The Virtual Brain

Available tutorials:

=== [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] ===

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//Level: beginner//

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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.

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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.

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=== [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] ===

//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

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=== [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===

//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>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===

//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>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Andreas Spiegler:

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Introduction to stimulation paradigm and stimulation techniques

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How to model brain stimulation with TVB

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Region-based stimulus

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Surface-based stimulus

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Examples of stimulated network dynamics using

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Human brain model

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Mouse brain model

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Example of Transcranial Direct-Current Stimulation (tDCS)

=== [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Randy McIntosh:

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General introduction to stroke

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TVB simulation workflow for stroke patients

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Structural reconstruction: “Virtual Brain Transplant”

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Parameter space exploration and fitting

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General introduction to dementia

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TVB simulation workflow for patients with dementia

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Pre-processing issues related to atrophy

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Two-stage modeling: sub- and full-brain network model

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Cognition predictor: model parameters vs. metrics of neuroimaging data

=== [[Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//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

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=== [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Create An Interactive Phase-Plane, Specifying Stochastic Integration,

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Simulate and Visualize

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=== [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Paul Triebkorn:

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Manipulation of the connectome

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Parameter space exploration

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Functional connectivity analysis

=== [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] ===

//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>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Patrik Bey:

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Importing Virtual Brain ready data into TVB

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Creating brain models in TVB

=== [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Michael Schirner:

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TVB processing pipelines with KG annotated outputs

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Software architecture

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Pipeline APIs

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Software maturity, integration, testing, versioning & deployment

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MINDS format

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Computing requirements

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Security requirements

=== [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

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

=== [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

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

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=== [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Julie Courtiol:

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Fundamentals of epilepsy

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How to build a virtual epileptic patient?

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Hand-on-guide through the iPython notebook

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Creating your own epilepsy simulations with TVB

=== [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

A script implementing the basic region imulation.

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=== [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

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

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=== [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

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

=== [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

In addition to the components discussed for a region simulation here we introduce one new major component, that is:

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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.

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We will also introduce two new Monitors that make more sense in the context of surface simulations

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=== [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] ===

//Level: advanced//

Topics covered in this lesson by Jil Meier:

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