Wiki source code of The Virtual Brain

Version 2.1 by jessicamitchell on 2023/09/11 11:44
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adavison 1.1 1 Available tutorials:
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jessicamitchell 2.1 3 === [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] ===
adavison 1.1 4
jessicamitchell 2.1 5 //Level: beginner//
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7 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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9 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.
10 === [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] ===
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12 //Level: beginner//
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14 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
15 === [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===
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17 //Level: beginner//
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19 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.
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21 <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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23 === [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===
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25 //Level: beginner//
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27 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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29 <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>
30 {{/html}}
31 === [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] ===
32
33 //Level: advanced//
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35 Topics covered in this lesson by Andreas Spiegler:
36 Introduction to stimulation paradigm and stimulation techniques
37 How to model brain stimulation with TVB
38 Region-based stimulus
39 Surface-based stimulus
40 Examples of stimulated network dynamics using
41 Human brain model
42 Mouse brain model
43 Example of Transcranial Direct-Current Stimulation (tDCS)
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45 <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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47 === [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
48
49 //Level: advanced//
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51 Topics covered in this lesson by Randy McIntosh:
52 General introduction to stroke
53 TVB simulation workflow for stroke patients
54 Structural reconstruction: “Virtual Brain Transplant”
55 Parameter space exploration and fitting
56 General introduction to dementia
57 TVB simulation workflow for patients with dementia
58 Pre-processing issues related to atrophy
59 Two-stage modeling: sub- and full-brain network model
60 Cognition predictor: model parameters vs. metrics of neuroimaging data
61 {{html}}
62 <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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64 === [[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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66 //Level: advanced//
67
68 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
69 === [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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71 //Level: advanced//
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73 Create An Interactive Phase-Plane, Specifying Stochastic Integration,
74 Simulate and Visualize
75 === [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===
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77 //Level: advanced//
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79 Topics covered in this lesson by Paul Triebkorn:
80 Manipulation of the connectome
81 Parameter space exploration
82 Functional connectivity analysis
83 {{html}}
84 <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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86 === [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] ===
87
88 //Level: advanced//
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90 How to use the TVB-NEST toolbox co-simulation in HBP collab
91 {{html}}
92 <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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94 === [[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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96 //Level: advanced//
97
98 Topics covered in this lesson by Patrik Bey:
99 Importing Virtual Brain ready data into TVB
100 Creating 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}}
104 === [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
105
106 //Level: advanced//
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108 Topics covered in this lesson by Michael Schirner:
109 TVB processing pipelines with KG annotated outputs
110 Software architecture
111 Pipeline APIs
112 Software maturity, integration, testing, versioning & deployment
113 MINDS format
114 Computing requirements
115 Security requirements
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117 <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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119 === [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
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121 //Level: advanced//
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123 Tutorial on how to simulate brain tumor brains with TVB (reproducing publication: Marinazzo et al. 2020 Neuroimage).
124 {{html}}
125 <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>
126 {{/html}}
127 === [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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129 //Level: advanced//
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131 Exploring the Epileptor model, Region based simulation of a temporal lobe seizure, Modeling surgical resection, Triggering a seizure by stimulation
132 === [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] ===
133
134 //Level: advanced//
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136 Topics covered in this lesson by Julie Courtiol:
137 Fundamentals of epilepsy
138 How to build a virtual epileptic patient?
139 Hand-on-guide through the iPython notebook
140 Creating your own epilepsy simulations with TVB
141 {{html}}
142 <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>
143 {{/html}}
144 === [[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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146 //Level: advanced//
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148 A script implementing the basic region imulation.
149 === [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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151 //Level: advanced//
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153 We will demonstrate some starting points for modeling resting state networks in TVB, using the default data set.
154 === [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] ===
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156 //Level: advanced//
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158 Step-by-step guide to simulating The Virtual Mouse Brain.
159 {{html}}
160 <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>
161 {{/html}}
162 === [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
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164 //Level: advanced//
165
166 In addition to the components discussed for a region simulation here we introduce one new major component, that is:
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168 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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170 We will also introduce two new Monitors that make more sense in the context of surface simulations
171 === [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] ===
172
173 //Level: advanced//
174
175 Topics covered in this lesson by Jil Meier:
176 Surface-based simulations: what? why? how?
177 Deep brain simulations: whay? why? how?
178 {{html}}
179 <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>
180 {{/html}}
181 === [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] ===
182
183 //Level: advanced//
184
185 Topics covered in this lesson by Meysam Hashemi:
186 Bayesian model inversion
187 BVEP workflow
188 Jupyter notebook example
189 Python & Stan interfaces
190 PyMC3 example
191 Comparing Stan & PyMC3 accuracy
192 {{html}}
193 <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>
194 {{/html}}
195 === [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
196
197 //Level: advanced//
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199 Topics covered in this lesson by Dionysios Perdikis:
200 Motivation; Software structure
201 Default workflow
202 EBRAINS collaboratory
203 Use cases
204 Modifications to the TVB simulator
205 Benchmarking
206 Parameters exploration
207 Future work
208 {{html}}
209 <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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