How to set different values of parameters in TVB?

[Jeriffer Smith]

Hi everyone,

     I have a question about suphopf model. I know 'omega' means the intrinsic frequency of each node which are estimated from the data, as given by the average peak frequency of the narrowband BOLD signals of each brain region.

    So how to set so many different values of different regions in TVB? I know we can set it in 'simulator-set up region model', however, if I use AAL atlas, there will be 90 different values to set, which is too complicated!

    How can I set them in a convenient way?

[WOODMAN Michael]

hi

Usually you will set all to default value and then modify just a few.  Unless you have data on 90 different values, or a hypothesis on the statistics (e.g. dispersion in intrinsic frequency) it usually isn't meaningful to specify them individually.  

In Python scripting, you would write something like

sim.model.omega = np.ones(90) * 2.3

sim.model.omega[[3,4,5]] = np.r_[3.0, 4.0, 5.0]

cheers,

Marmaduke

---

From: tvb-...@googlegroups.com <tvb-...@googlegroups.com> on behalf of Jeriffer Smith <jeriffe...@gmail.com>
Sent: Sunday, March 27, 2022 3:13:32 PM
To: TVB Users
Subject: [TVB] How to set different values of parameters in TVB?

 

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[Lia Domide]

Hi Jeniffer,

In TVB web GUI, you should first visit the "Phase Plane" GUI page[1] and define few model configurations (usually one default and few different regimes - as Marmaduke also suggests).

Then under "Setup Region model" [2] you link previously saved model configurations with the nodes: first link all regions with the "Default model configuration", then pick each of the special nodes and set the different configurations.

[1] https://docs.thevirtualbrain.org/manuals/UserGuide/UserGuide-UI_Simulator.html#the-phase-plane-page

[2] https://docs.thevirtualbrain.org/manuals/UserGuide/UserGuide-UI_Simulator.html#region-based-simulations 

Best,

Lia.

[Jeriffer Smith]

Thank you so much!

[nskplta]

Hi Lia, 

in the web GUI, is it possible to edit or delete already saved model configurations?

Thanks,

Belén.

[Lia Domide]

Hi Belén,

Currently it is not possible in tvb web GUI to remove or edit already saved Model configurations.

These entities are stored across projects, for a user.

If you have these entities stored in a shared installation of TVB, maybe I can help you to remove these from the DB directly - just indicate to me their names.

If you have those in a local TVB installation, then maybe you create another user for yourself to start fresh?

And meanwhile, we could create a new feature request for tvb to add this feature in the future for all users (although I can not guarantee a time when it will be done).

Best,

Lia.