State variables in ReducedWongWang NMMs

[Cathlin]

Hello!

I'm working with the ReducedWongWangExcInh and DecoBalancedExcInh neural mass models, both of which have S_e and S_i as state variables. Based on what I've gathered from associated papers and my understanding of the models' differential equations, these state variables appear to correspond to excitatory and inhibitory "synaptic gating variable[s]" (Deco et al. 2021. DOI:10.1126/sciadv.abf4752; page 10), respectively. However, in TVB's documentation, these state variables are instead described as corresponding to the "population firing rate." Is this indeed the case or is this an implementation bug on TVB's end?

(Also, if I may ask a follow-up question: if the latter is the case, is there an existing way through which we can access population firing rate in these models? E.g., if I'm not mistaken, population firing rate is captured in these models by H(x) (defined as H_e and H_i in TVB's documentation); is there a way to change the models' state variables to record these H(x) variables instead?)

Thank you!

Cathlin

[John Griffiths]

Hi Caitlin

S is indeed synaptic gating and not firing rate in this model, which is usually denoted by x. 

The docstring text you linked to looks like a typo / some original placeholder boilerplate text that was not updated. These things are unavoidable on large complex code bases, but it's good to have them flagged all the same.

You may find this (slightly old) tutorial useful for some of your Qs

https://github.com/krembilneuroinformatics/kcni-school-lessons/blob/master/day5/notebooks/WholeBrainModelling_02__RestingStateConnectivityAndBifurcations.ipynb

There is some general discussion of the original RWW model (the two you referred to are extensions of it), and replication of the main result from the original Deco 2013 paper. It also shows how you can subclass a TVB model, in this case adding some lines that (re-calculate) the firing rate for the state variables S (which can be done bc x is an auxiliary variable that is fully defined by the state variables and parameters), and returns it as an output for analysis 

HTH

Best,

john

[Cathlin]

Hi John,

This is most illuminating and extremely helpful. Thank you so very much for your help and for pointing me to this resource!

Best,
Cathlin