Wiki source code of The Virtual Brain

Version 91.1 by abonard on 2025/06/03 11:07
Hide last authors
adavison 1.1 1
2
abonard 3.1 3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
jessicamitchell 2.1 4
abonard 79.1 5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
6
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 76.1 14 === [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 15
abonard 76.1 16 **Level**: beginner(%%) **Type**: video tutorial
17
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>
21 {{/html}}
abonard 77.1 22 === [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===
abonard 76.1 23
abonard 77.1 24 **Level**: beginner(%%) **Type**: video tutorial
25
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.
27 {{html}}
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>
29 {{/html}}
abonard 78.1 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 77.1 31
abonard 78.1 32 **Level**: beginner(%%) **Type**: user documentation
33
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.
35
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 79.1 37 === **Advanced** ===
abonard 78.1 38
abonard 79.1 39 === [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] ===
40
41 **Level**: advanced(%%) **Type**: video tutorial
42
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.
44 {{html}}
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 80.1 47 === [[GUI tutorials – Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 79.1 48
abonard 80.1 49 **Level**: advanced(%%) **Type**: -
50
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.
52
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 81.1 54 === [[GUI tutorials – Resting State Networks>>https://docs.thevirtualbrain.org/tutorials/tutorial_2_RestingStateNetworks.html#tutorial-2-restingstatenetworks||rel=" noopener noreferrer" target="_blank"]] ===
abonard 80.1 55
abonard 81.1 56 **Level**: advanced(%%) **Type**: user documentation
57
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 82.1 59 === [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
abonard 81.1 60
abonard 82.1 61 **Level**: advanced(%%) **Type**: video tutorial
62
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>
66 {{/html}}
abonard 83.1 67 === [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
abonard 82.1 68
abonard 83.1 69 **Level**: advanced(%%) **Type**: video tutorial
70
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>
74 {{/html}}
abonard 84.1 75 === [[Scripting tutorials – Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 83.1 76
abonard 84.1 77 **Level**: advanced(%%) **Type**: interactive tutorial
78
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 85.1 80 === [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===
abonard 84.1 81
abonard 85.1 82 **Level**: advanced(%%) **Type**: video tutorial
83
84 Paul Triebkorn will guide you through manipulation of the connectomes, parameter space exploration and functional connectivity analysis.
85 {{html}}
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>
87 {{/html}}
abonard 86.1 88 === [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
abonard 85.1 89
abonard 86.1 90 **Level**: advanced(%%) **Type**: video tutorial
91
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>
95 {{/html}}
abonard 87.1 96 === [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] ===
abonard 86.1 97
abonard 87.1 98 **Level**: advanced(%%) **Type**: video tutorial
99
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>
103 {{/html}}
abonard 88.1 104 === [[TVB Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
abonard 87.1 105
abonard 88.1 106 **Level**: advanced(%%) **Type**: video tutorial
107
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.
109 {{html}}
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 89.1 112 === [[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 88.1 113
abonard 89.1 114 **Level**: advanced(%%) **Type**: interactive tutorial
115
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 90.1 117 === [[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 89.1 118
abonard 90.1 119 **Level**: advanced(%%) **Type**: interactive tutorial
120
121 Here you will learn how to use a script implementing the basic region imulation.
abonard 91.1 122 === [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] ===
abonard 90.1 123
abonard 91.1 124 **Level**: advanced(%%) **Type**: video tutorial
125
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>
129 {{/html}}
130