Wiki source code of The Virtual Brain

Version 26.1 by abonard on 2025/04/10 15:10
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adavison 1.1 1
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abonard 3.1 3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
jessicamitchell 2.1 4
abonard 7.1 5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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abonard 3.1 7 === **Beginner** ===
jessicamitchell 2.1 8
abonard 3.1 9 === [[GUI tutorials – Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 10
abonard 3.1 11 **Level**: beginner(%%) **Type**: user documentation
jessicamitchell 2.1 12
13 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
abonard 4.1 14 === [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 15
abonard 4.1 16 **Level**: beginner(%%) **Type**: video tutorial
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18 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.
19 {{html}}
20 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/326iA14UVzY" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 5.1 22 === [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===
abonard 4.1 23
abonard 5.1 24 **Level**: beginner(%%) **Type**: video tutorial
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26 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.
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28 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/Zo0HGwLHN3E" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 6.1 30 === [[GUI tutorials – Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] ===
abonard 5.1 31
abonard 6.1 32 **Level**: beginner(%%) **Type**: user documentation
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34 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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36 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.
abonard 7.1 37 === **Advanced** ===
abonard 6.1 38
abonard 7.1 39 === [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] ===
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41 **Level**: advanced(%%) **Type**: video tutorial
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43 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.
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45 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/4XghviA_1Uk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
46 {{/html}}
abonard 8.1 47 === [[GUI tutorials – Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 7.1 48
abonard 8.1 49 **Level**: advanced(%%) **Type**: -
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51 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.
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53 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.
abonard 9.1 54 === [[GUI tutorials – Resting State Networks>>https://docs.thevirtualbrain.org/tutorials/tutorial_2_RestingStateNetworks.html#tutorial-2-restingstatenetworks||rel=" noopener noreferrer" target="_blank"]] ===
abonard 8.1 55
abonard 9.1 56 **Level**: advanced(%%) **Type**: user documentation
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58 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.
abonard 10.1 59 === [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
abonard 9.1 60
abonard 10.1 61 **Level**: advanced(%%) **Type**: video tutorial
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63 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.
64 {{html}}
65 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/uUkq0K-xM0Q" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 11.1 67 === [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
abonard 10.1 68
abonard 11.1 69 **Level**: advanced(%%) **Type**: video tutorial
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71 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.
72 {{html}}
73 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/PppyGzWUxuE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 12.1 75 === [[Scripting tutorials – Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 11.1 76
abonard 12.1 77 **Level**: advanced(%%) **Type**: interactive tutorial
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79 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.
abonard 13.1 80 === [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===
abonard 12.1 81
abonard 13.1 82 **Level**: advanced(%%) **Type**: video tutorial
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84 Paul Triebkorn will guide you through manipulation of the connectomes, parameter space exploration and functional connectivity analysis.
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86 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/BDj9MLpt0io" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 14.1 88 === [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
abonard 13.1 89
abonard 14.1 90 **Level**: advanced(%%) **Type**: video tutorial
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92 Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage).
93 {{html}}
94 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/t9xyoHxTAmQ" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 15.1 96 === [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 15.1 98 **Level**: advanced(%%) **Type**: video tutorial
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100 Patrik Bey covers in this lesson how to import Virtual Brain ready data into TVB and how to create brain models in TVB.
101 {{html}}
102 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/OEOCFyiJgBM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 16.1 104 === [[TVB Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
abonard 15.1 105
abonard 16.1 106 **Level**: advanced(%%) **Type**: video tutorial
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108 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.
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110 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/ZA2UuHZiPnM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 17.1 112 === [[Scripting tutorials – Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 16.1 113
abonard 17.1 114 **Level**: advanced(%%) **Type**: interactive tutorial
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116 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.
abonard 18.1 117 === [[Scripting tutorials – Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 17.1 118
abonard 18.1 119 **Level**: advanced(%%) **Type**: interactive tutorial
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121 Here you will learn how to use a script implementing the basic region imulation.
abonard 19.1 122 === [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] ===
abonard 18.1 123
abonard 19.1 124 **Level**: advanced(%%) **Type**: video tutorial
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126 Step-by-step guide to simulating The Virtual Mouse Brain.
127 {{html}}
128 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/gxhJku8KRYY" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 20.1 130 === [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] ===
abonard 19.1 131
abonard 20.1 132 **Level**: advanced(%%) **Type**: video tutorial
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134 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?
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136 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/ZXLrvHc24xE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 21.1 138 === [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] ===
abonard 20.1 139
abonard 21.1 140 **Level**: advanced(%%) **Type**: video tutorial
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142 Learn how to use the TVB-NEST toolbox co-simulation in the HBP collab.
143 {{html}}
144 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/dUuQe_SI5lE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 22.1 146 === [[Scripting tutorials – Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 21.1 147
abonard 22.1 148 **Level**: advanced(%%) **Type**: interactive tutorial
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150 In addition to the components discussed for a region simulation here we introduce one new major component, that is:
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152 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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154 We will also introduce two new Monitors that make more sense in the context of surface simulations
abonard 23.1 155 === [[Scripting tutorials – Exploring a neural mass model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 22.1 156
abonard 23.1 157 **Level**: advanced(%%) **Type**: interactive tutorial
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159 In this tutorial we will look into creating an interactive phase-plane, specifying stochastic integration and finally learn how to simulate and visualise these models.
abonard 24.1 160 === [[Scripting tutorials – Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 23.1 161
abonard 24.1 162 **Level**: advanced(%%) **Type**: interactive tutorial
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164 We will demonstrate some starting points for modeling resting state networks in TVB, using the default data set.
abonard 25.1 165 === [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] ===
abonard 24.1 166
abonard 25.1 167 **Level**: advanced(%%) **Type**: video tutorial
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169 Topics covered in this lesson by Andreas Spiegler:
170 Introduction to stimulation paradigm and stimulation techniques
171 How to model brain stimulation with TVB
172 Region-based stimulus
173 Surface-based stimulus
174 Examples of stimulated network dynamics using
175 Human brain model
176 Mouse brain model
177 Example of Transcranial Direct-Current Stimulation (tDCS)
178 {{html}}
179 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/mskxBYKoeq0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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abonard 26.1 181 === [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] ===
abonard 25.1 182
abonard 26.1 183 **Level**: advanced(%%) **Type**: video tutorial
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185 Julie Courtiol is covering in this tutorial the fundamentals of epilepsy and closes in on the question on how to build a virtual epileptic patient? The lessons is followed with a hands-on-guide through the iPython notebook and with creating your own epilepsy simulations with TVB.
186 {{html}}
187 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/YrSxnMo6Lr8" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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