simulation. The mathematics of neural mass models and their integration to a coupled network are explained.

Bifurcation analysis is presented as an important technique in the understanding of non-linear systems and as a fundamental method in the des

This lecture introduces the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components.

Topics covered in this lesson by Randy McIntosh

• Motivation for The Virtual Brain
• The Virtual Brain Platform
• Architecture and access
• Dynamics
• Geometry & Connectivity
• Simulations & Data Generation
• The Virt

Related publication

Inferring multi-scale neural mechanisms with brain network modelling, published in eLife, January 2018, by Michael Schirner, Anthony Randal McIntosh, Viktor Jirsa, Gustavo Deco, Petra Ritter

doi: 10.7554/eLife.28927

Abstract

The neurophysiological processes underlying non-invasive brain activity m

This presentation on population models and phase plane 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... TVB is a full brain simulation platform.

Topics covered in this lesson by Dr. Michael Schirner

• What is a population model
• What is phase plane
• Cons

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.

Topics covered in this les

In this lecture we will focus on a paper called “The Virtual Epileptic Patient: Individualized whole-brain models of epilepsy spread”. Within their work, the authors used the epileptor model to simulate a patient's individual seizure.

To understand the concept we will have a closer look at the equations of the epileptor model and particular the epileptogenicity index which controls the excita

After introducing the local epileptor model, 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.

Topics covered in this lesson by P

This lecture gives an overview on the article “Individual brain structure and modelling predict seizure propagation” where 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.

Topics cov

The simulation of the virtual epileptic patient is presented as an example of advanced brain simulation as a translational approach to deliver improved results in clinics. The fundamentals of epilepsy are explained.

On this basis, the concept of epilepsy simulation is developed. By using an iPython notebook, the detailed process of this approach is explained step by step.

In the end, you

Along the example of a patient with bi-temporal epilepsy, we show step by step how to develop a Virtual Epileptic Patient (VEP) brain model and integrate patient-specific information such as brain connectivity, epileptogenic zone and MRI lesions.

The patient's brain network model is then evaluated via simulation, data fitting and mathematical analysis.

This lecture demonstrates how to dev

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.

Topics cov

This lecture on modeling epilepsy using TVB by Julie Courtiol 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Julie Courtiol

• Introduction to epilepsy
• How to model epilepsy with TVB

An overview of the Bayesian Virtual Epileptic Patient (BVEP), a research use case using TVB supported on the EBRAINS infrastructure.

Topics covered in this lesson by Meysam Hashemi

• Bayesian model inversion
• BVEP workflow
• Jupyter notebook example
• Python & Stan interfaces
• PyMC3 example
• Comparing Stan & PyMC3 accuracy

This lecture focuses on higher-level simulation scenarios using stimulation protocols. We demonstrate how to build stimulation patterns in TVB, and use them in a simulation to induced activity dissipating into experimentally known resting-state networks in human and mouse brain, a well as to obtain EEG recordings reproducing empirical findings of other researchers.

Topics covered in this les

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.

Topics covered in this lesson by Paul Triebkorn

• TVB graphical user interface
• Brain stimulation

This lecture on surface-based simulations and deep brain stimulations by Jil Meier 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Jil Meier

• Surface-based simulations: what? why? how?

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 data set in The Virtual Brain.

Topics cov

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

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. Afterwards the modified connectome will be used for simulations and the resulting activity will be analysed using functional connectivity.

Topics covered in this lesson by Pau

Tutorial on how to use the image processing pipeline with the HBP collab

Related publication

An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data, published in NeuroImage, August 2015, by Michael Schirner, Simon Rothmeier, Viktor K. Jirsa, Anthony Randal McIntosh, PetraRitter

doi: 10.1016/j.neuroimage.2015.03.055

Abst

This tutorial on importing and creating brain models in The Virtual Brain 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... TVB is a full brain simulation platform.

Topics covered in this lesson by Patrik Bey

• Importing Virtual Brain ready data into TVB
• Cr

This lecture on generating TVB ready imaging data 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Paul Triebkorn

• Pipeline overview
• Structural pre-processing
• Diffusion pre-process

Walk through of the Image Processing Pipeline, an integral part of the TVB on EBRAINS integrated workflows

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

An overview of the process of constructing models for TVB automatically on the EBRAINS infrastructure

Topics covered in this lesson by Michiel Van der Vlag and Sandra Diaz

• RateML
• Python vs CUDA models XML implementation
• Parameter Space Exploration on the GPU
• Current status

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.

Topics cove

Tutorial on how to perform multi-scale simulation of Alzheimer's disease on The Virtual Brain Simulation Platform

Related publication

Linking Molecular Pathways and Large-Scale Computational Modeling to Assess Candidate Disease Mechanisms and Pharmacodynamics in Alzheimer's Disease, published in frontiers

Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage). This tutorial comprises a didactic video, jupyter notebooks, and full data set for the construction of virtual brains from patients and health controls.

Related publication

[Modeling Brain Dynamics in Brain Tumor Patients Using the Virtual Brain](https://www.eneuro.org/con

This tutorial on simulating The Virutal Mouse Brain by Patrik Bey 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... TVB is a full brain simulation platform.

Topics covered in this lesson by Patrik Bey

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

This tutorlal on modeling a virtual macaque brain 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Julie Courtiol

• Step-by-step guide to modeling a virtual macaque brain using The Virtu

This lecture on generating 3D brain model outside The Virtual Brain 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... TVB is a full brain simulation platform.

Topics covered in this lesson by Michael Schirner

• 3D visualization with Python and mayavi (code)*

This presentation 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Dionysios Perdikis

• Introduction to TVB-multi-scale extension
• Introduction to TVB-multi-scale/TVB_nest interface

This lecture on multi-scale entropy 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. TVB is a full brain simulation platform.

Topics covered in this lesson by Jil Meier

• Introduction to entropy
• Introduction to multi-scale entropy (MSE)
• Evidence from clin

Tutorial on how to use the TVB-NEST toolbox co-simulation in HBP collab

Tutorial on how to use TVB-NEST toolbox on your local computer

An overview of The Virtual Brain integrated workflows on EBRAINS

Topics covered in this lesson by Petra Ritter

• Intro to TVB
• Running simulations with TVB
• Security of personal data
• Collaboration tools (jupyter notebooks)
• TVB datasets on EBRAINS

An overview of The Virtual Brain simulator and it's integration into the Human Brain Project Cloud and EBRAINS infrastructure

Topics covered in this lesson by Lia Domide

• Technical stack
• Packages
• TVB in HBP @ CSCS
• Plans & next steps

An overview of the EBRAINS integrated Fast TVB, a C implementation of TVB that is orders of magnitude faster than the original Python TVB, and capable of performing parallelizable simulations in the cloud.

Topics covered in this lesson by Michael Schirner

• What is Fast TVB
• Jupyter notebook review
• Data formats
• API
• Software maturity, integration, testing, versioning & deploymen

An overview of the process of developing the TVB-NEST co-simulation on the EBRAINS infrastructure, and its use cases

Topics covered in this lesson by Dionysios Perdikis

• Motivation; Software structure
• Default workflow
• EBRAINS collaboratory
• Use cases
• Modifications to the TVB simulator
• Benchmarking
• Parameters exploration
• Future work

An overview of the multi-scale co-simulation between TVB-NEST and Elephant on the EBRAINS infrastructure

Topics covered in this lesson by Wouter Klijn

• Alpha release workflow
• Co-simulation of NEST & TVP using Elephant
• Multiscale simulation design
• Motivation for this method