class R2(FreeParameterTemplate):
"""R2 = 1/T2, for linear T2Dec or other models."""
init_value = 5
lower_bound = 0.5
upper_bound = 500.0
parameter_transform = ScaleTransform(1e2)
class D_12(FreeParameterTemplate):
init_value = 0.1e-9
lower_bound = 0
upper_bound = 5e-9
parameter_transform = ScaleTransform(1e10)
sampling_proposal_std = 1e-10
numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class R2s(FreeParameterTemplate):
"""R2s = 1/T2s, for lineaR T2sDec or other models."""
init_value = 10
lower_bound = 1
upper_bound = 50.0
parameter_transform = ScaleTransform(1e2)
class time_dependent_characteristic_coefficient(FreeParameterTemplate):
"""The time dependent characteristic as used in the TimeDependentZeppelin model. Values are in m^2."""
init_value = 1e-6
lower_bound = 1e-7
upper_bound = 1e-5
parameter_transform = ScaleTransform(1e7)
sampling_proposal_std = 1e-7
class R1(FreeParameterTemplate):
"""R1 = 1/T1, for linear T1Dec or other models. """
init_value = 2
lower_bound = 0.25
upper_bound = 100.0
parameter_transform = ScaleTransform(1e2)
class matrix_element_param(FreeParameterTemplate):
name = 'W_{}{}{}{}'.format(*index)
init_value = _init_value
lower_bound = _lower_bound
upper_bound = 1e20
parameter_transform = ScaleTransform(100)
sampling_prior = _sampling_prior
sampling_proposal_std = 0.01
class d_exvivo(FreeParameterTemplate):
"""For use in ExpT1DecSTEAM model. It assumes ex-vivo values. For in-vivo use ``d`` instead."""
init_value = 5.0e-10
lower_bound = 0.0
upper_bound = 1.0e-8
parameter_transform = ScaleTransform(1e10)
sampling_proposal_std = 1e-11
numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class dperp1(FreeParameterTemplate):
init_value = 1.7e-11
lower_bound = 0
upper_bound = 1.0e-8
parameter_transform = ScaleTransform(1e10)
sampling_proposal_std = 1e-10
numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class kw(FreeParameterTemplate):
"""We optimize the ratio w = k1/k2 in the Ball&Racket and NODDI Bingham model"""
init_value = 2
lower_bound = 1
upper_bound = 64
sampling_proposal_std = 0.01
numdiff_info = {'use_upper_bound': False}
parameter_transform = ScaleTransform(1 / 64.)
class k1(FreeParameterTemplate):
"""The kappa parameter for the Ball&Racket and NODDI Bingham model"""
init_value = 1
lower_bound = 0
upper_bound = 64
sampling_proposal_std = 0.01
numdiff_info = {'use_upper_bound': False}
parameter_transform = ScaleTransform(1 / 64.)
class T2_b(FreeParameterTemplate):
"""T2_b"""
init_value = 10e-6
lower_bound = 1e-7
upper_bound = 100e-6
parameter_transform = ScaleTransform(1e6)
numdiff_info = {
'scale_factor': 1e5,
'use_upper_bound': False,
'use_lower_bound': False
}
class kappa(FreeParameterTemplate):
"""The kappa parameter used in the NODDI Watson model.
The NODDI-Watson model computes the spherical harmonic (SH) coefficients of the Watson distribution with the
concentration parameter k (kappa) up to the 12th order.
Truncating at the 12th order gives good approximation for kappa up to 64, as such we define kappa to be between
zero and 64.
"""
init_value = 1
lower_bound = 0
upper_bound = 64
sampling_proposal_std = 0.01
numdiff_info = {'use_upper_bound': False}
parameter_transform = ScaleTransform(1 / 64.)
class scale(FreeParameterTemplate):
init_value = 1e-6
lower_bound = 0.01e-6
upper_bound = 20e-6
parameter_transform = ScaleTransform(1e6)
sampling_proposal_std = 0.01e-6
class T2(FreeParameterTemplate):
init_value = 0.05
lower_bound = 1e-5
upper_bound = 2.0
parameter_transform = ScaleTransform(1e4)
class R(FreeParameterTemplate):
init_value = 1.0e-6
lower_bound = 1e-7
upper_bound = 20e-6
parameter_transform = ScaleTransform(1e7)
sampling_proposal_std = 1e-7