Changes for page SGA3 D1.2 Showcase 1

Last modified by fousekjan on 2022/07/04 18:31
From version 10.2
edited by fousekjan
on 2022/01/03 09:00
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To version 7.1
edited by fousekjan
on 2021/12/30 00:14
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21 21  The notebooks in this collab will load all required Python modules including Siibra and The Virtual Brain, and the interfaces for launching the computationally demanding parts in the HPC infrastructure. Running the notebooks requires an EBRANS account with permissions to access the Lab and the Knowledge Graph API. In addition, to be able to interact with the HPC infrastructure, the user has to have access to an active allocation on the corresponding FENIX site. 
22 22  
23 23  
24 -== Regional variability data ==
24 +== ==
25 25  
26 -The first step of the regional variability workflow loads the data from the Knowledge Graph and defines the regional bias on the model. In this case we require: 1) structural connectivity matrices, 2) GABA and AMPA receptor densities at each region, and 3) empirical resting-state fMRI data for fitting and validation of the simulations. The three datasets shall be characterised in the same parcellation.
27 -
28 -Link to the notebook:
29 -
30 -* [[regional_variability/notebooks/1_data_setup.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/1_data_setup.ipynb]]
31 -
32 -(% style="text-align:center" %)
33 -[[image:image-20220103095424-1.png]]
34 -
35 -== Fitting model parameters for models with regional bias ==
36 -
37 -A series of simulations of the whole-brain network model is launched in the EBRAINS HPC facilities in order to identify the optimal model parameters leading to simulated resting-state brain activity that best resembles the empirically observed activity.
38 -
39 -Link to the notebook:
40 -
41 -* [[regional_variability/notebooks/2_parameter_swep_proto.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/2_parameter_swep_proto.ipynb]]
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43 -[[image:image-20220103095948-1.png]]
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44 44  )))
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