Simulation on TVB

[Collin Qu]

Hey everyone,

When I run a simulation with a Jansin-Rit Model on the default project (so the default connectivity which means that it isn't a connectivity issue) that uses temporal average monitor (tracked y0,y1,y2 and y3), the time series visualizer for the temporal average monitor and all other monitors show a spike at the beginning and then it goes to 0 (this is true when I apply a region stimulus and when I don't apply a stimulus). Why is this happening?

Without Stimulus:

With Stimulus:

[Michelangelo Fabbrizzi]

Hi,

that is likely the initial transient, you can discard it, then you will see the following part in the proper scale on y-axis. I would suggest you use the python version, instead of the GUI version.

Regards,

Miche

[Collin Qu]

What do you mean by discarding it? I don't see an option to discard it. How do i get to the proper scale like you what mentioned? I will also use the python version from now on.

Also, thanks for responding so fast! I really appreciate the help!

[Collin Qu]

Looking at the full 1000ms sim, it stays at 0 for the rest of the data. Why is that happening?

Ignore the red, the sim that I showed you earlier is the blue one.

[Michelangelo Fabbrizzi]

Hi Collini,

I don’t think you can discard it in the GUI version, I would recommend to use the python version.

Regards,

Mic

Il giorno 28 mar 2025, alle ore 00:11, Collin Qu <coll...@gmail.com> ha scritto:

What do you mean by discarding it? I don't see an option to discard it. How do i get to the proper scale like you what mentioned? I will also use the python version from now on.

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[Hari Seldon]

I don’t have the details, however maybe you are using a set of parameters that is on a fixed point. Try to exlpore the parameter space to find better settings (maybe starting with mu, global coupling and noise).

You can also find other posts in this forum with suggestions on this topic.

Rgds,

Mic

Il giorno 28 mar 2025, alle ore 06:42, Collin Qu <coll...@gmail.com> ha scritto:

Looking at the full 1000ms sim, it stays at 0 for the rest of the data. Why is that happening?

Ignore the red, the sim that I showed you earlier is the blue one.

<image (1).jpeg>

On Thursday, March 27, 2025 at 4:11:02 PM UTC-7 Collin Qu wrote:

What do you mean by discarding it? I don't see an option to discard it. How do i get to the proper scale like you what mentioned? I will also use the python version from now on.

Also, thanks for responding so fast! I really appreciate the help!

On Thursday, March 27, 2025 at 3:38:09 PM UTC-7 mich...@gmail.com wrote:

Hi,

that is likely the initial transient, you can discard it, then you will see the following part in the proper scale on y-axis. I would suggest you use the python version, instead of the GUI version.

Regards,

Miche

On Thursday, March 27, 2025 at 10:58:43 PM UTC+1 coll...@gmail.com wrote:

Hey everyone,

When I run a simulation with a Jansin-Rit Model on the default project (so the default connectivity which means that it isn't a connectivity issue) that uses temporal average monitor (tracked y0,y1,y2 and y3), the time series visualizer for the temporal average monitor and all other monitors show a spike at the beginning and then it goes to 0 (this is true when I apply a region stimulus and when I don't apply a stimulus). Why is this happening?

Without Stimulus:

With Stimulus:

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<image (1).jpeg>

[Collin Qu]

Thanks for a quick response!

I'll play around with the parameters and let you know what further help I need.

[Lia Domide]

Dear all,

In TVB web you can also discard the initial conditions if you:
- run a fist short simulation (this to be discarded)

- the branch from it, you can also do slight adjustments to parameters (as long as the history of the simulator remains compatible, e.g. keep the same model class)

- the branch-ed simulation will start with the initial conditions left from the short first simulation.

I hope this helps a bit.

best,

Lia

[Collin Qu]

Appreciate the help! I tried branching the simulation after a short 10ms simulation at the start but the simulation is still going flat. Also, my parameters are just the default with 1000ms length and I'm using the Jansen-Rit model and monitoring variables y0,y1,y2,y3 using a temporal average monitor with defaults too. Could you run a simulation on your tvb using the Jansen-Rit model and show me what graph I should be seeing? Thank you so much!

[Lia Domide]

Hi,

Maybe this notebook can help you with to explore the model:

https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/simulate_region_jansen_rit.ipynb

Otherwise, in web GUI, you have the Simulator - > Phase Plane page

There you can change the param numeric values and see the effect immediately on the right-side.

This page does run a very short simulation as if it were a single node.

Best,

Lia