Wiki source code of The Virtual Brain

Version 66.1 by abonard on 2025/05/23 13:22
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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 55.1 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 52.1 14 === [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 15
abonard 52.1 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 53.1 22 === [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 53.1 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 54.1 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 53.1 31
abonard 54.1 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 55.1 37 === **Advanced** ===
abonard 54.1 38
abonard 55.1 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>
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abonard 56.1 47 === [[GUI tutorials – Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 55.1 48
abonard 56.1 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 57.1 54 === [[GUI tutorials – Resting State Networks>>https://docs.thevirtualbrain.org/tutorials/tutorial_2_RestingStateNetworks.html#tutorial-2-restingstatenetworks||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 57.1 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 58.1 59 === [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 58.1 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 59.1 67 === [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 59.1 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.
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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 60.1 75 === [[Scripting tutorials – Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 60.1 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 61.1 80 === [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 61.1 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 62.1 88 === [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 62.1 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).
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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 63.1 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 63.1 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 64.1 104 === [[TVB Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 64.1 106 **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>
111 {{/html}}
abonard 65.1 112 === [[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"]] ===
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abonard 65.1 114 **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 66.1 117 === [[Scripting tutorials – Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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abonard 66.1 119 **Level**: advanced(%%) **Type**: interactive tutorial
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121 Here you will learn how to use a script implementing the basic region imulation.
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