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Last modified by petkoski on 2025/09/06 16:12
From version 19.5
edited by petkoski
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To version 16.1
edited by mhashemi
on 2025/03/12 11:12
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1 -XWiki.petkoski
1 +XWiki.mhashemi
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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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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.
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.
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.
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 -
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 -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.
28 -
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.
30 -
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.
32 -
33 -
34 -These can all be found in the drive and accessed through the lab.
35 -
36 36  = Requirements =
37 37  
38 38  School participants should have EBRAINS accounts to be able to access and work on the tutorials.
39 39  
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.
25 +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.
41 41  
42 42  = Other tutorials =
43 43  
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45 45  
46 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/]]
47 47  
48 -[[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/>>https://wiki.ebrains.eu/bin/view/Collabs/automatic-dcm/]]
49 -
50 50  = References =
51 51  
52 52  (((
53 53  
54 54  
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.
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.
56 56  )))
57 57  
58 58  (((
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.
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 +
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.
61 61  )))
62 62  
63 63  (((
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.
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.
66 66  )))
67 67  
68 68  (((
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.
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.
70 70  )))
71 71  )))
72 72