JR Long-Range Coupling Parameter Name Change

[Minarose]

For the JR model fitting, the naming convention for the long-range coupling parameters between ROIs needs to be changed. The current naming scheme is as follows:

• Pyramidal to Inhibitory Cells: sc_m_b (from w_n_b>w_b>w_bb)
• Pyramidal to Excitatory Cells: sc_m_f (from w_n_f>w_f>w_ff)
• Pyramidal to Pyramidal Cells: sc_fitted (from w_n_l>w >w_ll)

This labeling is based on David (2005)’s hierarchical nomenclature for extrinsic coupling: backward (bottom-up), forward (top-down), and lateral connections.

However, this terminology seems inconsistent with how these couplings are fitted in WhoBPyt, as the fitting is done between all ROIs, not just in a hierarchical manner between sensory and higher-order regions as typically described in the Dynamic Causal Modeling (DCM) literature. Additionally, all three coupling types are fitted but only pyramidal to pyramidal is labelled as sc_fitted.

The suggestion is to rename these coupling variables to more accurately reflect their roles:

In whobpyt/models/JansenRit/jansen_rit.py
changed fitted sc vars:
sc_m_b -> sc_p_i for Pyramidal to Inhibitory
sc_m_f -> sc_p_e for Pyramidal to Excitatory
sc_fitted -> sc_p_p for Pyramidal to Pyramidal

change connection gain variables:
w_bb -> w_pi
w_b -> w_i
w_n_b ->w_n_pi

w_ff -> w_pe
w_f -> w_e
w_n_f ->w_n_pe

w_ll -> w_pp
w_l -> w_p
w_n_l->w_n_pp

In progress on Minarose/whobpyt:JR_sc

[Minarose]

How to deal with the use of sc_fitted in whobpyt/run/modelfitting.py -line 242 def train -
[[self.trainingStats.appendSC(self.model.sc_fitted.detach().cpu().numpy())](https://github.com/Minarose/whobpyt/blob/7e011a43e6e79fe3030291c7459e8f2d614f4d2a/whobpyt/run/modelfitting.py#L242)]

potential solution:

• add dictionary to assign sc_fitted for models
  ^^
  @JohnWangDataAnalyst