Changes for page The Virtual Brain

Last modified by abonard on 2025/06/03 11:07
From version 26.1
edited by abonard
on 2025/04/10 15:10
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To version 29.1
edited by abonard
on 2025/04/10 15:18
Change comment: There is no comment for this version

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2 2  
3 3  * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
4 4  
5 -* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
6 -
7 7  === **Beginner** ===
8 8  
9 9  === [[GUI tutorials – Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] ===
... ... @@ -27,163 +27,4 @@
27 27  {{html}}
28 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 29  {{/html}}
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"]] ===
31 31  
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.
37 -=== **Advanced** ===
38 -
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}}
47 -=== [[GUI tutorials – Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] ===
48 -
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.
54 -=== [[GUI tutorials – Resting State Networks>>https://docs.thevirtualbrain.org/tutorials/tutorial_2_RestingStateNetworks.html#tutorial-2-restingstatenetworks||rel=" noopener noreferrer" target="_blank"]] ===
55 -
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.
59 -=== [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
60 -
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}}
67 -=== [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
68 -
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}}
75 -=== [[Scripting tutorials – Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
76 -
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.
80 -=== [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] ===
81 -
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}}
88 -=== [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
89 -
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}}
96 -=== [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] ===
97 -
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}}
104 -=== [[TVB Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
105 -
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}}
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"]] ===
113 -
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.
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"]] ===
118 -
119 -**Level**: advanced(%%) **Type**: interactive tutorial
120 -
121 -Here you will learn how to use a script implementing the basic region imulation.
122 -=== [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] ===
123 -
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 -=== [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] ===
131 -
132 -**Level**: advanced(%%) **Type**: video tutorial
133 -
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?
135 -{{html}}
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>
137 -{{/html}}
138 -=== [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] ===
139 -
140 -**Level**: advanced(%%) **Type**: video tutorial
141 -
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>
145 -{{/html}}
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"]] ===
147 -
148 -**Level**: advanced(%%) **Type**: interactive tutorial
149 -
150 -In addition to the components discussed for a region simulation here we introduce one new major component, that is:
151 -
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.
153 -
154 -We will also introduce two new Monitors that make more sense in the context of surface simulations
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"]] ===
156 -
157 -**Level**: advanced(%%) **Type**: interactive tutorial
158 -
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.
160 -=== [[Scripting tutorials – Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
161 -
162 -**Level**: advanced(%%) **Type**: interactive tutorial
163 -
164 -We will demonstrate some starting points for modeling resting state networks in TVB, using the default data set.
165 -=== [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] ===
166 -
167 -**Level**: advanced(%%) **Type**: video tutorial
168 -
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>
180 -{{/html}}
181 -=== [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] ===
182 -
183 -**Level**: advanced(%%) **Type**: video tutorial
184 -
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>
188 -{{/html}}
189 -