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Version 19.5 by petkoski on 2025/09/05 15:41
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5 = Building personalized brain network models with TVB =
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7 Spase Petkoski and Marmaduke Woodman
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15 = What can I find here? =
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17 This collab contains access to the notebooks and reading materials that will be used during the EBRAINS Baltic-Nordic summer school 2024 [[https:~~/~~/lsmu.lt/en/events/ebrains/>>https://lsmu.lt/en/events/ebrains/]].
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19 The objective is to give to the participants an overview to building whole-brain network models with TVB.
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21 We will begin with the [[First steps of TVB>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/1_TVB_First_steps.ipynb||style="background-color: rgb(255, 255, 255);"]], where we will describe the building blocks of TVB through the paradigm of resting state activity.
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23 This will be followed by [[Modelling Epilepsy>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/2_TVB_Modelling_Epilepsy.ipynb||style="background-color: rgb(255, 255, 255);"]], where seizure propagation will be modeled.
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25 Then, there is one tutorial describing a deeper analysis of [[BOLD monitors>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/3_TVB_BOLD_digging_deeper.ipynb||style="background-color: rgb(255, 255, 255);"]].
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27 There is also a fourth tutorial which describes application of a fast back-end implementation of the Montbrio-Pazo-Roxin model used for modeling [[resting state fMRI >>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/MPR_rs.ipynb]]. This is a based on a previous showcase [[Degeneracy in neuroscience>>https://wiki.ebrains.eu/bin/view/Collabs/sga3-d1-5-showcase-1/]],  which described the interpersonal variability analyzed by the [[Virtual Ageing Brain>>https://www.sciencedirect.com/science/article/pii/S1053811923005542?via%3Dihub]] study.
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29 Lavanga, M., Stumme, J., Yalcinkaya, B. H., Fousek, J., Jockwitz, C., Sheheitli, H., Bittner, N., Hashemi, M., Petkoski, S., Caspers, S., & Jirsa, V. (2023). The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging. NeuroImage, 283, 120403.
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31 Finally, the collab contains one tutorial where a [[Bayesian approach>>https://wiki.ebrains.eu/bin/view/Collabs/ebrains-task-3-3/Drive#notebooks/EITN_tutorial||style="background-color: rgb(255, 255, 255);"]] is used on synthetic data to infer the posterior of the parameters foir a single brain region.
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34 These can all be found in the drive and accessed through the lab.
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36 = Requirements =
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38 School participants should have EBRAINS accounts to be able to access and work on the tutorials.
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40 They are also advised to install TVB locally in case of connection issues. After installation from the following link: https:~/~/www.thevirtualbrain.org/tvb/zwei/brainsimulator-software users can access many more tutorials. For inference, other tools such as Numpyro ([[https:~~/~~/github.com/ins-amu/DCM_ERP_PPLs>>https://github.com/ins-amu/DCM_ERP_PPLs]]) or VBI tool ([[https:~~/~~/github.com/ins-amu/vbi>>https://github.com/ins-amu/vbi]]) will be required.
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42 = Other tutorials =
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44 In addition to these notebooks, we also refer to the readers to the collab for the Showcase 1 of HBP: "Degeneracy in neuroscience - when is Big Data big enough"
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46 [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/sga3-d1-5-showcase-1/>>url:https://wiki.ebrains.eu/bin/view/Collabs/sga3-d1-5-showcase-1/]]
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48 [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/>>https://wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/]]
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50 = References =
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55 * Sanz-Leon P, Knock SA, Spiegler A, Jirsa VK. [[Mathematical framework for large-scale brain network modeling in The Virtual Brain>>https://www.sciencedirect.com/science/article/pii/S1053811915000051]]. Neuroimage. 2015 May 1;111:385-430.
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59 * Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A. [[Brain simulation as a cloud service: The Virtual Brain on EBRAINS>>https://www.sciencedirect.com/science/article/pii/S1053811922001021]]. NeuroImage. 2022 May 1;251:118973.
60 * Lavanga M, Stumme J, Yalcinkaya BH, Fousek J, Jockwitz C, Sheheitli H, Bittner N, Hashemi M, Petkoski S, Caspers S, Jirsa V. [[The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging>>https://www.sciencedirect.com/science/article/pii/S1053811923005542]]. NeuroImage. 2023 Dec 1;283:120403.
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64 * Wang HE, Triebkorn P, Breyton M, Dollomaja B, Lemarechal JD, Petkoski S, Sorrentino P, Depannemaecker D, Hashemi M, Jirsa VK. [[Virtual brain twins: from basic neuroscience to clinical use>>https://academic.oup.com/nsr/article/11/5/nwae079/7616087]]. National Science Review. 2024 May;11(5):nwae079.
65 * Baldy N, Woodman M, Jirsa V, Hashemi M. [[Dynamic Causal Modeling in Probabilistic Programming Languages>>https://www.biorxiv.org/content/10.1101/2024.11.06.622230v1.abstract]]. bioRxiv. 2024:2024-11.
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69 * Ziaeemehr A, Woodman M, Domide L, Petkoski S, Jirsa V, Hashemi M. [[Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models>>https://www.biorxiv.org/content/10.1101/2025.01.21.633922v1.abstract]] bioRxiv. 2025:2025-01.
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