Changes for page The Virtual Brain

Last modified by abonard on 2025/06/03 11:07
From version 34.1
edited by abonard
on 2025/04/10 15:18
Change comment: There is no comment for this version
To version 25.1
edited by abonard
on 2025/04/10 15:10
Change comment: There is no comment for this version

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64 64  {{html}}
65 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 66  {{/html}}
67 +=== [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] ===
67 67  
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 +