Last modified by mhashemi on 2025/03/12 11:20
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edited by mhashemi
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1 -TVB EBRAINS Baltic-Nordic school 2024
1 +EBRAINS Baltic-Nordic school 2024
Author
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1 -XWiki.mhashemi
1 +XWiki.petkoski
Content
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16 16  
17 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/]].
18 18  
19 -The objective is to give to the participants an overview to building whole-brain network models with TVB. 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. 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. 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);"]].  Finally, 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.  These can all be found in the drive and accessed through the lab.
19 +The objective is to give to the participants an overview to building whole-brain network models with TVB. We will begin with the [[First steps of TVB>>url:https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20tutorial%3A%20first%20steps/tvb_tutorials/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. This will be followed by [[Modelling Epilepsy>>url:https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20tutorial%3A%20first%20steps/tvb_tutorials/2_TVB_Modelling_Epilepsy.ipynb||style="background-color: rgb(255, 255, 255);"]], where seizure propagation will be modeled. Finally, there is one tutorial describing deeper analysis of [[BOLD monitors>>url:https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20tutorial%3A%20first%20steps/tvb_tutorials/3_TVB_BOLD_digging_deeper.ipynb||style="background-color: rgb(255, 255, 255);"]]. These can all be found in the following EBRAINS lab:
20 20  
21 +[[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20tutorial%3A%20first%20steps/tvb_tutorials>>url:https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20tutorial%3A%20first%20steps/tvb_tutorials]]
22 +
21 21  = Requirements =
22 22  
23 23  School participants should have EBRAINS accounts to be able to access and work on the tutorials.
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32 32  
33 33  = References =
34 34  
35 -(((
36 -
37 -
37 +* (((
38 38  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.
39 39  )))
40 -
41 -(((
40 +* (((
42 42  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.
43 -
42 +)))
43 +* (((
44 44  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.
45 45  )))
46 -
47 -(((
46 +* (((
48 48  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.
49 -
50 -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.
51 51  )))
52 -
53 -(((
54 -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.
55 55  )))
56 -)))
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58 58  
59 59  (% class="col-xs-12 col-sm-4" %)