cmp.stages.diffusion.reconstruction module¶

Reconstruction methods and workflows.

class cmp.stages.diffusion.reconstruction.Dipy_recon_config[source]¶

Bases: traits.has_traits.HasTraits

Class used to store Dipy diffusion reconstruction sub-workflow configuration parameters.

imaging_model¶

Diffusion imaging model (For instance ‘DTI’)

Type: Str

flip_table_axis¶

Axis to be flipped in the gradient table.

Type: traits.List([‘x’, ‘y’, ‘z’])

local_model_editor¶

List of reconstruction models

Type: {False: ‘1:Tensor’, True: ‘2:Constrained Spherical Deconvolution’}

local_model¶

Reconstruction model selected (See local_model_editor) (Default: True, meaning Tensor is performed)

Type: traits.Bool

lmax_order¶

Choices of maximal order to use for Constrained Spherical Deconvolution

Type: traits.Enum([2, 4, 6, 8, 10, 12, 14, 16])

single_fib_thr¶

FA threshold

Type: traits.Float(0.7, min=0, max=1)

recon_mode¶

Can be “Probabilistic” or “Deterministic”

Type: traits.Str

mapmri¶

Type: traits.Bool(False)

tracking_processing_tool¶

Type: traits.Enum(‘MRtrix’, ‘Dipy’)

laplacian_regularization¶

Apply laplacian regularization in MAP-MRI if True (Default: True)

Type: traits.Bool

laplacian_weighting¶

Laplacian regularization weight in MAP-MRI (Default: 0.05)

Type: traits.Float

positivity_constraint¶

Apply positivity constraint in MAP-MRI if True (Default: True)

Type: traits.Bool

radial_order¶

MAP-MRI radial order (Default: 8)

Type: traits.Int

small_delta¶

Small data for gradient table (pulse duration) used by MAP-MRI (Default: 0.02)

Type: traits.Float

big_delta¶

Big data for gradient table (time interval) used by MAP-MRI (Default: 0.5)

Type: traits.Float

radial_order_values¶

Choices of radial order values used by SHORE

Type: traits.List([2, 4, 6, 8, 10, 12])

shore_radial_order¶

Even number that represents the order of the basis (Default: 6)

Type: traits.Str

shore_zeta¶

Scale factor in SHORE (Default: 700)

Type: traits.Int

shore_lambda_n¶

Radial regularisation constant in SHORE (Default: 1e-8)

Type: traits.Float

shore_lambda_l¶

Angular regularisation constant in SHORE (Default: 1e-8)

Type: traits.Float

shore_tau¶

Diffusion time used by SHORE. By default the value that makes q equal to the square root of the b-value (Default: 0.025330295910584444)

Type: traits.Float

shore_constrain_e0¶

Constrain SHORE optimization such that E(0) = 1 (Default: False)

Type: traits.Bool

shore_positive_constraint¶

Constrain the SHORE propagator to be positive (Default: False)

Type: traits.Bool

class cmp.stages.diffusion.reconstruction.MRtrix_recon_config[source]¶