CNS*2020 Software Showcase: Brain Dynamics Toolbox

The Brain Dynamics Toolbox is an open-source matlab toolbox for simulating dynamical systems in neuroscience. I’ll be introducing the toolbox in Software Showcase S2. You may download the software in advance from https://bdtoolbox.org. Please use this topic to post any follow-up questions.

  • Stewart
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The slides for the talk can be downloaded from sched.

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Please post any follow-up questions here. I will keep checking this thread over the duration of the conference.

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Very nice and clear demo, Stewart! I was wondering, are there any built-in features to simulate stimulus-driven activity - in that context, I’d be especially interested not in TMS-like stimulations, but more like event-related potentials such as those observed in EEG. If not built-in, would you have any tips on how to achieve that? Thank you!

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Thank you Gleb. I’m glad it was helpful. There are no built-in stimulation protocols per se. You define such things explicitly in your model. In my demo, I used a constant stimulus (Je). Other common stimulation protocls are a step function and a square pulse. I like to use a step-function at t=0 because its very easy to code.

 dY = F(t,Y,J)
       % set the stimulus to J=0 for t<0
       if t < 0
            J=0
       end
       % your equations here
       dY = ..... + J
 end

You can then start your simulation at, say t=-100, to observe the stimulus onset at t=0. It is very easy to adjust the time domain in the graphical interface.

You do a similar thing with pulse stimuli. You just need to add another parameter for the stimulus duration.

 if t < 0 || t > dur
    J=0;
 end

As for event-related potentials in the EEG. Your model would need to describe the equations for the EEG. However you do that would be specific to your study. To get started, you could look at the BOLD Haemodynamic Response Function (BOLDHRF) that ships with the toolbox. That’s more for fMRI but it might give you some clues on how to proceed.

  • Stewart
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Stewart, thank you so much for the quick and detailed response! Sounds great, I will use the HRF as a reference on how I can inform my model to ‘react’ to stimuli and hopefully come up with a model that would modulate the synthetic ERPs in terms of their timings and amplitudes. Thanks again, have a great day! – Gleb

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