Changes for page The Virtual Brain

Last modified by abonard on 2025/06/03 11:07
From version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
Change comment: There is no comment for this version
To version 11.1
edited by abonard
on 2025/04/10 15:09
Change comment: There is no comment for this version

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1 -XWiki.jessicamitchell
1 +XWiki.abonard
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1 -Available tutorials:
2 2  
3 -=== [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] ===
4 4  
5 -//Level: beginner//
3 +* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
6 6  
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.
5 +* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
8 8  
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"]] ===
7 +=== **Beginner** ===
11 11  
12 -//Level: beginner//
9 +=== [[GUI tutorials – Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] ===
13 13  
11 +**Level**: beginner(%%) **Type**: user documentation
12 +
14 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 15  === [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] ===
16 16  
17 -//Level: beginner//
16 +**Level**: beginner(%%) **Type**: video tutorial
18 18  
19 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.
20 20  {{html}}
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22 22  {{/html}}
23 23  === [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] ===
24 24  
25 -//Level: beginner//
24 +**Level**: beginner(%%) **Type**: video tutorial
26 26  
27 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.
28 28  {{html}}
29 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 30  {{/html}}
31 -=== [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] ===
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"]] ===
32 32  
33 -//Level: advanced//
32 +**Level**: beginner(%%) **Type**: user documentation
34 34  
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)
44 -{{html}}
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>
46 -{{/html}}
47 -=== [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] ===
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.
48 48  
49 -//Level: advanced//
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** ===
50 50  
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>
63 -{{/html}}
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"]] ===
39 +=== [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] ===
65 65  
66 -//Level: advanced//
41 +**Level**: advanced(%%) **Type**: video tutorial
67 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"]] ===
70 -
71 -//Level: advanced//
72 -
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"]] ===
76 -
77 -//Level: advanced//
78 -
79 -Topics covered in this lesson by Paul Triebkorn:
80 -Manipulation of the connectome
81 -Parameter space exploration
82 -Functional connectivity analysis
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.
83 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>
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>
85 85  {{/html}}
86 -=== [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] ===
47 +=== [[GUI tutorials – Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] ===
87 87  
88 -//Level: advanced//
49 +**Level**: advanced(%%) **Type**: -
89 89  
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>
93 -{{/html}}
94 -=== [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] ===
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.
95 95  
96 -//Level: advanced//
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"]] ===
97 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}}
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.
104 104  === [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] ===
105 105  
106 -//Level: advanced//
61 +**Level**: advanced(%%) **Type**: video tutorial
107 107  
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
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.
116 116  {{html}}
117 117  <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>
118 118  {{/html}}
119 -=== [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] ===
120 -
121 -//Level: advanced//
122 -
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"]] ===
128 -
129 -//Level: advanced//
130 -
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//
135 -
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"]] ===
145 -
146 -//Level: advanced//
147 -
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"]] ===
150 -
151 -//Level: advanced//
152 -
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"]] ===
155 -
156 -//Level: advanced//
157 -
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"]] ===
163 -
164 -//Level: advanced//
165 -
166 -In addition to the components discussed for a region simulation here we introduce one new major component, that is:
167 -
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.
169 -
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}}
195 195  === [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
196 196  
197 -//Level: advanced//
69 +**Level**: advanced(%%) **Type**: video tutorial
198 198  
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
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.
208 208  {{html}}
209 209  <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>
210 210  {{/html}}