Example brain network parameter exploration: tune global coupling strength

neurolib_parameter_exploration.py

from neurolib.models.aln import ALNModel
from neurolib.utils.loadData import Dataset
from neurolib.optimize.exploration import BoxSearch
from neurolib.utils.parameterSpace import ParameterSpace

# load brain scan dataset
ds = Dataset("hcp")
# initialize brain network model
model = ALNModel(Cmat = ds.Cmat, Dmat = ds.Dmat)
# 5 minute simulation
model.params['duration'] = 5 * 60 * 1000 #ms
# define parameter range to search, 
# Ke_gl is global coupling strength between nodes
parameters = ParameterSpace({"Ke_gl" : np.linspace(150, 500, 8)})
# initialize search
search = BoxSearch(model, parameters)
# start exploration, run chunkwise to save RAM, simulate bold
search.run(chunkwise=True, bold=True)
# ...
# load the results
search.loadResults()