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.