Extracting interactions between only 3-4 nodes with SJ3D dynamics in Python

[Borjan Milinkovic]

Hi all,

I am interested in extracting 3 or 4 nodes uncoupled from the rest of the network in a scripting interface (ipython, python). I have been successful in doing it through the GUI, as its straight forward to save a connectivity with no in-weights and out-weights to the 4 specified nodes of interest. However, I am having trouble doing it in python as it is easier to implement in a total workflow for analysis. 

So, specifically, I would like to extract 3 or 4 nodes (Xi variable for the SJ3D models) from the default connectivity matrix in TVB without any interactions to and from the set of all other nodes. 

An example to go from for something like this would be of great help! I can't find much on this topic in the documentation/github.

Best wishes,

Boki

[WOODMAN Michael]

Hi

You can create a new connectivity based on the default one, e..g 

import numpy as np
from tvb.datatypes.connectivity import Connectivity

default = Connectivity.from_file()
default.configure()

idx = np.r_[2, 3, 5, 9, 12]
subset = Connectivity(
    weights=default.weights[idx][:,idx],
    tract_lengths=default.tract_lengths[idx][:,idx],
    centres=default.centres[idx],
    region_labels=default.region_labels[idx]
)
subset.configure()
print(subset)

cheers,

Marmaduke

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[Borjan Milinkovic]

Thanks Marmaduke,

This is incredibly helpful!

Cheers,

Boki