Tutorials & E-Library

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

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

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.

Presurgical planning for brain tumor resection aims at delineating eloquent tissue in the vicinity of the lesion to spare during surgery. To this end, noninvasive neuroimaging techniques such as functional MRI and diffusion-weighted imaging fiber tracking are currently employed.

However, taking into account this information is often still insufficient, as the complex nonlinear dynamics of the brain impede straightforward prediction of functional outcome after surgical intervention.

Large-scale brain network modeling carries the potential to bridge this gap by integrating neuroimaging data with biophysically based models to predict collective brain dynamics.

As a first step in this direction, an appropriate computational model has to be selected, after which suitable model parameter values have to be determined. To this end, we simulated large-scale brain dynamics in 25 human brain tumor patients and 11 human control participants using The Virtual Brain, an open-source neuroinformatics platform. Local and global model parameters of the Reduced Wong–Wang model were individually optimized and compared between brain tumor patients and control subjects. In addition, the relationship between model parameters and structural network topology and cognitive performance was assessed.

Results showed

(1) significantly improved prediction accuracy of individual functional connectivity when using individually optimized model parameters;
(2) local model parameters that can differentiate between regions directly affected by a tumor, regions distant from a tumor, and regions in a healthy brain;
and (3) interesting associations between individually optimized model parameters and structural network topology and cognitive performance.

Michael Schirner gives a walk through of the Image Processing Pipeline, an integral part of the TVB on EBRAINS integrated workflows.

TVB-EBRAINS workflows developed during SGA2 in Codesign Project The Virtual Brain in the EU Flagship Human Brain Project

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.

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.

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 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.

An overview of the Bayesian Virtual Epileptic Patient (BVEP), a research use case using TVB supported on the EBRAINS infrastructure.
In the end, you are able to perform simple epilepsy simulations your own.

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 are able to perform simple epilepsy simulations your own.

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.