Model configuration - daducci/AMICO GitHub Wiki

You can set models parameters by calling the set() method after selecting the model you want to fit:

import amico

ae = amico.Evaluation()
ae.set_model('MODEL_NAME')
ae.model.set(param1, param2)

NODDI parameters

__dPar__Parallel diffusivity [mm^2/s]. (default is 1.7E-3)

__dIso__Isotropic diffusivity [mm^2/s]. (default is 3.0E-3)

__IC_VFs__Intra-cellular volume fractions. (default is np.linspace(0.1, 0.99, 12))

__IC_ODs__Intra-cellular orientation dispersions. (default is np.hstack((np.array([0.03, 0.06]), np.linspace(0.09, 0.99, 10))))

__isExvivo__Is ex-vivo data. (default is False)

SANDI parameters

__d_is__Intra-soma diffusivity [mm^2/s]. (default is 3.0E-3)

__Rs__Radii of the soma [meters]. (default is np.linspace(1.0, 12.0, 5) * 1E-6)

__d_in__Intra-neurite diffusivities [mm^2/s]. (default is np.linspace(0.25, 3.0, 5) * 1E-3)

__d_isos__Extra-cellular isotropic mean diffusivities [mm^2/s]. (default is np.linspace(0.25, 3.0, 5) * 1E-3)

ActiveAx parameters

__d_par__Parallel diffusivity [mm^2/s]. (default is 0.6E-3)

__Rs__Radii of the axons [meters]. (default is np.concatenate(([0.01], np.linspace(0.5, 8.0, 20)) * 1E-6)

__d_perps__Perpendicular diffusivity(s) [mm^2/s]. (default is np.array([1.19E-3, 0.85E-3, 0.51E-3, 0.17E-3]))

__d_isos__Isotropic diffusivity(s) [mm^2/s]. (default is np.array([2.0E-3]))