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1 -TVB EBRAINS Baltic-Nordic school 2024
1 +EBRAINS Baltic-Nordic school 2024
Content
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4 4  (((
5 5  = Building personalized brain network models with TVB =
6 6  
7 -Spase Petkoski and Marmaduke Woodman
7 +Spase Petkoski, Damien Depannemaecker and Pierpaolo Sorrentino
8 8  )))
9 9  )))
10 10  
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14 14  (((
15 15  = What can I find here? =
16 16  
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/]].
17 +* A current topic in system neuroscience literature is the presence of brain activity in the absence of a task condition. These task-negative, spontaneous fluctuations occur in the so-called **rest state**, and a recurring theme of these fluctuations is that they have a network structure. Because TVB uses the structural connectivity of the brain as the backbone for simulating spontaneous activity, resting state activity and its network structure is a prime candidate for modeling in TVB.
18 18  
19 -The objective is to give to the participants an overview to building whole-brain network models with TVB.
19 += Who has access? =
20 20  
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.
21 +Describe the audience of this collab.
22 22  
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.
24 24  
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);"]].
26 -
27 -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.
28 -
29 -
30 -These can all be found in the drive and accessed through the lab.
31 -
32 -= Requirements =
33 -
34 -School participants should have EBRAINS accounts to be able to access and work on the tutorials.
35 -
36 -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.
37 -
38 -= Other tutorials =
39 -
40 -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"
41 -
42 -[[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/]]
43 -
44 -[[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/>>https://wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/]]
45 -
46 46  = References =
47 47  
48 -(((
49 -
50 -
51 -* 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.
26 +* (((
27 +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.
52 52  )))
53 -
54 -(((
55 -* 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.
56 -* 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.
29 +* (((
30 +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.
57 57  )))
58 -
59 -(((
60 -* 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.
61 -* 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.
32 +* (((
33 +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.
62 62  )))
63 -
64 -(((
65 -* 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.
35 +* (((
36 +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.
66 66  )))
67 67  )))
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