API Reference

• dipy
  • Diffusion Imaging in Python
    • Subpackages
    • Utilities
  • get_info
    • get_info()
• align
  • Module: align._public
  • Module: align.bundlemin
  • Module: align.cpd
    • Note
  • Module: align.crosscorr
  • Module: align.expectmax
  • Module: align.imaffine
    • References
  • Module: align.imwarp
  • Module: align.metrics
  • Module: align.parzenhist
  • Module: align.reslice
  • Module: align.scalespace
  • Module: align.streamlinear
  • Module: align.streamwarp
  • Module: align.sumsqdiff
  • Module: align.transforms
  • Module: align.vector_fields
    • Bunch
      • Bunch
        • Bunch.__init__()
    • VerbosityLevels
      • VerbosityLevels()
    • syn_registration
      • syn_registration()
    • register_dwi_to_template
      • register_dwi_to_template()
    • write_mapping
      • write_mapping()
    • read_mapping
      • read_mapping()
    • resample
      • resample()
    • affine_registration
      • affine_registration()
    • center_of_mass
      • center_of_mass()
    • translation
      • translation()
    • rigid
      • rigid()
    • rigid_isoscaling
      • rigid_isoscaling()
    • rigid_scaling
      • rigid_scaling()
    • affine
      • affine()
    • _METHOD_DICT
      • _METHOD_DICT()
    • register_series
      • register_series()
    • register_dwi_series
      • register_dwi_series()
    • motion_correction
      • motion_correction()
    • streamline_registration
      • streamline_registration()
    • determine_num_threads
      • determine_num_threads()
    • distance_matrix_mdf
      • distance_matrix_mdf()
    • DeformableRegistration
      • DeformableRegistration
        • DeformableRegistration.__init__()
        • DeformableRegistration.expectation()
        • DeformableRegistration.get_registration_parameters()
        • DeformableRegistration.iterate()
        • DeformableRegistration.maximization()
        • DeformableRegistration.register()
        • DeformableRegistration.transform_point_cloud()
        • DeformableRegistration.update_transform()
        • DeformableRegistration.update_variance()
    • gaussian_kernel
      • gaussian_kernel()
    • low_rank_eigen
      • low_rank_eigen()
    • initialize_sigma2
      • initialize_sigma2()
    • lowrankQS
      • lowrankQS()
    • compute_cc_backward_step_2d
      • compute_cc_backward_step_2d()
    • compute_cc_backward_step_3d
      • compute_cc_backward_step_3d()
    • compute_cc_forward_step_2d
      • compute_cc_forward_step_2d()
    • compute_cc_forward_step_3d
      • compute_cc_forward_step_3d()
    • precompute_cc_factors_2d
      • precompute_cc_factors_2d()
    • precompute_cc_factors_2d_test
      • precompute_cc_factors_2d_test()
    • precompute_cc_factors_3d
      • precompute_cc_factors_3d()
    • precompute_cc_factors_3d_test
      • precompute_cc_factors_3d_test()
    • compute_em_demons_step_2d
      • compute_em_demons_step_2d()
    • compute_em_demons_step_3d
      • compute_em_demons_step_3d()
    • compute_masked_class_stats_2d
      • compute_masked_class_stats_2d()
    • compute_masked_class_stats_3d
      • compute_masked_class_stats_3d()
    • quantize_positive_2d
      • quantize_positive_2d()
    • quantize_positive_3d
      • quantize_positive_3d()
    • AffineInversionError
      • AffineInversionError
        • AffineInversionError.__init__()
    • AffineInvalidValuesError
      • AffineInvalidValuesError
        • AffineInvalidValuesError.__init__()
    • AffineMap
      • AffineMap
        • AffineMap.__init__()
        • AffineMap.get_affine()
        • AffineMap.set_affine()
        • AffineMap.transform()
        • AffineMap.transform_inverse()
    • MutualInformationMetric
      • MutualInformationMetric
        • MutualInformationMetric.__init__()
        • MutualInformationMetric.distance()
        • MutualInformationMetric.distance_and_gradient()
        • MutualInformationMetric.gradient()
        • MutualInformationMetric.setup()
    • AffineRegistration
      • AffineRegistration
        • AffineRegistration.__init__()
        • AffineRegistration.docstring_addendum
        • AffineRegistration.optimize()
    • _transform_method
      • _transform_method()
    • transform_centers_of_mass
      • transform_centers_of_mass()
    • transform_geometric_centers
      • transform_geometric_centers()
    • transform_origins
      • transform_origins()
    • DiffeomorphicMap
      • DiffeomorphicMap
        • DiffeomorphicMap.__init__()
        • DiffeomorphicMap.allocate()
        • DiffeomorphicMap.compute_inversion_error()
        • DiffeomorphicMap.expand_fields()
        • DiffeomorphicMap.get_backward_field()
        • DiffeomorphicMap.get_forward_field()
        • DiffeomorphicMap.get_simplified_transform()
        • DiffeomorphicMap.interpret_matrix()
        • DiffeomorphicMap.inverse()
        • DiffeomorphicMap.shallow_copy()
        • DiffeomorphicMap.transform()
        • DiffeomorphicMap.transform_inverse()
        • DiffeomorphicMap.transform_points()
        • DiffeomorphicMap.transform_points_inverse()
        • DiffeomorphicMap.warp_endomorphism()
    • DiffeomorphicRegistration
      • DiffeomorphicRegistration
        • DiffeomorphicRegistration.__init__()
        • DiffeomorphicRegistration.get_map()
        • DiffeomorphicRegistration.optimize()
        • DiffeomorphicRegistration.set_level_iters()
    • SymmetricDiffeomorphicRegistration
      • SymmetricDiffeomorphicRegistration
        • SymmetricDiffeomorphicRegistration.__init__()
        • SymmetricDiffeomorphicRegistration.get_map()
        • SymmetricDiffeomorphicRegistration.optimize()
        • SymmetricDiffeomorphicRegistration.update()
    • RegistrationStages
      • RegistrationStages()
    • logger
      • logger()
    • mult_aff
      • mult_aff()
    • get_direction_and_spacings
      • get_direction_and_spacings()
    • SimilarityMetric
      • SimilarityMetric
        • SimilarityMetric.__init__()
        • SimilarityMetric.compute_backward()
        • SimilarityMetric.compute_forward()
        • SimilarityMetric.free_iteration()
        • SimilarityMetric.get_energy()
        • SimilarityMetric.initialize_iteration()
        • SimilarityMetric.set_levels_above()
        • SimilarityMetric.set_levels_below()
        • SimilarityMetric.set_moving_image()
        • SimilarityMetric.set_static_image()
        • SimilarityMetric.use_moving_image_dynamics()
        • SimilarityMetric.use_static_image_dynamics()
    • CCMetric
      • CCMetric
        • CCMetric.__init__()
        • CCMetric.compute_backward()
        • CCMetric.compute_forward()
        • CCMetric.free_iteration()
        • CCMetric.get_energy()
        • CCMetric.initialize_iteration()
    • EMMetric
      • EMMetric
        • EMMetric.__init__()
        • EMMetric.compute_backward()
        • EMMetric.compute_demons_step()
        • EMMetric.compute_forward()
        • EMMetric.compute_gauss_newton_step()
        • EMMetric.free_iteration()
        • EMMetric.get_energy()
        • EMMetric.initialize_iteration()
        • EMMetric.use_moving_image_dynamics()
        • EMMetric.use_static_image_dynamics()
    • SSDMetric
      • SSDMetric
        • SSDMetric.__init__()
        • SSDMetric.compute_backward()
        • SSDMetric.compute_demons_step()
        • SSDMetric.compute_forward()
        • SSDMetric.compute_gauss_newton_step()
        • SSDMetric.free_iteration()
        • SSDMetric.get_energy()
        • SSDMetric.initialize_iteration()
    • v_cycle_2d
      • v_cycle_2d()
    • v_cycle_3d
      • v_cycle_3d()
    • ParzenJointHistogram
      • ParzenJointHistogram
        • ParzenJointHistogram.__init__()
        • ParzenJointHistogram.bin_index()
        • ParzenJointHistogram.bin_normalize_moving()
        • ParzenJointHistogram.bin_normalize_static()
        • ParzenJointHistogram.setup()
        • ParzenJointHistogram.update_gradient_dense()
        • ParzenJointHistogram.update_gradient_sparse()
        • ParzenJointHistogram.update_pdfs_dense()
        • ParzenJointHistogram.update_pdfs_sparse()
    • compute_parzen_mi
      • compute_parzen_mi()
    • cubic_spline
      • cubic_spline()
    • cubic_spline_derivative
      • cubic_spline_derivative()
    • sample_domain_regular
      • sample_domain_regular()
    • reslice
      • reslice()
    • ScaleSpace
      • ScaleSpace
        • ScaleSpace.__init__()
        • ScaleSpace.get_affine()
        • ScaleSpace.get_affine_inv()
        • ScaleSpace.get_domain_shape()
        • ScaleSpace.get_expand_factors()
        • ScaleSpace.get_image()
        • ScaleSpace.get_scaling()
        • ScaleSpace.get_sigmas()
        • ScaleSpace.get_spacing()
        • ScaleSpace.print_level()
    • IsotropicScaleSpace
      • IsotropicScaleSpace
        • IsotropicScaleSpace.__init__()
    • logger
      • logger()
    • StreamlineDistanceMetric
      • StreamlineDistanceMetric
        • StreamlineDistanceMetric.__init__()
        • StreamlineDistanceMetric.distance()
        • StreamlineDistanceMetric.setup()
    • BundleMinDistanceMetric
      • BundleMinDistanceMetric
        • BundleMinDistanceMetric.__init__()
        • BundleMinDistanceMetric.distance()
        • BundleMinDistanceMetric.setup()
    • BundleMinDistanceMatrixMetric
      • BundleMinDistanceMatrixMetric
        • BundleMinDistanceMatrixMetric.__init__()
        • BundleMinDistanceMatrixMetric.distance()
        • BundleMinDistanceMatrixMetric.setup()
    • BundleMinDistanceAsymmetricMetric
      • BundleMinDistanceAsymmetricMetric
        • BundleMinDistanceAsymmetricMetric.__init__()
        • BundleMinDistanceAsymmetricMetric.distance()
    • BundleSumDistanceMatrixMetric
      • BundleSumDistanceMatrixMetric
        • BundleSumDistanceMatrixMetric.__init__()
        • BundleSumDistanceMatrixMetric.distance()
    • JointBundleMinDistanceMetric
      • JointBundleMinDistanceMetric
        • JointBundleMinDistanceMetric.__init__()
        • JointBundleMinDistanceMetric.distance()
        • JointBundleMinDistanceMetric.setup()
    • StreamlineLinearRegistration
      • StreamlineLinearRegistration
        • StreamlineLinearRegistration.__init__()
        • StreamlineLinearRegistration.optimize()
    • StreamlineRegistrationMap
      • StreamlineRegistrationMap
        • StreamlineRegistrationMap.__init__()
        • StreamlineRegistrationMap.transform()
    • JointStreamlineRegistrationMap
      • JointStreamlineRegistrationMap
        • JointStreamlineRegistrationMap.__init__()
        • JointStreamlineRegistrationMap.transform()
    • logger
      • logger()
    • bundle_sum_distance
      • bundle_sum_distance()
    • bundle_min_distance
      • bundle_min_distance()
    • bundle_min_distance_fast
      • bundle_min_distance_fast()
    • bundle_min_distance_asymmetric_fast
      • bundle_min_distance_asymmetric_fast()
    • remove_clusters_by_size
      • remove_clusters_by_size()
    • progressive_slr
      • progressive_slr()
    • slr_with_qbx
      • slr_with_qbx()
    • groupwise_slr
      • groupwise_slr()
    • get_unique_pairs
      • get_unique_pairs()
    • compose_matrix44
      • compose_matrix44()
    • decompose_matrix44
      • decompose_matrix44()
    • average_bundle_length
      • average_bundle_length()
    • find_missing
      • find_missing()
    • bundlewarp
      • bundlewarp()
    • bundlewarp_vector_filed
      • bundlewarp_vector_filed()
    • bundlewarp_shape_analysis
      • bundlewarp_shape_analysis()
    • compute_energy_ssd_2d
      • compute_energy_ssd_2d()
    • compute_energy_ssd_3d
      • compute_energy_ssd_3d()
    • compute_residual_displacement_field_ssd_2d
      • compute_residual_displacement_field_ssd_2d()
    • compute_residual_displacement_field_ssd_3d
      • compute_residual_displacement_field_ssd_3d()
    • compute_ssd_demons_step_2d
      • compute_ssd_demons_step_2d()
    • compute_ssd_demons_step_3d
      • compute_ssd_demons_step_3d()
    • iterate_residual_displacement_field_ssd_2d
      • iterate_residual_displacement_field_ssd_2d()
    • iterate_residual_displacement_field_ssd_3d
      • iterate_residual_displacement_field_ssd_3d()
    • solve_2d_symmetric_positive_definite
      • solve_2d_symmetric_positive_definite()
    • solve_3d_symmetric_positive_definite
      • solve_3d_symmetric_positive_definite()
    • AffineTransform2D
      • AffineTransform2D
        • AffineTransform2D.__init__()
    • AffineTransform3D
      • AffineTransform3D
        • AffineTransform3D.__init__()
    • RigidIsoScalingTransform2D
      • RigidIsoScalingTransform2D
        • RigidIsoScalingTransform2D.__init__()
    • RigidIsoScalingTransform3D
      • RigidIsoScalingTransform3D
        • RigidIsoScalingTransform3D.__init__()
    • RigidScalingTransform2D
      • RigidScalingTransform2D
        • RigidScalingTransform2D.__init__()
    • RigidScalingTransform3D
      • RigidScalingTransform3D
        • RigidScalingTransform3D.__init__()
    • RigidTransform2D
      • RigidTransform2D
        • RigidTransform2D.__init__()
    • RigidTransform3D
      • RigidTransform3D
        • RigidTransform3D.__init__()
    • RotationTransform2D
      • RotationTransform2D
        • RotationTransform2D.__init__()
    • RotationTransform3D
      • RotationTransform3D
        • RotationTransform3D.__init__()
    • ScalingTransform2D
      • ScalingTransform2D
        • ScalingTransform2D.__init__()
    • ScalingTransform3D
      • ScalingTransform3D
        • ScalingTransform3D.__init__()
    • Transform
      • Transform
        • Transform.__init__()
        • Transform.get_dim()
        • Transform.get_identity_parameters()
        • Transform.get_number_of_parameters()
        • Transform.jacobian()
        • Transform.param_to_matrix()
    • TranslationTransform2D
      • TranslationTransform2D
        • TranslationTransform2D.__init__()
    • TranslationTransform3D
      • TranslationTransform3D
        • TranslationTransform3D.__init__()
    • compose_vector_fields_2d
      • compose_vector_fields_2d()
    • compose_vector_fields_3d
      • compose_vector_fields_3d()
    • create_circle
      • create_circle()
    • create_harmonic_fields_2d
      • create_harmonic_fields_2d()
    • create_harmonic_fields_3d
      • create_harmonic_fields_3d()
    • create_random_displacement_2d
      • create_random_displacement_2d()
    • create_random_displacement_3d
      • create_random_displacement_3d()
    • create_sphere
      • create_sphere()
    • downsample_displacement_field_2d
      • downsample_displacement_field_2d()
    • downsample_displacement_field_3d
      • downsample_displacement_field_3d()
    • downsample_scalar_field_2d
      • downsample_scalar_field_2d()
    • downsample_scalar_field_3d
      • downsample_scalar_field_3d()
    • gradient
      • gradient()
    • invert_vector_field_fixed_point_2d
      • invert_vector_field_fixed_point_2d()
    • invert_vector_field_fixed_point_3d
      • invert_vector_field_fixed_point_3d()
    • is_valid_affine
      • is_valid_affine()
    • reorient_vector_field_2d
      • reorient_vector_field_2d()
    • reorient_vector_field_3d
      • reorient_vector_field_3d()
    • resample_displacement_field_2d
      • resample_displacement_field_2d()
    • resample_displacement_field_3d
      • resample_displacement_field_3d()
    • simplify_warp_function_2d
      • simplify_warp_function_2d()
    • simplify_warp_function_3d
      • simplify_warp_function_3d()
    • sparse_gradient
      • sparse_gradient()
    • transform_2d_affine
      • transform_2d_affine()
    • transform_2d_affine_nn
      • transform_2d_affine_nn()
    • transform_3d_affine
      • transform_3d_affine()
    • transform_3d_affine_nn
      • transform_3d_affine_nn()
    • warp_2d
      • warp_2d()
    • warp_2d_nn
      • warp_2d_nn()
    • warp_3d
      • warp_3d()
    • warp_3d_nn
      • warp_3d_nn()
    • warp_coordinates_2d
      • warp_coordinates_2d()
    • warp_coordinates_3d
      • warp_coordinates_3d()
• core
  • Module: core.geometry
  • Module: core.gradients
  • Module: core.graph
  • Module: core.histeq
  • Module: core.interpolation
  • Module: core.ndindex
  • Module: core.onetime
    • References
  • Module: core.optimize
  • Module: core.profile
  • Module: core.rng
  • Module: core.sphere
  • Module: core.sphere_stats
  • Module: core.subdivide_octahedron
  • Module: core.wavelet
    • _TUPLE2AXES
      • _TUPLE2AXES()
    • sphere2cart
      • sphere2cart()
    • cart2sphere
      • cart2sphere()
    • sph2latlon
      • sph2latlon()
    • normalized_vector
      • normalized_vector()
    • vector_norm
      • vector_norm()
    • rodrigues_axis_rotation
      • rodrigues_axis_rotation()
    • nearest_pos_semi_def
      • nearest_pos_semi_def()
    • sphere_distance
      • sphere_distance()
    • cart_distance
      • cart_distance()
    • vector_cosine
      • vector_cosine()
    • lambert_equal_area_projection_polar
      • lambert_equal_area_projection_polar()
    • lambert_equal_area_projection_cart
      • lambert_equal_area_projection_cart()
    • euler_matrix
      • euler_matrix()
    • compose_matrix
      • compose_matrix()
    • decompose_matrix
      • decompose_matrix()
    • circumradius
      • circumradius()
    • vec2vec_rotmat
      • vec2vec_rotmat()
    • compose_transformations
      • compose_transformations()
    • perpendicular_directions
      • perpendicular_directions()
    • dist_to_corner
      • dist_to_corner()
    • is_hemispherical
      • is_hemispherical()
    • GradientTable
      • GradientTable
        • GradientTable.__init__()
        • GradientTable.b0s_mask()
        • GradientTable.bvals()
        • GradientTable.bvecs()
        • GradientTable.gradient_strength()
        • GradientTable.info
        • GradientTable.qvals()
        • GradientTable.tau()
    • logger
      • logger()
    • unique_bvals
      • unique_bvals()
    • b0_threshold_empty_gradient_message
      • b0_threshold_empty_gradient_message()
    • b0_threshold_update_slicing_message
      • b0_threshold_update_slicing_message()
    • mask_non_weighted_bvals
      • mask_non_weighted_bvals()
    • gradient_table_from_bvals_bvecs
      • gradient_table_from_bvals_bvecs()
    • gradient_table_from_qvals_bvecs
      • gradient_table_from_qvals_bvecs()
    • gradient_table_from_gradient_strength_bvecs
      • gradient_table_from_gradient_strength_bvecs()
    • gradient_table
      • gradient_table()
    • reorient_bvecs
      • reorient_bvecs()
    • generate_bvecs
      • generate_bvecs()
    • round_bvals
      • round_bvals()
    • unique_bvals_tolerance
      • unique_bvals_tolerance()
    • get_bval_indices
      • get_bval_indices()
    • unique_bvals_magnitude
      • unique_bvals_magnitude()
    • check_multi_b
      • check_multi_b()
    • btens_to_params
      • btens_to_params()
    • params_to_btens
      • params_to_btens()
    • ornt_mapping
      • ornt_mapping()
    • reorient_vectors
      • reorient_vectors()
    • reorient_on_axis
      • reorient_on_axis()
    • orientation_from_string
      • orientation_from_string()
    • orientation_to_string
      • orientation_to_string()
    • Graph
      • Graph
        • Graph.__init__()
        • Graph.add_edge()
        • Graph.add_node()
        • Graph.all_paths()
        • Graph.children()
        • Graph.del_node()
        • Graph.del_node_and_edges()
        • Graph.down()
        • Graph.down_short()
        • Graph.parents()
        • Graph.shortest_path()
        • Graph.up()
        • Graph.up_short()
    • histeq
      • histeq()
    • Interpolator
      • Interpolator
        • Interpolator.__init__()
    • NearestNeighborInterpolator
      • NearestNeighborInterpolator
        • NearestNeighborInterpolator.__init__()
    • OutsideImage
      • OutsideImage
        • OutsideImage.__init__()
    • TriLinearInterpolator
      • TriLinearInterpolator
        • TriLinearInterpolator.__init__()
    • interp_rbf
      • interp_rbf()
    • interpolate_scalar_2d
      • interpolate_scalar_2d()
    • interpolate_scalar_3d
      • interpolate_scalar_3d()
    • interpolate_scalar_nn_2d
      • interpolate_scalar_nn_2d()
    • interpolate_scalar_nn_3d
      • interpolate_scalar_nn_3d()
    • interpolate_vector_2d
      • interpolate_vector_2d()
    • interpolate_vector_3d
      • interpolate_vector_3d()
    • map_coordinates_trilinear_iso
      • map_coordinates_trilinear_iso()
    • nearestneighbor_interpolate
      • nearestneighbor_interpolate()
    • trilinear_interp
      • trilinear_interp()
    • trilinear_interpolate4d
      • trilinear_interpolate4d()
    • ndindex
      • ndindex()
    • ResetMixin
      • ResetMixin
        • ResetMixin.__init__()
        • ResetMixin.reset()
    • OneTimeProperty
      • OneTimeProperty
        • OneTimeProperty.__init__()
    • auto_attr
      • auto_attr()
    • Optimizer
      • Optimizer
        • Optimizer.__init__()
        • Optimizer.evolution
        • Optimizer.fopt
        • Optimizer.message
        • Optimizer.nfev
        • Optimizer.nit
        • Optimizer.print_summary()
        • Optimizer.xopt
    • SKLearnLinearSolver
      • SKLearnLinearSolver
        • SKLearnLinearSolver.__init__()
        • SKLearnLinearSolver.fit()
        • SKLearnLinearSolver.predict()
    • NonNegativeLeastSquares
      • NonNegativeLeastSquares
        • NonNegativeLeastSquares.__init__()
        • NonNegativeLeastSquares.fit()
    • PositiveDefiniteLeastSquares
      • PositiveDefiniteLeastSquares
        • PositiveDefiniteLeastSquares.__init__()
        • PositiveDefiniteLeastSquares.solve()
    • spdot
      • spdot()
    • sparse_nnls
      • sparse_nnls()
    • Profiler
      • Profiler
        • Profiler.__init__()
        • Profiler.print_stats()
    • WichmannHill2006
      • WichmannHill2006()
    • WichmannHill1982
      • WichmannHill1982()
    • LEcuyer
      • LEcuyer()
    • Sphere
      • Sphere
        • Sphere.__init__()
        • Sphere.edges()
        • Sphere.faces()
        • Sphere.find_closest()
        • Sphere.subdivide()
        • Sphere.vertices()
        • Sphere.x
        • Sphere.y
        • Sphere.z
    • HemiSphere
      • HemiSphere
        • HemiSphere.__init__()
        • HemiSphere.faces()
        • HemiSphere.find_closest()
        • HemiSphere.from_sphere()
        • HemiSphere.mirror()
        • HemiSphere.subdivide()
    • faces_from_sphere_vertices
      • faces_from_sphere_vertices()
    • unique_edges
      • unique_edges()
    • unique_sets
      • unique_sets()
    • disperse_charges
      • disperse_charges()
    • fibonacci_sphere
      • fibonacci_sphere()
    • disperse_charges_alt
      • disperse_charges_alt()
    • euler_characteristic_check
      • euler_characteristic_check()
    • octahedron_vertices
      • octahedron_vertices()
    • octahedron_faces
      • octahedron_faces()
    • icosahedron_vertices
      • icosahedron_vertices()
    • icosahedron_faces
      • icosahedron_faces()
    • unit_octahedron
      • unit_octahedron()
    • unit_icosahedron
      • unit_icosahedron()
    • hemi_icosahedron
      • hemi_icosahedron()
    • random_uniform_on_sphere
      • random_uniform_on_sphere()
    • eigenstats
      • eigenstats()
    • compare_orientation_sets
      • compare_orientation_sets()
    • angular_similarity
      • angular_similarity()
    • create_unit_sphere
      • create_unit_sphere()
    • create_unit_hemisphere
      • create_unit_hemisphere()
    • cshift3D
      • cshift3D()
    • permutationinverse
      • permutationinverse()
    • afb3D_A
      • afb3D_A()
    • sfb3D_A
      • sfb3D_A()
    • sfb3D
      • sfb3D()
    • afb3D
      • afb3D()
    • dwt3D
      • dwt3D()
    • idwt3D
      • idwt3D()
• data
  • Module: data.fetcher
    • DataError
      • DataError
        • DataError.__init__()
    • loads_compat
      • loads_compat()
    • DATA_DIR
      • DATA_DIR()
    • get_sim_voxels
      • get_sim_voxels()
    • get_skeleton
      • get_skeleton()
    • get_sphere
      • get_sphere()
    • default_sphere
      • default_sphere()
    • small_sphere
      • small_sphere()
    • get_3shell_gtab
      • get_3shell_gtab()
    • get_isbi2013_2shell_gtab
      • get_isbi2013_2shell_gtab()
    • get_gtab_taiwan_dsi
      • get_gtab_taiwan_dsi()
    • dsi_voxels
      • dsi_voxels()
    • dsi_deconv_voxels
      • dsi_deconv_voxels()
    • mrtrix_spherical_functions
      • mrtrix_spherical_functions()
    • get_cmap
      • get_cmap()
    • two_cingulum_bundles
      • two_cingulum_bundles()
    • matlab_life_results
      • matlab_life_results()
    • load_sdp_constraints
      • load_sdp_constraints()
    • copyfileobj_withprogress
      • copyfileobj_withprogress()
    • check_md5
      • check_md5()
    • fetch_data
      • fetch_data()
    • fetch_isbi2013_2shell
      • fetch_isbi2013_2shell()
    • fetch_stanford_labels
      • fetch_stanford_labels()
    • fetch_sherbrooke_3shell
      • fetch_sherbrooke_3shell()
    • fetch_stanford_hardi
      • fetch_stanford_hardi()
    • fetch_resdnn_weights
      • fetch_resdnn_weights()
    • fetch_synb0_weights
      • fetch_synb0_weights()
    • fetch_synb0_test
      • fetch_synb0_test()
    • fetch_deepn4_weights
      • fetch_deepn4_weights()
    • fetch_deepn4_test
      • fetch_deepn4_test()
    • fetch_evac_weights
      • fetch_evac_weights()
    • fetch_evac_test
      • fetch_evac_test()
    • fetch_stanford_t1
      • fetch_stanford_t1()
    • fetch_stanford_pve_maps
      • fetch_stanford_pve_maps()
    • fetch_stanford_tracks
      • fetch_stanford_tracks()
    • fetch_taiwan_ntu_dsi
      • fetch_taiwan_ntu_dsi()
    • fetch_syn_data
      • fetch_syn_data()
    • fetch_mni_template
      • fetch_mni_template()
    • fetch_scil_b0
      • fetch_scil_b0()
    • fetch_bundles_2_subjects
      • fetch_bundles_2_subjects()
    • fetch_ivim
      • fetch_ivim()
    • fetch_cfin_multib
      • fetch_cfin_multib()
    • fetch_file_formats
      • fetch_file_formats()
    • fetch_bundle_atlas_hcp842
      • fetch_bundle_atlas_hcp842()
    • fetch_target_tractogram_hcp
      • fetch_target_tractogram_hcp()
    • fetch_bundle_fa_hcp
      • fetch_bundle_fa_hcp()
    • fetch_qtdMRI_test_retest_2subjects
      • fetch_qtdMRI_test_retest_2subjects()
    • fetch_gold_standard_io
      • fetch_gold_standard_io()
    • fetch_qte_lte_pte
      • fetch_qte_lte_pte()
    • fetch_cti_rat1
      • fetch_cti_rat1()
    • fetch_fury_surface
      • fetch_fury_surface()
    • fetch_DiB_70_lte_pte_ste
      • fetch_DiB_70_lte_pte_ste()
    • fetch_DiB_217_lte_pte_ste
      • fetch_DiB_217_lte_pte_ste()
    • fetch_ptt_minimal_dataset
      • fetch_ptt_minimal_dataset()
    • fetch_bundle_warp_dataset
      • fetch_bundle_warp_dataset()
    • get_fnames
      • get_fnames()
    • read_qtdMRI_test_retest_2subjects
      • read_qtdMRI_test_retest_2subjects()
    • read_scil_b0
      • read_scil_b0()
    • read_siemens_scil_b0
      • read_siemens_scil_b0()
    • read_isbi2013_2shell
      • read_isbi2013_2shell()
    • read_sherbrooke_3shell
      • read_sherbrooke_3shell()
    • read_stanford_labels
      • read_stanford_labels()
    • read_stanford_hardi
      • read_stanford_hardi()
    • read_stanford_t1
      • read_stanford_t1()
    • read_stanford_pve_maps
      • read_stanford_pve_maps()
    • read_taiwan_ntu_dsi
      • read_taiwan_ntu_dsi()
    • read_syn_data
      • read_syn_data()
    • fetch_tissue_data
      • fetch_tissue_data()
    • read_tissue_data
      • read_tissue_data()
    • read_mni_template
      • read_mni_template()
    • fetch_cenir_multib
      • fetch_cenir_multib()
    • read_cenir_multib
      • read_cenir_multib()
    • read_bundles_2_subjects
      • read_bundles_2_subjects()
    • read_ivim
      • read_ivim()
    • read_cfin_dwi
      • read_cfin_dwi()
    • read_cfin_t1
      • read_cfin_t1()
    • get_file_formats
      • get_file_formats()
    • get_bundle_atlas_hcp842
      • get_bundle_atlas_hcp842()
    • get_two_hcp842_bundles
      • get_two_hcp842_bundles()
    • get_target_tractogram_hcp
      • get_target_tractogram_hcp()
    • read_qte_lte_pte
      • read_qte_lte_pte()
    • read_DiB_70_lte_pte_ste
      • read_DiB_70_lte_pte_ste()
    • read_DiB_217_lte_pte_ste
      • read_DiB_217_lte_pte_ste()
    • extract_example_tracts
      • extract_example_tracts()
    • read_five_af_bundles
      • read_five_af_bundles()
    • to_bids_description
      • to_bids_description()
    • fetch_hcp
      • fetch_hcp()
    • fetch_hbn
      • fetch_hbn()
• denoise
  • Module: denoise.adaptive_soft_matching
  • Module: denoise.denspeed
  • Module: denoise.enhancement_kernel
  • Module: denoise.gibbs
  • Module: denoise.localpca
  • Module: denoise.nlmeans
  • Module: denoise.nlmeans_block
  • Module: denoise.noise_estimate
  • Module: denoise.non_local_means
  • Module: denoise.patch2self
  • Module: denoise.pca_noise_estimate
    • PCA Based Local Noise Estimation
  • Module: denoise.shift_twist_convolution
    • adaptive_soft_matching
      • adaptive_soft_matching()
    • add_padding_reflection
      • add_padding_reflection()
    • correspond_indices
      • correspond_indices()
    • determine_num_threads
      • determine_num_threads()
    • nlmeans_3d
      • nlmeans_3d()
    • remove_padding
      • remove_padding()
    • EnhancementKernel
      • EnhancementKernel
        • EnhancementKernel.__init__()
        • EnhancementKernel.evaluate_kernel()
        • EnhancementKernel.get_lookup_table()
        • EnhancementKernel.get_orientations()
        • EnhancementKernel.get_sphere()
    • HemiSphere
      • HemiSphere
        • HemiSphere.__init__()
        • HemiSphere.faces()
        • HemiSphere.find_closest()
        • HemiSphere.from_sphere()
        • HemiSphere.mirror()
        • HemiSphere.subdivide()
    • Sphere
      • Sphere
        • Sphere.__init__()
        • Sphere.edges()
        • Sphere.faces()
        • Sphere.find_closest()
        • Sphere.subdivide()
        • Sphere.vertices()
        • Sphere.x
        • Sphere.y
        • Sphere.z
    • ceil
      • ceil()
    • disperse_charges
      • disperse_charges()
    • get_sphere
      • get_sphere()
    • gettempdir
      • gettempdir()
    • gibbs_removal
      • gibbs_removal()
    • dimensionality_problem_message
      • dimensionality_problem_message()
    • create_patch_radius_arr
      • create_patch_radius_arr()
    • compute_patch_size
      • compute_patch_size()
    • compute_num_samples
      • compute_num_samples()
    • compute_suggested_patch_radius
      • compute_suggested_patch_radius()
    • genpca
      • genpca()
    • localpca
      • localpca()
    • mppca
      • mppca()
    • nlmeans
      • nlmeans()
    • firdn
      • firdn()
    • nlmeans_block
      • nlmeans_block()
    • upfir
      • upfir()
    • piesno
      • piesno()
    • estimate_sigma
      • estimate_sigma()
    • non_local_means
      • non_local_means()
    • patch2self
      • patch2self()
    • pca_noise_estimate
      • pca_noise_estimate()
    • warn
      • warn()
    • convolve
      • convolve()
    • convolve_sf
      • convolve_sf()
    • deprecated_params
      • deprecated_params()
    • determine_num_threads
      • determine_num_threads()
    • sf_to_sh
      • sf_to_sh()
    • sh_to_sf
      • sh_to_sf()
• direction
  • Module: direction.bootstrap_direction_getter
  • Module: direction.closest_peak_direction_getter
  • Module: direction.peaks
  • Module: direction.pmf
  • Module: direction.probabilistic_direction_getter
  • Module: direction.ptt_direction_getter
    • BootDirectionGetter
      • BootDirectionGetter
        • BootDirectionGetter.__init__()
        • BootDirectionGetter.from_data()
        • BootDirectionGetter.get_pmf()
        • BootDirectionGetter.get_pmf_no_boot()
        • BootDirectionGetter.initial_direction()
    • peak_directions
      • peak_directions()
    • BaseDirectionGetter
      • BaseDirectionGetter
        • BaseDirectionGetter.__init__()
    • BasePmfDirectionGetter
      • BasePmfDirectionGetter
        • BasePmfDirectionGetter.__init__()
        • BasePmfDirectionGetter.initial_direction()
    • ClosestPeakDirectionGetter
      • ClosestPeakDirectionGetter
        • ClosestPeakDirectionGetter.__init__()
    • PmfGenDirectionGetter
      • PmfGenDirectionGetter
        • PmfGenDirectionGetter.__init__()
        • PmfGenDirectionGetter.from_pmf()
        • PmfGenDirectionGetter.from_shcoeff()
    • peak_directions
      • peak_directions()
    • PeaksAndMetrics
      • PeaksAndMetrics
        • PeaksAndMetrics.__init__()
    • peak_directions_nl
      • peak_directions_nl()
    • peak_directions
      • peak_directions()
    • peaks_from_model
      • peaks_from_model()
    • reshape_peaks_for_visualization
      • reshape_peaks_for_visualization()
    • PmfGen
      • PmfGen
        • PmfGen.__init__()
        • PmfGen.get_pmf()
        • PmfGen.get_pmf_value()
    • SHCoeffPmfGen
      • SHCoeffPmfGen
        • SHCoeffPmfGen.__init__()
    • SimplePmfGen
      • SimplePmfGen
        • SimplePmfGen.__init__()
    • DeterministicMaximumDirectionGetter
      • DeterministicMaximumDirectionGetter
        • DeterministicMaximumDirectionGetter.__init__()
    • ProbabilisticDirectionGetter
      • ProbabilisticDirectionGetter
        • ProbabilisticDirectionGetter.__init__()
    • random
      • random()
    • PTTDirectionGetter
      • PTTDirectionGetter
        • PTTDirectionGetter.__init__()
        • PTTDirectionGetter.generate_streamline()
    • min_radius_curvature_from_angle
      • min_radius_curvature_from_angle()
• io
  • Module: io.dpy
    • References
  • Module: io.gradients
  • Module: io.image
  • Module: io.peaks
  • Module: io.pickles
  • Module: io.stateful_tractogram
  • Module: io.streamline
  • Module: io.surface
  • Module: io.utils
  • Module: io.vtk
    • Dpy
      • Dpy
        • Dpy.__init__()
        • Dpy.close()
        • Dpy.read_track()
        • Dpy.read_tracks()
        • Dpy.read_tracksi()
        • Dpy.version()
        • Dpy.write_track()
        • Dpy.write_tracks()
    • read_bvals_bvecs
      • read_bvals_bvecs()
    • load_nifti_data
      • load_nifti_data()
    • load_nifti
      • load_nifti()
    • save_nifti
      • save_nifti()
    • save_qa_metric
      • save_qa_metric()
    • load_peaks
      • load_peaks()
    • save_peaks
      • save_peaks()
    • peaks_to_niftis
      • peaks_to_niftis()
    • save_pickle
      • save_pickle()
    • load_pickle
      • load_pickle()
    • Space
      • Space
        • Space.__init__()
        • Space.RASMM
        • Space.VOX
        • Space.VOXMM
    • Origin
      • Origin
        • Origin.__init__()
        • Origin.NIFTI
        • Origin.TRACKVIS
    • StatefulTractogram
      • StatefulTractogram
        • StatefulTractogram.__init__()
        • StatefulTractogram.affine
        • StatefulTractogram.are_compatible()
        • StatefulTractogram.compute_bounding_box()
        • StatefulTractogram.data_per_point
        • StatefulTractogram.data_per_streamline
        • StatefulTractogram.dimensions
        • StatefulTractogram.dtype_dict
        • StatefulTractogram.from_sft()
        • StatefulTractogram.get_data_per_point_keys()
        • StatefulTractogram.get_data_per_streamline_keys()
        • StatefulTractogram.get_streamlines_copy()
        • StatefulTractogram.is_bbox_in_vox_valid()
        • StatefulTractogram.origin
        • StatefulTractogram.remove_invalid_streamlines()
        • StatefulTractogram.space
        • StatefulTractogram.space_attributes
        • StatefulTractogram.streamlines
        • StatefulTractogram.to_center()
        • StatefulTractogram.to_corner()
        • StatefulTractogram.to_origin()
        • StatefulTractogram.to_rasmm()
        • StatefulTractogram.to_space()
        • StatefulTractogram.to_vox()
        • StatefulTractogram.to_voxmm()
        • StatefulTractogram.voxel_order
        • StatefulTractogram.voxel_sizes
    • logger
      • logger()
    • set_sft_logger_level
      • set_sft_logger_level()
    • save_tractogram
      • save_tractogram()
    • load_tractogram
      • load_tractogram()
    • load_generator
      • load_generator()
    • save_generator
      • save_generator()
    • load_trk
      • load_trk()
    • load_tck
      • load_tck()
    • load_trx
      • load_trx()
    • load_vtk
      • load_vtk()
    • load_vtp
      • load_vtp()
    • load_fib
      • load_fib()
    • load_dpy
      • load_dpy()
    • save_trk
      • save_trk()
    • save_tck
      • save_tck()
    • save_trx
      • save_trx()
    • save_vtk
      • save_vtk()
    • save_vtp
      • save_vtp()
    • save_fib
      • save_fib()
    • save_dpy
      • save_dpy()
    • load_pial
      • load_pial()
    • load_gifti
      • load_gifti()
    • nifti1_symmat
      • nifti1_symmat()
    • make5d
      • make5d()
    • decfa
      • decfa()
    • decfa_to_float
      • decfa_to_float()
    • is_reference_info_valid
      • is_reference_info_valid()
    • split_name_with_gz
      • split_name_with_gz()
    • get_reference_info
      • get_reference_info()
    • is_header_compatible
      • is_header_compatible()
    • create_tractogram_header
      • create_tractogram_header()
    • create_nifti_header
      • create_nifti_header()
    • save_buan_profiles_hdf5
      • save_buan_profiles_hdf5()
    • read_img_arr_or_path
      • read_img_arr_or_path()
    • load_polydata
      • load_polydata()
    • save_polydata
      • save_polydata()
    • save_vtk_streamlines
      • save_vtk_streamlines()
    • load_vtk_streamlines
      • load_vtk_streamlines()
• nn
  • Module: nn.cnn_1d_denoising
    • Title : Denoising diffusion weighted imaging data using CNN
      • Reference
  • Module: nn.deepn4
  • Module: nn.evac
  • Module: nn.histo_resdnn
  • Module: nn.model
  • Module: nn.synb0
  • Module: nn.utils
    • Cnn1DDenoiser
      • Cnn1DDenoiser
        • Cnn1DDenoiser.__init__()
        • Cnn1DDenoiser.compile()
        • Cnn1DDenoiser.evaluate()
        • Cnn1DDenoiser.fit()
        • Cnn1DDenoiser.load_weights()
        • Cnn1DDenoiser.predict()
        • Cnn1DDenoiser.save_weights()
        • Cnn1DDenoiser.summary()
        • Cnn1DDenoiser.train_test_split()
    • EncoderBlock
      • EncoderBlock
        • EncoderBlock.__init__()
        • EncoderBlock.call()
    • DecoderBlock
      • DecoderBlock
        • DecoderBlock.__init__()
        • DecoderBlock.call()
    • DeepN4
      • DeepN4
        • DeepN4.__init__()
        • DeepN4.fetch_default_weights()
        • DeepN4.load_model_weights()
        • DeepN4.load_resample()
        • DeepN4.pad()
        • DeepN4.predict()
    • logger
      • logger()
    • UNet3D
      • UNet3D()
    • Block
      • Block
        • Block.__init__()
        • Block.call()
    • ChannelSum
      • ChannelSum
        • ChannelSum.__init__()
        • ChannelSum.call()
    • EVACPlus
      • EVACPlus
        • EVACPlus.__init__()
        • EVACPlus.fetch_default_weights()
        • EVACPlus.load_model_weights()
        • EVACPlus.predict()
    • logger
      • logger()
    • prepare_img
      • prepare_img()
    • init_model
      • init_model()
    • HistoResDNN
      • HistoResDNN
        • HistoResDNN.__init__()
        • HistoResDNN.fetch_default_weights()
        • HistoResDNN.load_model_weights()
        • HistoResDNN.predict()
    • logger
      • logger()
    • SingleLayerPerceptron
      • SingleLayerPerceptron
        • SingleLayerPerceptron.__init__()
        • SingleLayerPerceptron.evaluate()
        • SingleLayerPerceptron.fit()
        • SingleLayerPerceptron.predict()
        • SingleLayerPerceptron.summary()
    • MultipleLayerPercepton
      • MultipleLayerPercepton
        • MultipleLayerPercepton.__init__()
        • MultipleLayerPercepton.evaluate()
        • MultipleLayerPercepton.fit()
        • MultipleLayerPercepton.predict()
        • MultipleLayerPercepton.summary()
    • EncoderBlock
      • EncoderBlock
        • EncoderBlock.__init__()
        • EncoderBlock.call()
    • DecoderBlock
      • DecoderBlock
        • DecoderBlock.__init__()
        • DecoderBlock.call()
    • Synb0
      • Synb0
        • Synb0.__init__()
        • Synb0.fetch_default_weights()
        • Synb0.load_model_weights()
        • Synb0.predict()
    • logger
      • logger()
    • UNet3D
      • UNet3D()
    • normalize
      • normalize()
    • unnormalize
      • unnormalize()
    • set_logger_level
      • set_logger_level()
    • transform_img
      • transform_img()
    • recover_img
      • recover_img()
    • correct_minor_errors
      • correct_minor_errors()
• reconst
  • Module: reconst.base
  • Module: reconst.cache
  • Module: reconst.cross_validation
  • Module: reconst.csdeconv
  • Module: reconst.cti
  • Module: reconst.dki
  • Module: reconst.dki_micro
  • Module: reconst.dsi
  • Module: reconst.dti
  • Module: reconst.eudx_direction_getter
  • Module: reconst.forecast
  • Module: reconst.fwdti
  • Module: reconst.gqi
  • Module: reconst.ivim
  • Module: reconst.mapmri
  • Module: reconst.mcsd
  • Module: reconst.msdki
  • Module: reconst.multi_voxel
  • Module: reconst.odf
  • Module: reconst.qtdmri
  • Module: reconst.qti
  • Module: reconst.quick_squash
  • Module: reconst.recspeed
  • Module: reconst.rumba
  • Module: reconst.sfm
  • Module: reconst.shm
    • References
  • Module: reconst.shore
  • Module: reconst.utils
  • Module: reconst.vec_val_sum
    • ReconstModel
      • ReconstModel
        • ReconstModel.__init__()
        • ReconstModel.fit()
    • ReconstFit
      • ReconstFit
        • ReconstFit.__init__()
    • Cache
      • Cache
        • Cache.__init__()
        • Cache.cache_clear()
        • Cache.cache_get()
        • Cache.cache_set()
    • coeff_of_determination
      • coeff_of_determination()
    • kfold_xval
      • kfold_xval()
    • AxSymShResponse
      • AxSymShResponse
        • AxSymShResponse.__init__()
        • AxSymShResponse.basis()
        • AxSymShResponse.on_sphere()
    • ConstrainedSphericalDeconvModel
      • ConstrainedSphericalDeconvModel
        • ConstrainedSphericalDeconvModel.__init__()
        • ConstrainedSphericalDeconvModel.fit()
        • ConstrainedSphericalDeconvModel.predict()
    • ConstrainedSDTModel
      • ConstrainedSDTModel
        • ConstrainedSDTModel.__init__()
        • ConstrainedSDTModel.fit()
    • auto_response
      • auto_response()
    • response_from_mask
      • response_from_mask()
    • estimate_response
      • estimate_response()
    • forward_sdt_deconv_mat
      • forward_sdt_deconv_mat()
    • csdeconv
      • csdeconv()
    • odf_deconv
      • odf_deconv()
    • odf_sh_to_sharp
      • odf_sh_to_sharp()
    • mask_for_response_ssst
      • mask_for_response_ssst()
    • response_from_mask_ssst
      • response_from_mask_ssst()
    • auto_response_ssst
      • auto_response_ssst()
    • recursive_response
      • recursive_response()
    • fa_trace_to_lambdas
      • fa_trace_to_lambdas()
    • CorrelationTensorModel
      • CorrelationTensorModel
        • CorrelationTensorModel.__init__()
        • CorrelationTensorModel.fit()
        • CorrelationTensorModel.predict()
    • CorrelationTensorFit
      • CorrelationTensorFit
        • CorrelationTensorFit.__init__()
        • CorrelationTensorFit.K_aniso
        • CorrelationTensorFit.K_iso
        • CorrelationTensorFit.K_micro
        • CorrelationTensorFit.K_total()
        • CorrelationTensorFit.ct
        • CorrelationTensorFit.predict()
    • from_qte_to_cti
      • from_qte_to_cti()
    • multi_gaussian_k_from_c
      • multi_gaussian_k_from_c()
    • split_cti_params
      • split_cti_params()
    • cti_prediction
      • cti_prediction()
    • params_to_cti_params
      • params_to_cti_params()
    • ls_fit_cti
      • ls_fit_cti()
    • DiffusionKurtosisModel
      • DiffusionKurtosisModel
        • DiffusionKurtosisModel.__init__()
        • DiffusionKurtosisModel.fit()
        • DiffusionKurtosisModel.multi_fit()
        • DiffusionKurtosisModel.predict()
    • DiffusionKurtosisFit
      • DiffusionKurtosisFit
        • DiffusionKurtosisFit.__init__()
        • DiffusionKurtosisFit.ak()
        • DiffusionKurtosisFit.akc()
        • DiffusionKurtosisFit.kfa
        • DiffusionKurtosisFit.kmax()
        • DiffusionKurtosisFit.kt
        • DiffusionKurtosisFit.mk()
        • DiffusionKurtosisFit.mkt()
        • DiffusionKurtosisFit.predict()
        • DiffusionKurtosisFit.rk()
    • carlson_rf
      • carlson_rf()
    • carlson_rd
      • carlson_rd()
    • directional_diffusion
      • directional_diffusion()
    • directional_diffusion_variance
      • directional_diffusion_variance()
    • directional_kurtosis
      • directional_kurtosis()
    • apparent_kurtosis_coef
      • apparent_kurtosis_coef()
    • mean_kurtosis
      • mean_kurtosis()
    • radial_kurtosis
      • radial_kurtosis()
    • axial_kurtosis
      • axial_kurtosis()
    • kurtosis_maximum
      • kurtosis_maximum()
    • mean_kurtosis_tensor
      • mean_kurtosis_tensor()
    • kurtosis_fractional_anisotropy
      • kurtosis_fractional_anisotropy()
    • dki_prediction
      • dki_prediction()
    • params_to_dki_params
      • params_to_dki_params()
    • ls_fit_dki
      • ls_fit_dki()
    • cls_fit_dki
      • cls_fit_dki()
    • Wrotate
      • Wrotate()
    • Wrotate_element
      • Wrotate_element()
    • Wcons
      • Wcons()
    • split_dki_param
      • split_dki_param()
    • KurtosisMicrostructureModel
      • KurtosisMicrostructureModel
        • KurtosisMicrostructureModel.__init__()
        • KurtosisMicrostructureModel.fit()
        • KurtosisMicrostructureModel.predict()
    • KurtosisMicrostructuralFit
      • KurtosisMicrostructuralFit
        • KurtosisMicrostructuralFit.__init__()
        • KurtosisMicrostructuralFit.awf
        • KurtosisMicrostructuralFit.axonal_diffusivity
        • KurtosisMicrostructuralFit.hindered_ad
        • KurtosisMicrostructuralFit.hindered_evals
        • KurtosisMicrostructuralFit.hindered_rd
        • KurtosisMicrostructuralFit.predict()
        • KurtosisMicrostructuralFit.restricted_evals
        • KurtosisMicrostructuralFit.tortuosity
    • axonal_water_fraction
      • axonal_water_fraction()
    • diffusion_components
      • diffusion_components()
    • dkimicro_prediction
      • dkimicro_prediction()
    • tortuosity
      • tortuosity()
    • DiffusionSpectrumModel
      • DiffusionSpectrumModel
        • DiffusionSpectrumModel.__init__()
        • DiffusionSpectrumModel.fit()
    • DiffusionSpectrumFit
      • DiffusionSpectrumFit
        • DiffusionSpectrumFit.__init__()
        • DiffusionSpectrumFit.msd_discrete()
        • DiffusionSpectrumFit.odf()
        • DiffusionSpectrumFit.pdf()
        • DiffusionSpectrumFit.rtop_pdf()
        • DiffusionSpectrumFit.rtop_signal()
    • DiffusionSpectrumDeconvModel
      • DiffusionSpectrumDeconvModel
        • DiffusionSpectrumDeconvModel.__init__()
        • DiffusionSpectrumDeconvModel.fit()
    • DiffusionSpectrumDeconvFit
      • DiffusionSpectrumDeconvFit
        • DiffusionSpectrumDeconvFit.__init__()
        • DiffusionSpectrumDeconvFit.pdf()
    • create_qspace
      • create_qspace()
    • create_qtable
      • create_qtable()
    • hanning_filter
      • hanning_filter()
    • pdf_interp_coords
      • pdf_interp_coords()
    • pdf_odf
      • pdf_odf()
    • half_to_full_qspace
      • half_to_full_qspace()
    • project_hemisph_bvecs
      • project_hemisph_bvecs()
    • threshold_propagator
      • threshold_propagator()
    • gen_PSF
      • gen_PSF()
    • LR_deconv
      • LR_deconv()
    • TensorModel
      • TensorModel
        • TensorModel.__init__()
        • TensorModel.fit()
        • TensorModel.predict()
    • TensorFit
      • TensorFit
        • TensorFit.__init__()
        • TensorFit.S0_hat
        • TensorFit.ad()
        • TensorFit.adc()
        • TensorFit.color_fa()
        • TensorFit.directions
        • TensorFit.evals
        • TensorFit.evecs
        • TensorFit.fa()
        • TensorFit.ga()
        • TensorFit.linearity()
        • TensorFit.lower_triangular()
        • TensorFit.md()
        • TensorFit.mode()
        • TensorFit.odf()
        • TensorFit.planarity()
        • TensorFit.predict()
        • TensorFit.quadratic_form
        • TensorFit.rd()
        • TensorFit.shape
        • TensorFit.sphericity()
        • TensorFit.trace()
    • fractional_anisotropy
      • fractional_anisotropy()
    • geodesic_anisotropy
      • geodesic_anisotropy()
    • mean_diffusivity
      • mean_diffusivity()
    • axial_diffusivity
      • axial_diffusivity()
    • radial_diffusivity
      • radial_diffusivity()
    • trace
      • trace()
    • color_fa
      • color_fa()
    • determinant
      • determinant()
    • isotropic
      • isotropic()
    • deviatoric
      • deviatoric()
    • norm
      • norm()
    • mode
      • mode()
    • linearity
      • linearity()
    • planarity
      • planarity()
    • sphericity
      • sphericity()
    • apparent_diffusion_coef
      • apparent_diffusion_coef()
    • tensor_prediction
      • tensor_prediction()
    • iter_fit_tensor
      • iter_fit_tensor()
    • wls_fit_tensor
      • wls_fit_tensor()
    • ols_fit_tensor
      • ols_fit_tensor()
    • nlls_fit_tensor
      • nlls_fit_tensor()
    • restore_fit_tensor
      • restore_fit_tensor()
    • _lt_indices
      • _lt_indices()
    • from_lower_triangular
      • from_lower_triangular()
    • _lt_rows
      • _lt_rows()
    • _lt_cols
      • _lt_cols()
    • lower_triangular
      • lower_triangular()
    • decompose_tensor
      • decompose_tensor()
    • design_matrix
      • design_matrix()
    • quantize_evecs
      • quantize_evecs()
    • eig_from_lo_tri
      • eig_from_lo_tri()
    • EuDXDirectionGetter
      • EuDXDirectionGetter
        • EuDXDirectionGetter.__init__()
        • EuDXDirectionGetter.ang_thr
        • EuDXDirectionGetter.initial_direction()
        • EuDXDirectionGetter.qa_thr
        • EuDXDirectionGetter.total_weight
    • ForecastModel
      • ForecastModel
        • ForecastModel.__init__()
        • ForecastModel.fit()
    • ForecastFit
      • ForecastFit
        • ForecastFit.__init__()
        • ForecastFit.dpar
        • ForecastFit.dperp
        • ForecastFit.fractional_anisotropy()
        • ForecastFit.mean_diffusivity()
        • ForecastFit.odf()
        • ForecastFit.predict()
        • ForecastFit.sh_coeff
    • find_signal_means
      • find_signal_means()
    • forecast_error_func
      • forecast_error_func()
    • psi_l
      • psi_l()
    • forecast_matrix
      • forecast_matrix()
    • rho_matrix
      • rho_matrix()
    • lb_forecast
      • lb_forecast()
    • FreeWaterTensorModel
      • FreeWaterTensorModel
        • FreeWaterTensorModel.__init__()
        • FreeWaterTensorModel.fit()
        • FreeWaterTensorModel.predict()
    • FreeWaterTensorFit
      • FreeWaterTensorFit
        • FreeWaterTensorFit.__init__()
        • FreeWaterTensorFit.f
        • FreeWaterTensorFit.predict()
    • fwdti_prediction
      • fwdti_prediction()
    • wls_iter
      • wls_iter()
    • wls_fit_tensor
      • wls_fit_tensor()
    • nls_iter
      • nls_iter()
    • nls_fit_tensor
      • nls_fit_tensor()
    • lower_triangular_to_cholesky
      • lower_triangular_to_cholesky()
    • cholesky_to_lower_triangular
      • cholesky_to_lower_triangular()
    • GeneralizedQSamplingModel
      • GeneralizedQSamplingModel
        • GeneralizedQSamplingModel.__init__()
        • GeneralizedQSamplingModel.fit()
    • GeneralizedQSamplingFit
      • GeneralizedQSamplingFit
        • GeneralizedQSamplingFit.__init__()
        • GeneralizedQSamplingFit.odf()
    • normalize_qa
      • normalize_qa()
    • squared_radial_component
      • squared_radial_component()
    • npa
      • npa()
    • equatorial_zone_vertices
      • equatorial_zone_vertices()
    • polar_zone_vertices
      • polar_zone_vertices()
    • upper_hemi_map
      • upper_hemi_map()
    • equatorial_maximum
      • equatorial_maximum()
    • patch_vertices
      • patch_vertices()
    • patch_maximum
      • patch_maximum()
    • odf_sum
      • odf_sum()
    • patch_sum
      • patch_sum()
    • triple_odf_maxima
      • triple_odf_maxima()
    • IvimModelTRR
      • IvimModelTRR
        • IvimModelTRR.__init__()
        • IvimModelTRR.estimate_f_D_star()
        • IvimModelTRR.estimate_linear_fit()
        • IvimModelTRR.fit()
        • IvimModelTRR.predict()
    • IvimModelVP
      • IvimModelVP
        • IvimModelVP.__init__()
        • IvimModelVP.cvx_fit()
        • IvimModelVP.fit()
        • IvimModelVP.ivim_mix_cost_one()
        • IvimModelVP.nlls_cost()
        • IvimModelVP.phi()
        • IvimModelVP.stoc_search_cost()
        • IvimModelVP.x_and_f_to_x_f()
        • IvimModelVP.x_f_to_x_and_f()
    • IvimFit
      • IvimFit
        • IvimFit.__init__()
        • IvimFit.D
        • IvimFit.D_star
        • IvimFit.S0_predicted
        • IvimFit.perfusion_fraction
        • IvimFit.predict()
        • IvimFit.shape
    • ivim_prediction
      • ivim_prediction()
    • f_D_star_prediction
      • f_D_star_prediction()
    • f_D_star_error
      • f_D_star_error()
    • ivim_model_selector
      • ivim_model_selector()
    • MapmriModel
      • MapmriModel
        • MapmriModel.__init__()
        • MapmriModel.fit()
    • MapmriFit
      • MapmriFit
        • MapmriFit.__init__()
        • MapmriFit.fitted_signal()
        • MapmriFit.mapmri_R
        • MapmriFit.mapmri_coeff
        • MapmriFit.mapmri_mu
        • MapmriFit.msd()
        • MapmriFit.ng()
        • MapmriFit.ng_parallel()
        • MapmriFit.ng_perpendicular()
        • MapmriFit.norm_of_laplacian_signal()
        • MapmriFit.odf()
        • MapmriFit.odf_sh()
        • MapmriFit.pdf()
        • MapmriFit.predict()
        • MapmriFit.qiv()
        • MapmriFit.rtap()
        • MapmriFit.rtop()
        • MapmriFit.rtpp()
    • isotropic_scale_factor
      • isotropic_scale_factor()
    • mapmri_index_matrix
      • mapmri_index_matrix()
    • b_mat
      • b_mat()
    • b_mat_isotropic
      • b_mat_isotropic()
    • mapmri_phi_1d
      • mapmri_phi_1d()
    • mapmri_phi_matrix
      • mapmri_phi_matrix()
    • mapmri_psi_1d
      • mapmri_psi_1d()
    • mapmri_psi_matrix
      • mapmri_psi_matrix()
    • mapmri_odf_matrix
      • mapmri_odf_matrix()
    • mapmri_isotropic_phi_matrix
      • mapmri_isotropic_phi_matrix()
    • mapmri_isotropic_radial_signal_basis
      • mapmri_isotropic_radial_signal_basis()
    • mapmri_isotropic_M_mu_independent
      • mapmri_isotropic_M_mu_independent()
    • mapmri_isotropic_M_mu_dependent
      • mapmri_isotropic_M_mu_dependent()
    • mapmri_isotropic_psi_matrix
      • mapmri_isotropic_psi_matrix()
    • mapmri_isotropic_radial_pdf_basis
      • mapmri_isotropic_radial_pdf_basis()
    • mapmri_isotropic_K_mu_independent
      • mapmri_isotropic_K_mu_independent()
    • mapmri_isotropic_K_mu_dependent
      • mapmri_isotropic_K_mu_dependent()
    • binomialfloat
      • binomialfloat()
    • mapmri_isotropic_odf_matrix
      • mapmri_isotropic_odf_matrix()
    • mapmri_isotropic_odf_sh_matrix
      • mapmri_isotropic_odf_sh_matrix()
    • mapmri_isotropic_laplacian_reg_matrix
      • mapmri_isotropic_laplacian_reg_matrix()
    • mapmri_isotropic_laplacian_reg_matrix_from_index_matrix
      • mapmri_isotropic_laplacian_reg_matrix_from_index_matrix()
    • mapmri_isotropic_index_matrix
      • mapmri_isotropic_index_matrix()
    • create_rspace
      • create_rspace()
    • delta
      • delta()
    • map_laplace_u
      • map_laplace_u()
    • map_laplace_t
      • map_laplace_t()
    • map_laplace_s
      • map_laplace_s()
    • mapmri_STU_reg_matrices
      • mapmri_STU_reg_matrices()
    • mapmri_laplacian_reg_matrix
      • mapmri_laplacian_reg_matrix()
    • generalized_crossvalidation_array
      • generalized_crossvalidation_array()
    • generalized_crossvalidation
      • generalized_crossvalidation()
    • gcv_cost_function
      • gcv_cost_function()
    • MultiShellResponse
      • MultiShellResponse
        • MultiShellResponse.__init__()
        • MultiShellResponse.iso
    • MultiShellDeconvModel
      • MultiShellDeconvModel
        • MultiShellDeconvModel.__init__()
        • MultiShellDeconvModel.fit()
        • MultiShellDeconvModel.predict()
    • MSDeconvFit
      • MSDeconvFit
        • MSDeconvFit.__init__()
        • MSDeconvFit.all_shm_coeff
        • MSDeconvFit.shm_coeff
        • MSDeconvFit.volume_fractions
    • QpFitter
      • QpFitter
        • QpFitter.__init__()
    • multi_tissue_basis
      • multi_tissue_basis()
    • solve_qp
      • solve_qp()
    • multi_shell_fiber_response
      • multi_shell_fiber_response()
    • mask_for_response_msmt
      • mask_for_response_msmt()
    • response_from_mask_msmt
      • response_from_mask_msmt()
    • auto_response_msmt
      • auto_response_msmt()
    • MeanDiffusionKurtosisModel
      • MeanDiffusionKurtosisModel
        • MeanDiffusionKurtosisModel.__init__()
        • MeanDiffusionKurtosisModel.fit()
        • MeanDiffusionKurtosisModel.predict()
    • MeanDiffusionKurtosisFit
      • MeanDiffusionKurtosisFit
        • MeanDiffusionKurtosisFit.__init__()
        • MeanDiffusionKurtosisFit.S0_hat
        • MeanDiffusionKurtosisFit.msd()
        • MeanDiffusionKurtosisFit.msk()
        • MeanDiffusionKurtosisFit.predict()
        • MeanDiffusionKurtosisFit.smt2di()
        • MeanDiffusionKurtosisFit.smt2f()
        • MeanDiffusionKurtosisFit.smt2uFA()
    • mean_signal_bvalue
      • mean_signal_bvalue()
    • msk_from_awf
      • msk_from_awf()
    • awf_from_msk
      • awf_from_msk()
    • msdki_prediction
      • msdki_prediction()
    • wls_fit_msdki
      • wls_fit_msdki()
    • design_matrix
      • design_matrix()
    • MultiVoxelFit
      • MultiVoxelFit
        • MultiVoxelFit.__init__()
        • MultiVoxelFit.predict()
        • MultiVoxelFit.shape
    • CallableArray
      • CallableArray
        • CallableArray.__init__()
    • multi_voxel_fit
      • multi_voxel_fit()
    • OdfModel
      • OdfModel
        • OdfModel.__init__()
        • OdfModel.fit()
    • OdfFit
      • OdfFit
        • OdfFit.__init__()
        • OdfFit.odf()
    • gfa
      • gfa()
    • minmax_normalize
      • minmax_normalize()
    • QtdmriModel
      • QtdmriModel
        • QtdmriModel.__init__()
        • QtdmriModel.fit()
    • QtdmriFit
      • QtdmriFit
        • QtdmriFit.__init__()
        • QtdmriFit.fitted_signal()
        • QtdmriFit.msd()
        • QtdmriFit.norm_of_laplacian_signal()
        • QtdmriFit.odf()
        • QtdmriFit.odf_sh()
        • QtdmriFit.pdf()
        • QtdmriFit.predict()
        • QtdmriFit.qiv()
        • QtdmriFit.qtdmri_to_mapmri_coef()
        • QtdmriFit.rtap()
        • QtdmriFit.rtop()
        • QtdmriFit.rtpp()
        • QtdmriFit.sparsity_abs()
        • QtdmriFit.sparsity_density()
    • qtdmri_to_mapmri_matrix
      • qtdmri_to_mapmri_matrix()
    • qtdmri_isotropic_to_mapmri_matrix
      • qtdmri_isotropic_to_mapmri_matrix()
    • qtdmri_temporal_normalization
      • qtdmri_temporal_normalization()
    • qtdmri_mapmri_normalization
      • qtdmri_mapmri_normalization()
    • qtdmri_mapmri_isotropic_normalization
      • qtdmri_mapmri_isotropic_normalization()
    • qtdmri_signal_matrix_
      • qtdmri_signal_matrix_()
    • qtdmri_signal_matrix
      • qtdmri_signal_matrix()
    • qtdmri_eap_matrix
      • qtdmri_eap_matrix()
    • qtdmri_isotropic_signal_matrix_
      • qtdmri_isotropic_signal_matrix_()
    • qtdmri_isotropic_signal_matrix
      • qtdmri_isotropic_signal_matrix()
    • qtdmri_eap_matrix_
      • qtdmri_eap_matrix_()
    • qtdmri_isotropic_eap_matrix_
      • qtdmri_isotropic_eap_matrix_()
    • qtdmri_isotropic_eap_matrix
      • qtdmri_isotropic_eap_matrix()
    • radial_basis_opt
      • radial_basis_opt()
    • angular_basis_opt
      • angular_basis_opt()
    • radial_basis_EAP_opt
      • radial_basis_EAP_opt()
    • angular_basis_EAP_opt
      • angular_basis_EAP_opt()
    • temporal_basis
      • temporal_basis()
    • qtdmri_index_matrix
      • qtdmri_index_matrix()
    • qtdmri_isotropic_index_matrix
      • qtdmri_isotropic_index_matrix()
    • qtdmri_laplacian_reg_matrix
      • qtdmri_laplacian_reg_matrix()
    • qtdmri_isotropic_laplacian_reg_matrix
      • qtdmri_isotropic_laplacian_reg_matrix()
    • part23_reg_matrix_q
      • part23_reg_matrix_q()
    • part23_iso_reg_matrix_q
      • part23_iso_reg_matrix_q()
    • part4_reg_matrix_q
      • part4_reg_matrix_q()
    • part4_iso_reg_matrix_q
      • part4_iso_reg_matrix_q()
    • part1_reg_matrix_tau
      • part1_reg_matrix_tau()
    • part23_reg_matrix_tau
      • part23_reg_matrix_tau()
    • part4_reg_matrix_tau
      • part4_reg_matrix_tau()
    • H
      • H()
    • generalized_crossvalidation
      • generalized_crossvalidation()
    • GCV_cost_function
      • GCV_cost_function()
    • qtdmri_isotropic_scaling
      • qtdmri_isotropic_scaling()
    • qtdmri_anisotropic_scaling
      • qtdmri_anisotropic_scaling()
    • design_matrix_spatial
      • design_matrix_spatial()
    • create_rt_space_grid
      • create_rt_space_grid()
    • qtdmri_number_of_coefficients
      • qtdmri_number_of_coefficients()
    • l1_crossvalidation
      • l1_crossvalidation()
    • elastic_crossvalidation
      • elastic_crossvalidation()
    • visualise_gradient_table_G_Delta_rainbow
      • visualise_gradient_table_G_Delta_rainbow()
    • QtiModel
      • QtiModel
        • QtiModel.__init__()
        • QtiModel.fit()
        • QtiModel.predict()
    • QtiFit
      • QtiFit
        • QtiFit.__init__()
        • QtiFit.S0_hat()
        • QtiFit.c_c()
        • QtiFit.c_m()
        • QtiFit.c_md()
        • QtiFit.c_mu()
        • QtiFit.d_sq()
        • QtiFit.fa()
        • QtiFit.k_bulk()
        • QtiFit.k_mu()
        • QtiFit.k_shear()
        • QtiFit.md()
        • QtiFit.mean_d_sq()
        • QtiFit.mk()
        • QtiFit.predict()
        • QtiFit.ufa()
        • QtiFit.v_iso()
        • QtiFit.v_md()
        • QtiFit.v_shear()
    • from_3x3_to_6x1
      • from_3x3_to_6x1()
    • from_6x1_to_3x3
      • from_6x1_to_3x3()
    • from_6x6_to_21x1
      • from_6x6_to_21x1()
    • from_21x1_to_6x6
      • from_21x1_to_6x6()
    • cvxpy_1x6_to_3x3
      • cvxpy_1x6_to_3x3()
    • cvxpy_1x21_to_6x6
      • cvxpy_1x21_to_6x6()
    • dtd_covariance
      • dtd_covariance()
    • qti_signal
      • qti_signal()
    • design_matrix
      • design_matrix()
    • quick_squash
      • quick_squash()
    • reduce
      • reduce()
    • adj_to_countarrs
      • adj_to_countarrs()
    • argmax_from_adj
      • argmax_from_adj()
    • argmax_from_countarrs
      • argmax_from_countarrs()
    • le_to_odf
      • le_to_odf()
    • local_maxima
      • local_maxima()
    • proc_reco_args
      • proc_reco_args()
    • remove_similar_vertices
      • remove_similar_vertices()
    • search_descending
      • search_descending()
    • sum_on_blocks_1d
      • sum_on_blocks_1d()
    • RumbaSDModel
      • RumbaSDModel
        • RumbaSDModel.__init__()
    • RumbaFit
      • RumbaFit
        • RumbaFit.__init__()
        • RumbaFit.combined_odf_iso()
        • RumbaFit.f_csf()
        • RumbaFit.f_gm()
        • RumbaFit.f_iso()
        • RumbaFit.f_wm()
        • RumbaFit.odf()
        • RumbaFit.predict()
    • logger
      • logger()
    • rumba_deconv
      • rumba_deconv()
    • mbessel_ratio
      • mbessel_ratio()
    • generate_kernel
      • generate_kernel()
    • rumba_deconv_global
      • rumba_deconv_global()
    • IsotropicModel
      • IsotropicModel
        • IsotropicModel.__init__()
        • IsotropicModel.fit()
    • IsotropicFit
      • IsotropicFit
        • IsotropicFit.__init__()
        • IsotropicFit.predict()
    • ExponentialIsotropicModel
      • ExponentialIsotropicModel
        • ExponentialIsotropicModel.__init__()
        • ExponentialIsotropicModel.fit()
    • ExponentialIsotropicFit
      • ExponentialIsotropicFit
        • ExponentialIsotropicFit.__init__()
        • ExponentialIsotropicFit.predict()
    • SparseFascicleModel
      • SparseFascicleModel
        • SparseFascicleModel.__init__()
        • SparseFascicleModel.design_matrix()
        • SparseFascicleModel.fit()
    • SparseFascicleFit
      • SparseFascicleFit
        • SparseFascicleFit.__init__()
        • SparseFascicleFit.odf()
        • SparseFascicleFit.predict()
    • sfm_design_matrix
      • sfm_design_matrix()
    • SphHarmModel
      • SphHarmModel
        • SphHarmModel.__init__()
        • SphHarmModel.sampling_matrix()
    • QballBaseModel
      • QballBaseModel
        • QballBaseModel.__init__()
        • QballBaseModel.fit()
    • SphHarmFit
      • SphHarmFit
        • SphHarmFit.__init__()
        • SphHarmFit.gfa()
        • SphHarmFit.odf()
        • SphHarmFit.predict()
        • SphHarmFit.shape
        • SphHarmFit.shm_coeff
    • CsaOdfModel
      • CsaOdfModel
        • CsaOdfModel.__init__()
        • CsaOdfModel.max
        • CsaOdfModel.min
    • OpdtModel
      • OpdtModel
        • OpdtModel.__init__()
    • QballModel
      • QballModel
        • QballModel.__init__()
    • ResidualBootstrapWrapper
      • ResidualBootstrapWrapper
        • ResidualBootstrapWrapper.__init__()
    • forward_sdeconv_mat
      • forward_sdeconv_mat()
    • sh_to_rh
      • sh_to_rh()
    • gen_dirac
      • gen_dirac()
    • spherical_harmonics
      • spherical_harmonics()
    • real_sph_harm
      • real_sph_harm()
    • real_sh_tournier_from_index
      • real_sh_tournier_from_index()
    • real_sh_descoteaux_from_index
      • real_sh_descoteaux_from_index()
    • real_sh_tournier
      • real_sh_tournier()
    • real_sh_descoteaux
      • real_sh_descoteaux()
    • real_sym_sh_mrtrix
      • real_sym_sh_mrtrix()
    • real_sym_sh_basis
      • real_sym_sh_basis()
    • sph_harm_ind_list
      • sph_harm_ind_list()
    • order_from_ncoef
      • order_from_ncoef()
    • smooth_pinv
      • smooth_pinv()
    • lazy_index
      • lazy_index()
    • normalize_data
      • normalize_data()
    • hat
      • hat()
    • lcr_matrix
      • lcr_matrix()
    • bootstrap_data_array
      • bootstrap_data_array()
    • bootstrap_data_voxel
      • bootstrap_data_voxel()
    • sf_to_sh
      • sf_to_sh()
    • sh_to_sf
      • sh_to_sf()
    • sh_to_sf_matrix
      • sh_to_sf_matrix()
    • calculate_max_order
      • calculate_max_order()
    • anisotropic_power
      • anisotropic_power()
    • convert_sh_to_full_basis
      • convert_sh_to_full_basis()
    • convert_sh_from_legacy
      • convert_sh_from_legacy()
    • convert_sh_to_legacy
      • convert_sh_to_legacy()
    • convert_sh_descoteaux_tournier
      • convert_sh_descoteaux_tournier()
    • ShoreModel
      • ShoreModel
        • ShoreModel.__init__()
        • ShoreModel.fit()
    • ShoreFit
      • ShoreFit
        • ShoreFit.__init__()
        • ShoreFit.fitted_signal()
        • ShoreFit.msd()
        • ShoreFit.odf()
        • ShoreFit.odf_sh()
        • ShoreFit.pdf()
        • ShoreFit.pdf_grid()
        • ShoreFit.rtop_pdf()
        • ShoreFit.rtop_signal()
        • ShoreFit.shore_coeff
    • shore_matrix
      • shore_matrix()
    • shore_matrix_pdf
      • shore_matrix_pdf()
    • shore_matrix_odf
      • shore_matrix_odf()
    • l_shore
      • l_shore()
    • n_shore
      • n_shore()
    • create_rspace
      • create_rspace()
    • shore_indices
      • shore_indices()
    • shore_order
      • shore_order()
    • dki_design_matrix
      • dki_design_matrix()
    • cti_design_matrix
      • cti_design_matrix()
    • convert_tensors
      • convert_tensors()
    • vec_val_vect
      • vec_val_vect()
• segment
  • Module: segment.bundles
  • Module: segment.clustering
  • Module: segment.clustering_algorithms
  • Module: segment.clusteringspeed
  • Module: segment.cythonutils
  • Module: segment.featurespeed
  • Module: segment.fss
  • Module: segment.mask
  • Module: segment.metric
  • Module: segment.metricspeed
  • Module: segment.mrf
  • Module: segment.threshold
  • Module: segment.tissue
    • RecoBundles
      • RecoBundles
        • RecoBundles.__init__()
        • RecoBundles.evaluate_results()
        • RecoBundles.recognize()
        • RecoBundles.refine()
    • check_range
      • check_range()
    • logger
      • logger()
    • bundle_adjacency
      • bundle_adjacency()
    • ba_analysis
      • ba_analysis()
    • cluster_bundle
      • cluster_bundle()
    • bundle_shape_similarity
      • bundle_shape_similarity()
    • Identity
      • Identity
        • Identity.__init__()
    • Cluster
      • Cluster
        • Cluster.__init__()
        • Cluster.assign()
    • ClusterCentroid
      • ClusterCentroid
        • ClusterCentroid.__init__()
        • ClusterCentroid.assign()
        • ClusterCentroid.update()
    • ClusterMap
      • ClusterMap
        • ClusterMap.__init__()
        • ClusterMap.add_cluster()
        • ClusterMap.clear()
        • ClusterMap.clusters
        • ClusterMap.clusters_sizes()
        • ClusterMap.get_large_clusters()
        • ClusterMap.get_small_clusters()
        • ClusterMap.refdata
        • ClusterMap.remove_cluster()
        • ClusterMap.size()
    • ClusterMapCentroid
      • ClusterMapCentroid
        • ClusterMapCentroid.__init__()
        • ClusterMapCentroid.centroids
    • Clustering
      • Clustering
        • Clustering.__init__()
        • Clustering.cluster()
    • QuickBundles
      • QuickBundles
        • QuickBundles.__init__()
        • QuickBundles.cluster()
    • QuickBundlesX
      • QuickBundlesX
        • QuickBundlesX.__init__()
        • QuickBundlesX.cluster()
    • TreeCluster
      • TreeCluster
        • TreeCluster.__init__()
        • TreeCluster.add()
        • TreeCluster.is_leaf
        • TreeCluster.return_indices()
    • TreeClusterMap
      • TreeClusterMap
        • TreeClusterMap.__init__()
        • TreeClusterMap.get_clusters()
        • TreeClusterMap.iter_preorder()
        • TreeClusterMap.refdata
        • TreeClusterMap.traverse_postorder()
    • logger
      • logger()
    • qbx_and_merge
      • qbx_and_merge()
    • ClusterCentroid
      • ClusterCentroid
        • ClusterCentroid.__init__()
        • ClusterCentroid.assign()
        • ClusterCentroid.update()
    • ClusterMapCentroid
      • ClusterMapCentroid
        • ClusterMapCentroid.__init__()
        • ClusterMapCentroid.centroids
    • DTYPE
      • DTYPE
    • clusters_centroid2clustermap_centroid
      • clusters_centroid2clustermap_centroid()
    • peek
      • peek()
    • quickbundles
      • quickbundles()
    • quickbundlesx
      • quickbundlesx()
    • ClusterCentroid
      • ClusterCentroid
        • ClusterCentroid.__init__()
        • ClusterCentroid.assign()
        • ClusterCentroid.update()
    • ClusterMapCentroid
      • ClusterMapCentroid
        • ClusterMapCentroid.__init__()
        • ClusterMapCentroid.centroids
    • Clusters
      • Clusters
        • Clusters.__init__()
    • ClustersCentroid
      • ClustersCentroid
        • ClustersCentroid.__init__()
    • DTYPE
      • DTYPE
    • QuickBundles
      • QuickBundles
        • QuickBundles.__init__()
        • QuickBundles.get_cluster_map()
        • QuickBundles.get_stats()
    • QuickBundlesX
      • QuickBundlesX
        • QuickBundlesX.__init__()
        • QuickBundlesX.get_stats()
        • QuickBundlesX.get_tree_cluster_map()
        • QuickBundlesX.insert()
    • TreeCluster
      • TreeCluster
        • TreeCluster.__init__()
        • TreeCluster.add()
        • TreeCluster.is_leaf
        • TreeCluster.return_indices()
    • TreeClusterMap
      • TreeClusterMap
        • TreeClusterMap.__init__()
        • TreeClusterMap.get_clusters()
        • TreeClusterMap.iter_preorder()
        • TreeClusterMap.refdata
        • TreeClusterMap.traverse_postorder()
    • evaluate_aabb_checks
      • evaluate_aabb_checks()
    • ArcLengthFeature
      • ArcLengthFeature
        • ArcLengthFeature.__init__()
    • CenterOfMassFeature
      • CenterOfMassFeature
        • CenterOfMassFeature.__init__()
    • CythonFeature
      • CythonFeature
        • CythonFeature.__init__()
        • CythonFeature.extract()
        • CythonFeature.infer_shape()
    • Feature
      • Feature
        • Feature.__init__()
        • Feature.extract()
        • Feature.infer_shape()
        • Feature.is_order_invariant
    • IdentityFeature
      • IdentityFeature
        • IdentityFeature.__init__()
    • MidpointFeature
      • MidpointFeature
        • MidpointFeature.__init__()
    • ResampleFeature
      • ResampleFeature
        • ResampleFeature.__init__()
    • VectorOfEndpointsFeature
      • VectorOfEndpointsFeature
        • VectorOfEndpointsFeature.__init__()
    • extract
      • extract()
    • infer_shape
      • infer_shape()
    • FastStreamlineSearch
      • FastStreamlineSearch
        • FastStreamlineSearch.__init__()
        • FastStreamlineSearch.radius_search()
    • nearest_from_matrix_row
      • nearest_from_matrix_row()
    • nearest_from_matrix_col
      • nearest_from_matrix_col()
    • multi_median
      • multi_median()
    • applymask
      • applymask()
    • bounding_box
      • bounding_box()
    • crop
      • crop()
    • median_otsu
      • median_otsu()
    • segment_from_cfa
      • segment_from_cfa()
    • clean_cc_mask
      • clean_cc_mask()
    • mdf
      • mdf()
    • mean_manhattan_distance
      • mean_manhattan_distance()
    • mean_euclidean_distance
      • mean_euclidean_distance()
    • AveragePointwiseEuclideanMetric
      • AveragePointwiseEuclideanMetric
        • AveragePointwiseEuclideanMetric.__init__()
    • CosineMetric
      • CosineMetric
        • CosineMetric.__init__()
    • CythonMetric
      • CythonMetric
        • CythonMetric.__init__()
        • CythonMetric.are_compatible()
        • CythonMetric.dist()
    • Metric
      • Metric
        • Metric.__init__()
        • Metric.are_compatible()
        • Metric.dist()
        • Metric.feature
        • Metric.is_order_invariant
    • MinimumAverageDirectFlipMetric
      • MinimumAverageDirectFlipMetric
        • MinimumAverageDirectFlipMetric.__init__()
        • MinimumAverageDirectFlipMetric.is_order_invariant
    • SumPointwiseEuclideanMetric
      • SumPointwiseEuclideanMetric
        • SumPointwiseEuclideanMetric.__init__()
    • dist
      • dist()
    • distance_matrix
      • distance_matrix()
    • ConstantObservationModel
      • ConstantObservationModel
        • ConstantObservationModel.__init__()
        • ConstantObservationModel.initialize_param_uniform()
        • ConstantObservationModel.negloglikelihood()
        • ConstantObservationModel.prob_image()
        • ConstantObservationModel.seg_stats()
        • ConstantObservationModel.update_param()
    • IteratedConditionalModes
      • IteratedConditionalModes
        • IteratedConditionalModes.__init__()
        • IteratedConditionalModes.icm_ising()
        • IteratedConditionalModes.initialize_maximum_likelihood()
        • IteratedConditionalModes.prob_neighborhood()
    • otsu
      • otsu()
    • upper_bound_by_rate
      • upper_bound_by_rate()
    • upper_bound_by_percent
      • upper_bound_by_percent()
    • TissueClassifierHMRF
      • TissueClassifierHMRF
        • TissueClassifierHMRF.__init__()
        • TissueClassifierHMRF.classify()
• sims
  • Module: sims.phantom
  • Module: sims.voxel
    • add_noise
      • add_noise()
    • diff2eigenvectors
      • diff2eigenvectors()
    • orbital_phantom
      • orbital_phantom()
    • diffusion_evals
      • diffusion_evals()
    • add_noise
      • add_noise()
    • sticks_and_ball
      • sticks_and_ball()
    • callaghan_perpendicular
      • callaghan_perpendicular()
    • gaussian_parallel
      • gaussian_parallel()
    • cylinders_and_ball_soderman
      • cylinders_and_ball_soderman()
    • single_tensor
      • single_tensor()
    • multi_tensor
      • multi_tensor()
    • multi_tensor_dki
      • multi_tensor_dki()
    • kurtosis_element
      • kurtosis_element()
    • dki_signal
      • dki_signal()
    • single_tensor_odf
      • single_tensor_odf()
    • all_tensor_evecs
      • all_tensor_evecs()
    • multi_tensor_odf
      • multi_tensor_odf()
    • single_tensor_rtop
      • single_tensor_rtop()
    • multi_tensor_rtop
      • multi_tensor_rtop()
    • single_tensor_pdf
      • single_tensor_pdf()
    • multi_tensor_pdf
      • multi_tensor_pdf()
    • single_tensor_msd
      • single_tensor_msd()
    • multi_tensor_msd
      • multi_tensor_msd()
• stats
  • Module: stats.analysis
    • peak_values
      • peak_values()
    • anatomical_measures
      • anatomical_measures()
    • assignment_map
      • assignment_map()
    • gaussian_weights
      • gaussian_weights()
    • afq_profile
      • afq_profile()
• tracking
  • Module: tracking._utils
  • Module: tracking.direction_getter
  • Module: tracking.distances
  • Module: tracking.fbcmeasures
  • Module: tracking.learning
  • Module: tracking.life
  • Module: tracking.local_tracking
  • Module: tracking.localtrack
  • Module: tracking.mesh
  • Module: tracking.metrics
  • Module: tracking.propspeed
  • Module: tracking.stopping_criterion
  • Module: tracking.streamline
  • Module: tracking.streamlinespeed
  • Module: tracking.utils
    • Important Notes
  • Module: tracking.vox2track
    • DirectionGetter
      • DirectionGetter
        • DirectionGetter.__init__()
        • DirectionGetter.generate_streamline()
        • DirectionGetter.get_direction()
        • DirectionGetter.initial_direction()
    • add_3vecs
      • add_3vecs()
    • approx_polygon_track
      • approx_polygon_track()
    • approximate_mdl_trajectory
      • approximate_mdl_trajectory()
    • bundles_distances_mam
      • bundles_distances_mam()
    • bundles_distances_mdf
      • bundles_distances_mdf()
    • cut_plane
      • cut_plane()
    • inner_3vecs
      • inner_3vecs()
    • intersect_segment_cylinder
      • intersect_segment_cylinder()
    • larch_3merge
      • larch_3merge()
    • larch_3split
      • larch_3split()
    • lee_angle_distance
      • lee_angle_distance()
    • lee_perpendicular_distance
      • lee_perpendicular_distance()
    • local_skeleton_clustering
      • local_skeleton_clustering()
    • local_skeleton_clustering_3pts
      • local_skeleton_clustering_3pts()
    • mam_distances
      • mam_distances()
    • minimum_closest_distance
      • minimum_closest_distance()
    • most_similar_track_mam
      • most_similar_track_mam()
    • mul_3vec
      • mul_3vec()
    • mul_3vecs
      • mul_3vecs()
    • norm_3vec
      • norm_3vec()
    • normalized_3vec
      • normalized_3vec()
    • point_segment_sq_distance
      • point_segment_sq_distance()
    • point_track_sq_distance_check
      • point_track_sq_distance_check()
    • sub_3vecs
      • sub_3vecs()
    • track_dist_3pts
      • track_dist_3pts()
    • track_roi_intersection_check
      • track_roi_intersection_check()
    • warn
      • warn()
    • FBCMeasures
      • FBCMeasures
        • FBCMeasures.__init__()
        • FBCMeasures.get_points_rfbc_thresholded()
    • KDTree
      • KDTree
        • KDTree.__init__()
        • KDTree.count_neighbors()
        • KDTree.innernode
          • KDTree.innernode.children
          • KDTree.innernode.split
          • KDTree.innernode.split_dim
        • KDTree.leafnode
          • KDTree.leafnode.children
          • KDTree.leafnode.idx
        • KDTree.node
        • KDTree.query()
        • KDTree.query_ball_point()
        • KDTree.query_ball_tree()
        • KDTree.query_pairs()
        • KDTree.sparse_distance_matrix()
        • KDTree.tree
    • interp1d
      • interp1d
        • interp1d.__init__()
        • interp1d.dtype
        • interp1d.fill_value
    • compute_rfbc
      • compute_rfbc()
    • determine_num_threads
      • determine_num_threads()
    • min_moving_average
      • min_moving_average()
    • detect_corresponding_tracks
      • detect_corresponding_tracks()
    • detect_corresponding_tracks_plus
      • detect_corresponding_tracks_plus()
    • LifeSignalMaker
      • LifeSignalMaker
        • LifeSignalMaker.__init__()
        • LifeSignalMaker.calc_signal()
        • LifeSignalMaker.streamline_signal()
    • FiberModel
      • FiberModel
        • FiberModel.__init__()
        • FiberModel.fit()
        • FiberModel.setup()
    • FiberFit
      • FiberFit
        • FiberFit.__init__()
        • FiberFit.predict()
    • gradient
      • gradient()
    • streamline_gradients
      • streamline_gradients()
    • grad_tensor
      • grad_tensor()
    • streamline_tensors
      • streamline_tensors()
    • streamline_signal
      • streamline_signal()
    • voxel2streamline
      • voxel2streamline()
    • LocalTracking
      • LocalTracking
        • LocalTracking.__init__()
    • ParticleFilteringTracking
      • ParticleFilteringTracking
        • ParticleFilteringTracking.__init__()
    • local_tracker
      • local_tracker()
    • pft_tracker
      • pft_tracker()
    • random
      • random()
    • random_coordinates_from_surface
      • random_coordinates_from_surface()
    • seeds_from_surface_coordinates
      • seeds_from_surface_coordinates()
    • triangles_area
      • triangles_area()
    • vertices_to_triangles_values
      • vertices_to_triangles_values()
    • winding
      • winding()
    • length
      • length()
    • bytes
      • bytes()
    • midpoint
      • midpoint()
    • downsample
      • downsample()
    • center_of_mass
      • center_of_mass()
    • magn
      • magn()
    • frenet_serret
      • frenet_serret()
    • mean_curvature
      • mean_curvature()
    • mean_orientation
      • mean_orientation()
    • generate_combinations
      • generate_combinations()
    • longest_track_bundle
      • longest_track_bundle()
    • intersect_sphere
      • intersect_sphere()
    • inside_sphere
      • inside_sphere()
    • inside_sphere_points
      • inside_sphere_points()
    • spline
      • spline()
    • startpoint
      • startpoint()
    • endpoint
      • endpoint()
    • arbitrarypoint
      • arbitrarypoint()
    • principal_components
      • principal_components()
    • midpoint2point
      • midpoint2point()
    • eudx_both_directions
      • eudx_both_directions()
    • ndarray_offset
      • ndarray_offset()
    • ActStoppingCriterion
      • ActStoppingCriterion
        • ActStoppingCriterion.__init__()
    • AnatomicalStoppingCriterion
      • AnatomicalStoppingCriterion
        • AnatomicalStoppingCriterion.__init__()
        • AnatomicalStoppingCriterion.from_pve()
        • AnatomicalStoppingCriterion.get_exclude()
        • AnatomicalStoppingCriterion.get_include()
    • BinaryStoppingCriterion
      • BinaryStoppingCriterion
        • BinaryStoppingCriterion.__init__()
    • CmcStoppingCriterion
      • CmcStoppingCriterion
        • CmcStoppingCriterion.__init__()
    • StoppingCriterion
      • StoppingCriterion
        • StoppingCriterion.__init__()
        • StoppingCriterion.check_point()
    • StreamlineStatus
      • StreamlineStatus
        • StreamlineStatus.__init__()
        • StreamlineStatus.ENDPOINT
        • StreamlineStatus.INVALIDPOINT
        • StreamlineStatus.OUTSIDEIMAGE
        • StreamlineStatus.PYERROR
        • StreamlineStatus.TRACKPOINT
    • ThresholdStoppingCriterion
      • ThresholdStoppingCriterion
        • ThresholdStoppingCriterion.__init__()
    • unlist_streamlines
      • unlist_streamlines()
    • relist_streamlines
      • relist_streamlines()
    • center_streamlines
      • center_streamlines()
    • deform_streamlines
      • deform_streamlines()
    • transform_streamlines
      • transform_streamlines()
    • select_random_set_of_streamlines
      • select_random_set_of_streamlines()
    • select_by_rois
      • select_by_rois()
    • cluster_confidence
      • cluster_confidence()
    • orient_by_rois
      • orient_by_rois()
    • orient_by_streamline
      • orient_by_streamline()
    • values_from_volume
      • values_from_volume()
    • nbytes
      • nbytes()
    • Streamlines
      • Streamlines
    • compress_streamlines
      • compress_streamlines()
    • length
      • length()
    • set_number_of_points
      • set_number_of_points()
    • density_map
      • density_map()
    • connectivity_matrix
      • connectivity_matrix()
    • ndbincount
      • ndbincount()
    • reduce_labels
      • reduce_labels()
    • subsegment
      • subsegment()
    • seeds_from_mask
      • seeds_from_mask()
    • random_seeds_from_mask
      • random_seeds_from_mask()
    • target
      • target()
    • target_line_based
      • target_line_based()
    • streamline_near_roi
      • streamline_near_roi()
    • near_roi
      • near_roi()
    • length
      • length()
    • unique_rows
      • unique_rows()
    • transform_tracking_output
      • transform_tracking_output()
    • reduce_rois
      • reduce_rois()
    • path_length
      • path_length()
    • max_angle_from_curvature
      • max_angle_from_curvature()
    • min_radius_curvature_from_angle
      • min_radius_curvature_from_angle()
    • streamline_mapping
      • streamline_mapping()
    • track_counts
      • track_counts()
• viz
  • Module: viz.gmem
  • Module: viz.horizon
  • Module: viz.horizon.app
  • Module: viz.horizon.tab
  • Module: viz.horizon.tab.base
  • Module: viz.horizon.tab.cluster
  • Module: viz.horizon.tab.peak
  • Module: viz.horizon.tab.roi
  • Module: viz.horizon.tab.slice
  • Module: viz.horizon.tab.surface
  • Module: viz.horizon.util
  • Module: viz.horizon.visualizer
  • Module: viz.horizon.visualizer.cluster
  • Module: viz.horizon.visualizer.peak
  • Module: viz.horizon.visualizer.slice
  • Module: viz.horizon.visualizer.surface
  • Module: viz.panel
  • Module: viz.plotting
  • Module: viz.projections
  • Module: viz.regtools
  • Module: viz.streamline
    • GlobalHorizon
      • GlobalHorizon
        • GlobalHorizon.__init__()
    • Horizon
      • Horizon
        • Horizon.__init__()
        • Horizon.build_scene()
        • Horizon.build_show()
    • horizon
      • horizon()
    • HorizonUIElement
      • HorizonUIElement
        • HorizonUIElement.__init__()
        • HorizonUIElement.obj
        • HorizonUIElement.position
        • HorizonUIElement.selected_value
        • HorizonUIElement.size
        • HorizonUIElement.visibility
    • HorizonTab
      • HorizonTab
        • HorizonTab.__init__()
        • HorizonTab.build()
        • HorizonTab.elements
        • HorizonTab.name
        • HorizonTab.on_tab_selected()
        • HorizonTab.register_elements()
    • TabManager
      • TabManager
        • TabManager.__init__()
        • TabManager.handle_text_overflows()
        • TabManager.reposition()
        • TabManager.synchronize_slices()
        • TabManager.synchronize_volumes()
        • TabManager.tab_ui
    • build_label
      • build_label()
    • build_slider
      • build_slider()
    • build_checkbox
      • build_checkbox()
    • build_switcher
      • build_switcher()
    • color_single_slider
      • color_single_slider()
    • color_double_slider
      • color_double_slider()
    • ClustersTab
      • ClustersTab
        • ClustersTab.__init__()
        • ClustersTab.build()
        • ClustersTab.name
    • PeaksTab
      • PeaksTab
        • PeaksTab.__init__()
        • PeaksTab.actors
        • PeaksTab.build()
        • PeaksTab.name
        • PeaksTab.on_tab_selected()
        • PeaksTab.tab_id
        • PeaksTab.update_slices()
    • ROIsTab
      • ROIsTab
        • ROIsTab.__init__()
        • ROIsTab.build()
        • ROIsTab.name
    • SlicesTab
      • SlicesTab
        • SlicesTab.__init__()
        • SlicesTab.actors
        • SlicesTab.build()
        • SlicesTab.file_name
        • SlicesTab.name
        • SlicesTab.on_tab_selected()
        • SlicesTab.tab_id
        • SlicesTab.update_slices()
        • SlicesTab.update_volume()
    • SurfaceTab
      • SurfaceTab
        • SurfaceTab.__init__()
        • SurfaceTab.actors
        • SurfaceTab.build()
        • SurfaceTab.name
        • SurfaceTab.tab_id
    • check_img_shapes
      • check_img_shapes()
    • check_img_dtype
      • check_img_dtype()
    • show_ellipsis
      • show_ellipsis()
    • unpack_image
      • unpack_image()
    • unpack_surface
      • unpack_surface()
    • is_binary_image
      • is_binary_image()
    • check_peak_size
      • check_peak_size()
    • ClustersVisualizer
      • ClustersVisualizer
        • ClustersVisualizer.__init__()
        • ClustersVisualizer.add_cluster_actors()
        • ClustersVisualizer.centroid_actors
        • ClustersVisualizer.cluster_actors
        • ClustersVisualizer.lengths
        • ClustersVisualizer.recluster_tractograms()
        • ClustersVisualizer.sizes
        • ClustersVisualizer.tractogram_clusters
    • PeakActor
      • PeakActor
        • PeakActor.__init__()
        • PeakActor.cross_section
        • PeakActor.display_cross_section()
        • PeakActor.display_extent()
        • PeakActor.global_opacity
        • PeakActor.high_ranges
        • PeakActor.is_range
        • PeakActor.linewidth
        • PeakActor.low_ranges
        • PeakActor.max_centers
        • PeakActor.min_centers
    • PeaksVisualizer
      • PeaksVisualizer
        • PeaksVisualizer.__init__()
        • PeaksVisualizer.actors
    • peak
      • peak()
    • SlicesVisualizer
      • SlicesVisualizer
        • SlicesVisualizer.__init__()
        • SlicesVisualizer.change_volume()
        • SlicesVisualizer.data_shape
        • SlicesVisualizer.intensities_range
        • SlicesVisualizer.register_picker_callback()
        • SlicesVisualizer.rgb
        • SlicesVisualizer.selected_slices
        • SlicesVisualizer.slice_actors
        • SlicesVisualizer.volume_max
        • SlicesVisualizer.volume_min
    • SurfaceVisualizer
      • SurfaceVisualizer
        • SurfaceVisualizer.__init__()
        • SurfaceVisualizer.actors
    • build_label
      • build_label()
    • slicer_panel
      • slicer_panel()
    • compare_maps
      • compare_maps()
    • compare_qti_maps
      • compare_qti_maps()
    • bundle_shape_profile
      • bundle_shape_profile()
    • sph_project
      • sph_project()
    • simple_plot
      • simple_plot()
    • overlay_images
      • overlay_images()
    • draw_lattice_2d
      • draw_lattice_2d()
    • plot_2d_diffeomorphic_map
      • plot_2d_diffeomorphic_map()
    • plot_slices
      • plot_slices()
    • overlay_slices
      • overlay_slices()
    • show_bundles
      • show_bundles()
    • viz_two_bundles
      • viz_two_bundles()
    • viz_vector_field
      • viz_vector_field()
    • viz_displacement_mag
      • viz_displacement_mag()
• workflows
  • Module: workflows.align
  • Module: workflows.base
  • Module: workflows.cli
  • Module: workflows.combined_workflow
  • Module: workflows.denoise
  • Module: workflows.docstring_parser
  • Module: workflows.flow_runner
  • Module: workflows.io
  • Module: workflows.mask
  • Module: workflows.multi_io
  • Module: workflows.nn
  • Module: workflows.reconst
  • Module: workflows.segment
  • Module: workflows.stats
  • Module: workflows.tracking
  • Module: workflows.viz
  • Module: workflows.workflow
    • ResliceFlow
      • ResliceFlow
        • ResliceFlow.__init__()
        • ResliceFlow.get_short_name()
        • ResliceFlow.run()
    • SlrWithQbxFlow
      • SlrWithQbxFlow
        • SlrWithQbxFlow.__init__()
        • SlrWithQbxFlow.get_short_name()
        • SlrWithQbxFlow.run()
    • ImageRegistrationFlow
      • ImageRegistrationFlow
        • ImageRegistrationFlow.__init__()
        • ImageRegistrationFlow.run()
    • ApplyTransformFlow
      • ApplyTransformFlow
        • ApplyTransformFlow.__init__()
        • ApplyTransformFlow.run()
    • SynRegistrationFlow
      • SynRegistrationFlow
        • SynRegistrationFlow.__init__()
        • SynRegistrationFlow.run()
    • MotionCorrectionFlow
      • MotionCorrectionFlow
        • MotionCorrectionFlow.__init__()
        • MotionCorrectionFlow.run()
    • BundleWarpFlow
      • BundleWarpFlow
        • BundleWarpFlow.__init__()
        • BundleWarpFlow.get_short_name()
        • BundleWarpFlow.run()
    • check_dimensions
      • check_dimensions()
    • IntrospectiveArgumentParser
      • IntrospectiveArgumentParser
        • IntrospectiveArgumentParser.__init__()
        • IntrospectiveArgumentParser.add_description()
        • IntrospectiveArgumentParser.add_epilogue()
        • IntrospectiveArgumentParser.add_sub_flow_args()
        • IntrospectiveArgumentParser.add_workflow()
        • IntrospectiveArgumentParser.get_flow_args()
        • IntrospectiveArgumentParser.optional_parameters
        • IntrospectiveArgumentParser.output_parameters
        • IntrospectiveArgumentParser.positional_parameters
        • IntrospectiveArgumentParser.show_argument()
        • IntrospectiveArgumentParser.update_argument()
    • get_args_default
      • get_args_default()
    • none_or_dtype
      • none_or_dtype()
    • run
      • run()
    • CombinedWorkflow
      • CombinedWorkflow
        • CombinedWorkflow.__init__()
        • CombinedWorkflow.get_optionals()
        • CombinedWorkflow.get_sub_runs()
        • CombinedWorkflow.run_sub_flow()
        • CombinedWorkflow.set_sub_flows_optionals()
    • Patch2SelfFlow
      • Patch2SelfFlow
        • Patch2SelfFlow.__init__()
        • Patch2SelfFlow.get_short_name()
        • Patch2SelfFlow.run()
    • NLMeansFlow
      • NLMeansFlow
        • NLMeansFlow.__init__()
        • NLMeansFlow.get_short_name()
        • NLMeansFlow.run()
    • LPCAFlow
      • LPCAFlow
        • LPCAFlow.__init__()
        • LPCAFlow.get_short_name()
        • LPCAFlow.run()
    • MPPCAFlow
      • MPPCAFlow
        • MPPCAFlow.__init__()
        • MPPCAFlow.get_short_name()
        • MPPCAFlow.run()
    • GibbsRingingFlow
      • GibbsRingingFlow
        • GibbsRingingFlow.__init__()
        • GibbsRingingFlow.get_short_name()
        • GibbsRingingFlow.run()
    • Reader
      • Reader
        • Reader.__init__()
        • Reader.eof()
        • Reader.is_empty()
        • Reader.peek()
        • Reader.read()
        • Reader.read_to_condition()
        • Reader.read_to_next_empty_line()
        • Reader.read_to_next_unindented_line()
        • Reader.reset()
        • Reader.seek_next_non_empty_line()
    • NumpyDocString
      • NumpyDocString
        • NumpyDocString.__init__()
    • dedent_lines
      • dedent_lines()
    • get_level
      • get_level()
    • run_flow
      • run_flow()
    • IoInfoFlow
      • IoInfoFlow
        • IoInfoFlow.__init__()
        • IoInfoFlow.get_short_name()
        • IoInfoFlow.run()
    • FetchFlow
      • FetchFlow
        • FetchFlow.__init__()
        • FetchFlow.get_fetcher_datanames()
        • FetchFlow.get_short_name()
        • FetchFlow.load_module()
        • FetchFlow.run()
    • SplitFlow
      • SplitFlow
        • SplitFlow.__init__()
        • SplitFlow.get_short_name()
        • SplitFlow.run()
    • ConcatenateTractogramFlow
      • ConcatenateTractogramFlow
        • ConcatenateTractogramFlow.__init__()
        • ConcatenateTractogramFlow.get_short_name()
        • ConcatenateTractogramFlow.run()
    • ConvertSHFlow
      • ConvertSHFlow
        • ConvertSHFlow.__init__()
        • ConvertSHFlow.get_short_name()
        • ConvertSHFlow.run()
    • ConvertTensorsFlow
      • ConvertTensorsFlow
        • ConvertTensorsFlow.__init__()
        • ConvertTensorsFlow.get_short_name()
        • ConvertTensorsFlow.run()
    • ConvertTractogramFlow
      • ConvertTractogramFlow
        • ConvertTractogramFlow.__init__()
        • ConvertTractogramFlow.get_short_name()
        • ConvertTractogramFlow.run()
    • MaskFlow
      • MaskFlow
        • MaskFlow.__init__()
        • MaskFlow.get_short_name()
        • MaskFlow.run()
    • IOIterator
      • IOIterator
        • IOIterator.__init__()
        • IOIterator.create_directories()
        • IOIterator.create_outputs()
        • IOIterator.file_existence_check()
        • IOIterator.set_inputs()
        • IOIterator.set_out_dir()
        • IOIterator.set_out_fnames()
        • IOIterator.set_output_keys()
    • common_start
      • common_start()
    • slash_to_under
      • slash_to_under()
    • connect_output_paths
      • connect_output_paths()
    • concatenate_inputs
      • concatenate_inputs()
    • basename_without_extension
      • basename_without_extension()
    • io_iterator
      • io_iterator()
    • io_iterator_
      • io_iterator_()
    • EVACPlusFlow
      • EVACPlusFlow
        • EVACPlusFlow.__init__()
        • EVACPlusFlow.get_short_name()
        • EVACPlusFlow.run()
    • ReconstMAPMRIFlow
      • ReconstMAPMRIFlow
        • ReconstMAPMRIFlow.__init__()
        • ReconstMAPMRIFlow.get_short_name()
        • ReconstMAPMRIFlow.run()
    • ReconstDtiFlow
      • ReconstDtiFlow
        • ReconstDtiFlow.__init__()
        • ReconstDtiFlow.get_fitted_tensor()
        • ReconstDtiFlow.get_short_name()
        • ReconstDtiFlow.run()
    • ReconstDsiFlow
      • ReconstDsiFlow
        • ReconstDsiFlow.__init__()
        • ReconstDsiFlow.get_short_name()
        • ReconstDsiFlow.run()
    • ReconstCSDFlow
      • ReconstCSDFlow
        • ReconstCSDFlow.__init__()
        • ReconstCSDFlow.get_short_name()
        • ReconstCSDFlow.run()
    • ReconstCSAFlow
      • ReconstCSAFlow
        • ReconstCSAFlow.__init__()
        • ReconstCSAFlow.get_short_name()
        • ReconstCSAFlow.run()
    • ReconstDkiFlow
      • ReconstDkiFlow
        • ReconstDkiFlow.__init__()
        • ReconstDkiFlow.get_fitted_tensor()
        • ReconstDkiFlow.get_short_name()
        • ReconstDkiFlow.run()
    • ReconstIvimFlow
      • ReconstIvimFlow
        • ReconstIvimFlow.__init__()
        • ReconstIvimFlow.get_fitted_ivim()
        • ReconstIvimFlow.get_short_name()
        • ReconstIvimFlow.run()
    • ReconstRUMBAFlow
      • ReconstRUMBAFlow
        • ReconstRUMBAFlow.__init__()
        • ReconstRUMBAFlow.get_short_name()
        • ReconstRUMBAFlow.run()
    • MedianOtsuFlow
      • MedianOtsuFlow
        • MedianOtsuFlow.__init__()
        • MedianOtsuFlow.get_short_name()
        • MedianOtsuFlow.run()
    • RecoBundlesFlow
      • RecoBundlesFlow
        • RecoBundlesFlow.__init__()
        • RecoBundlesFlow.get_short_name()
        • RecoBundlesFlow.run()
    • LabelsBundlesFlow
      • LabelsBundlesFlow
        • LabelsBundlesFlow.__init__()
        • LabelsBundlesFlow.get_short_name()
        • LabelsBundlesFlow.run()
    • SNRinCCFlow
      • SNRinCCFlow
        • SNRinCCFlow.__init__()
        • SNRinCCFlow.get_short_name()
        • SNRinCCFlow.run()
    • BundleAnalysisTractometryFlow
      • BundleAnalysisTractometryFlow
        • BundleAnalysisTractometryFlow.__init__()
        • BundleAnalysisTractometryFlow.get_short_name()
        • BundleAnalysisTractometryFlow.run()
    • LinearMixedModelsFlow
      • LinearMixedModelsFlow
        • LinearMixedModelsFlow.__init__()
        • LinearMixedModelsFlow.get_metric_name()
        • LinearMixedModelsFlow.get_short_name()
        • LinearMixedModelsFlow.run()
        • LinearMixedModelsFlow.save_lmm_plot()
    • BundleShapeAnalysis
      • BundleShapeAnalysis
        • BundleShapeAnalysis.__init__()
        • BundleShapeAnalysis.get_short_name()
        • BundleShapeAnalysis.run()
    • buan_bundle_profiles
      • buan_bundle_profiles()
    • LocalFiberTrackingPAMFlow
      • LocalFiberTrackingPAMFlow
        • LocalFiberTrackingPAMFlow.__init__()
        • LocalFiberTrackingPAMFlow.get_short_name()
        • LocalFiberTrackingPAMFlow.run()
    • PFTrackingPAMFlow
      • PFTrackingPAMFlow
        • PFTrackingPAMFlow.__init__()
        • PFTrackingPAMFlow.get_short_name()
        • PFTrackingPAMFlow.run()
    • HorizonFlow
      • HorizonFlow
        • HorizonFlow.__init__()
        • HorizonFlow.get_short_name()
        • HorizonFlow.run()
    • Workflow
      • Workflow
        • Workflow.__init__()
        • Workflow.get_io_iterator()
        • Workflow.get_short_name()
        • Workflow.get_sub_runs()
        • Workflow.manage_output_overwrite()
        • Workflow.run()