Extracting connectivity matrix from gpickle

[milad7093]

Dear Sebastian

I have just gotten some outputs of cmp3 (connectivity matrices) in the gpickle format and need to extract connectivity matrices base on the following parameters:
fa mean
adc mean
number of fibers

Can you help me?

Please help me

Thanks in advance

Best regards,

-Milad

[sebastientourbier]

Dear Milad,

You can do it using the networkx library as follows:

import networx as nx
conn_mats = {}
connectivity_weights = ['FA_mean', 'ADC_mean', 'number_of_fibers']
G = nx.read_gpickle('path/to/connectome.gpickle')
for weight in connectivity_weights:
    conn_mats[weight] = nx.to_numpy_array(G, weight=weight)

which will store in conn_mats['FA_mean'], conn_mats['ADC_mean'], and conn_mats['number_of_fibers'] each of the connectivity matrices.

You can have an example on how to handle the connectome file here in the documentation.

Hope this helps,
Best,
Seb