API ReferenceΒΆ
dipy__config__align- Module:
align.imaffine - Module:
align.imwarp - Module:
align.metrics - Module:
align.reslice - Module:
align.scalespace - Module:
align.streamlinearBunchfloatingAffineInvalidValuesErrorAffineInversionErrorAffineMapAffineRegistrationIsotropicScaleSpaceMutualInformationMetricOptimizerParzenJointHistogramScaleSpace- compute_parzen_mi
- get_direction_and_spacings
- interpolate_scalar_2d
- interpolate_scalar_3d
- sample_domain_regular
- transform_centers_of_mass
- transform_geometric_centers
- transform_origins
- warn
BunchDiffeomorphicMapDiffeomorphicRegistrationScaleSpaceSymmetricDiffeomorphicRegistrationfloating- get_direction_and_spacings
- mult_aff
CCMetricEMMetricSSDMetricSimilarityMetricfloating- gradient
- v_cycle_2d
- v_cycle_3d
- Pool
- affine_transform
- cpu_count
- reslice
IsotropicScaleSpaceScaleSpacefloatingBundleMinDistanceAsymmetricMetricBundleMinDistanceMatrixMetricBundleMinDistanceMetricBundleSumDistanceMatrixMetricOptimizerStreamlineDistanceMetricStreamlineLinearRegistrationStreamlineRegistrationMapStreamlines- bundle_min_distance
- bundle_min_distance_asymmetric_fast
- bundle_min_distance_fast
- bundle_sum_distance
- center_streamlines
- compose_matrix
- compose_matrix44
- compose_transformations
- decompose_matrix
- decompose_matrix44
- distance_matrix_mdf
- length
- progressive_slr
- qbx_and_merge
- remove_clusters_by_size
- select_random_set_of_streamlines
- set_number_of_points
- slr_with_qbx
- time
- transform_streamlines
- unlist_streamlines
- whole_brain_slr
- Module:
bootscore- Module:
core.geometry - Module:
core.gradients - Module:
core.graph - Module:
core.histeq - Module:
core.ndindex - Module:
core.onetime - Module:
core.optimize - Module:
core.profile - Module:
core.rng - Module:
core.sphere - Module:
core.sphere_stats - Module:
core.subdivide_octahedron - Module:
core.wavelet- test
- cart2sphere
- cart_distance
- circumradius
- compose_matrix
- compose_transformations
- decompose_matrix
- dist_to_corner
- euler_matrix
- is_hemispherical
- lambert_equal_area_projection_cart
- lambert_equal_area_projection_polar
- nearest_pos_semi_def
- normalized_vector
- perpendicular_directions
- rodrigues_axis_rotation
- sph2latlon
- sphere2cart
- sphere_distance
- vec2vec_rotmat
- vector_cosine
- vector_norm
GradientTableHemiSphere- auto_attr
- check_multi_b
- disperse_charges
- generate_bvecs
- gradient_table
- gradient_table_from_bvals_bvecs
- gradient_table_from_gradient_strength_bvecs
- gradient_table_from_qvals_bvecs
- inv
- polar
- reorient_bvecs
- round_bvals
- unique_bvals
- vector_norm
- warn
Graph- histeq
- as_strided
- ndindex
OneTimePropertyResetMixin- auto_attr
NonNegativeLeastSquaresOptimizerSKLearnLinearSolver- minimize
- sparse_nnls
- spdot
Profiler- optional_package
- LEcuyer
- WichmannHill1982
- WichmannHill2006
- architecture
- floor
HemiSphereSphere- auto_attr
- cart2sphere
- disperse_charges
- euler_characteristic_check
- faces_from_sphere_vertices
- remove_similar_vertices
- sphere2cart
- unique_edges
- unique_sets
- vector_norm
permutations- angular_similarity
- compare_orientation_sets
- eigenstats
- random_uniform_on_sphere
HemiSphere- create_unit_hemisphere
- create_unit_sphere
- afb3D
- afb3D_A
- cshift3D
- dwt3D
- idwt3D
- permutationinverse
- sfb3D
- sfb3D_A
- Module:
data- Module:
data.fetcherDataErrorGradientTableHemiSphereSphere- as_native_array
- dirname
- dsi_deconv_voxels
- dsi_voxels
- fetch_bundle_atlas_hcp842
- fetch_bundle_fa_hcp
- fetch_bundles_2_subjects
- fetch_cenir_multib
- fetch_cfin_multib
- fetch_gold_standard_io
- fetch_isbi2013_2shell
- fetch_ivim
- fetch_mni_template
- fetch_scil_b0
- fetch_sherbrooke_3shell
- fetch_stanford_hardi
- fetch_stanford_labels
- fetch_stanford_pve_maps
- fetch_stanford_t1
- fetch_syn_data
- fetch_taiwan_ntu_dsi
- fetch_target_tractogram_hcp
- fetch_tissue_data
- get_3shell_gtab
- get_bundle_atlas_hcp842
- get_cmap
- get_fnames
- get_gtab_taiwan_dsi
- get_isbi2013_2shell_gtab
- get_sim_voxels
- get_skeleton
- get_sphere
- get_target_tractogram_hcp
- gradient_table
- load
- loads_compat
- matlab_life_results
- mrtrix_spherical_functions
- pjoin
- read_bundles_2_subjects
- read_cenir_multib
- read_cfin_dwi
- read_cfin_t1
- read_isbi2013_2shell
- read_ivim
- read_mni_template
- read_scil_b0
- read_sherbrooke_3shell
- read_stanford_hardi
- read_stanford_labels
- read_stanford_pve_maps
- read_stanford_t1
- read_syn_data
- read_taiwan_ntu_dsi
- read_tissue_data
- relist_streamlines
- sticks_and_ball
- two_cingulum_bundles
FetcherError- check_md5
- copyfileobj
- copyfileobj_withprogress
- fetch_bundle_atlas_hcp842
- fetch_bundle_fa_hcp
- fetch_bundles_2_subjects
- fetch_cenir_multib
- fetch_cfin_multib
- fetch_data
- fetch_file_formats
- fetch_gold_standard_io
- fetch_isbi2013_2shell
- fetch_ivim
- fetch_mni_template
- fetch_qtdMRI_test_retest_2subjects
- fetch_scil_b0
- fetch_sherbrooke_3shell
- fetch_stanford_hardi
- fetch_stanford_labels
- fetch_stanford_pve_maps
- fetch_stanford_t1
- fetch_syn_data
- fetch_taiwan_ntu_dsi
- fetch_target_tractogram_hcp
- fetch_tissue_data
- get_bundle_atlas_hcp842
- get_file_formats
- get_target_tractogram_hcp
- get_two_hcp842_bundles
- gradient_table
- gradient_table_from_gradient_strength_bvecs
- md5
- pjoin
- read_bundles_2_subjects
- read_bvals_bvecs
- read_cenir_multib
- read_cfin_dwi
- read_cfin_t1
- read_isbi2013_2shell
- read_ivim
- read_mni_template
- read_qtdMRI_test_retest_2subjects
- read_scil_b0
- read_sherbrooke_3shell
- read_siemens_scil_b0
- read_stanford_hardi
- read_stanford_labels
- read_stanford_pve_maps
- read_stanford_t1
- read_syn_data
- read_taiwan_ntu_dsi
- read_tissue_data
- update_progressbar
- urlopen
- Module:
denoisedirection- Module:
direction.peaksBootDirectionGetterClosestPeakDirectionGetterDeterministicMaximumDirectionGetterEuDXDirectionGetterInTemporaryDirectoryPeaksAndMetricsProbabilisticDirectionGetterSphererepeat- Pool
- cpu_count
- gfa
- local_maxima
- ndindex
- peak_directions
- peak_directions_nl
- peaks_from_model
- remove_similar_vertices
- reshape_peaks_for_visualization
- search_descending
- sh_to_sf_matrix
- warn
EuDXDirectionGetterInTemporaryDirectoryPeaksAndMetricsSphererepeat- Pool
- cpu_count
- gfa
- local_maxima
- ndindex
- peak_directions
- peak_directions_nl
- peaks_from_model
- remove_similar_vertices
- reshape_peaks_for_visualization
- search_descending
- sh_to_sf_matrix
- warn
- Module:
io- Module:
io.bvectxt - Module:
io.dpy - Module:
io.gradients - Module:
io.image - Module:
io.peaks - Module:
io.pickles - Module:
io.stateful_tractogram - Module:
io.streamline - Module:
io.utils - Module:
io.vtkDpy- load_pickle
- orientation_from_string
- orientation_to_string
- ornt_mapping
- read_bvals_bvecs
- read_bvec_file
- reorient_on_axis
- reorient_vectors
- save_pickle
- orientation_from_string
- orientation_to_string
- ornt_mapping
- read_bvec_file
- reorient_on_axis
- reorient_vectors
- splitext
DpyStreamlinesInTemporaryDirectory- read_bvals_bvecs
- splitext
- load_nifti
- save_nifti
- save_qa_metric
PeaksAndMetricsSphere- load_peaks
- peaks_to_niftis
- reshape_peaks_for_visualization
- save_nifti
- save_peaks
- load_pickle
- save_pickle
PerArrayDictPerArraySequenceDictSpaceStatefulTractogramStreamlinesTractogramitemgetterproduct- apply_affine
- bisect
- deepcopy
- get_reference_info
DpySpaceStatefulTractogramTractogram- create_tractogram_header
- deepcopy
- detect_format
- is_header_compatible
- load_dpy
- load_fib
- load_tck
- load_tractogram
- load_trk
- load_vtk
- load_vtk_streamlines
- save_dpy
- save_fib
- save_tck
- save_tractogram
- save_trk
- save_vtk
- save_vtk_streamlines
Nifti1Image- create_nifti_header
- create_tractogram_header
- decfa
- decfa_to_float
- detect_format
- get_reference_info
- is_header_compatible
- make5d
- nifti1_symmat
- load_polydata
- load_vtk_streamlines
- optional_package
- save_polydata
- save_vtk_streamlines
- setup_module
- transform_streamlines
- Module:
reconst- Module:
reconst.base - Module:
reconst.benchmarks - Module:
reconst.benchmarks.bench_bounding_box - Module:
reconst.benchmarks.bench_csd - Module:
reconst.benchmarks.bench_peaks - Module:
reconst.benchmarks.bench_squash - Module:
reconst.benchmarks.bench_vec_val_sum - Module:
reconst.cache - Module:
reconst.cross_validation - Module:
reconst.csdeconv - Module:
reconst.dki - Module:
reconst.dki_micro - Module:
reconst.dsi - Module:
reconst.dti - 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.sfm - Module:
reconst.shm - Module:
reconst.shore - Module:
reconst.utils- bench
- test
ReconstFitReconstModel- bench_bounding_box
- bounding_box
- measure
ConstrainedSphericalDeconvModelGradientTable- bench_csdeconv
- num_grad
- read_stanford_labels
- bench_local_maxima
- local_maxima
- measure
- unique_edges
- bench_quick_squash
- measure
- ndindex
- old_squash
- quick_squash
- reduce
- bench_vec_val_vect
- measure
- randn
- vec_val_vect
- with_einsum
Cache- auto_attr
- coeff_of_determination
- kfold_xval
AxSymShResponseConstrainedSDTModelConstrainedSphericalDeconvModelSphHarmFitSphHarmModelTensorModel- auto_response
- cart2sphere
- csdeconv
- estimate_response
- fa_inferior
- fa_superior
- fa_trace_to_lambdas
- forward_sdeconv_mat
- forward_sdt_deconv_mat
- fractional_anisotropy
- get_sphere
- lazy_index
- lpn
- multi_voxel_fit
- ndindex
- odf_deconv
- odf_sh_to_sharp
- peaks_from_model
- quad
- real_sph_harm
- real_sym_sh_basis
- recursive_response
- response_from_mask
- sh_to_rh
- single_tensor
- sph_harm_ind_list
- vec2vec_rotmat
DiffusionKurtosisFitDiffusionKurtosisModelReconstModelTensorFit- Wcons
- Wrotate
- Wrotate_element
- apparent_kurtosis_coef
- axial_kurtosis
- carlson_rd
- carlson_rf
- cart2sphere
- check_multi_b
- decompose_tensor
- design_matrix
- directional_diffusion
- directional_diffusion_variance
- directional_kurtosis
- dki_prediction
- from_lower_triangular
- get_sphere
- kurtosis_maximum
- local_maxima
- lower_triangular
- mean_diffusivity
- mean_kurtosis
- ndindex
- ols_fit_dki
- radial_kurtosis
- sphere2cart
- split_dki_param
- vec_val_vect
- wls_fit_dki
DiffusionKurtosisFitDiffusionKurtosisModelKurtosisMicrostructuralFitKurtosisMicrostructureModel- axial_diffusivity
- axonal_water_fraction
- decompose_tensor
- diffusion_components
- directional_diffusion
- directional_kurtosis
- dkimicro_prediction
- dti_design_matrix
- from_lower_triangular
- get_sphere
- kurtosis_maximum
- lower_triangular
- mean_diffusivity
- ndindex
- radial_diffusivity
- split_dki_param
- tortuosity
- trace
- vec_val_vect
CacheDiffusionSpectrumDeconvFitDiffusionSpectrumDeconvModelDiffusionSpectrumFitDiffusionSpectrumModelOdfFitOdfModel- LR_deconv
- create_qspace
- create_qtable
- fftn
- fftshift
- gen_PSF
- half_to_full_qspace
- hanning_filter
- ifftshift
- map_coordinates
- multi_voxel_fit
- pdf_interp_coords
- pdf_odf
- project_hemisph_bvecs
- threshold_propagator
ReconstModelTensorFitTensorModel- apparent_diffusion_coef
- auto_attr
- axial_diffusivity
- color_fa
- decompose_tensor
- design_matrix
- determinant
- deviatoric
- eig_from_lo_tri
- fractional_anisotropy
- from_lower_triangular
- geodesic_anisotropy
- get_sphere
- gradient_table
- isotropic
- iter_fit_tensor
- linearity
- lower_triangular
- mean_diffusivity
- mode
- nlls_fit_tensor
- norm
- ols_fit_tensor
- pinv
- planarity
- quantize_evecs
- radial_diffusivity
- restore_fit_tensor
- sphericity
- tensor_prediction
- trace
- vec_val_vect
- vector_norm
- wls_fit_tensor
CacheForecastFitForecastModelOdfFitOdfModel- cart2sphere
- csdeconv
- find_signal_means
- forecast_error_func
- forecast_matrix
- lb_forecast
- leastsq
- multi_voxel_fit
- optional_package
- psi_l
- real_sph_harm
- rho_matrix
- warn
FreeWaterTensorFitFreeWaterTensorModelReconstModelTensorFit- check_multi_b
- cholesky_to_lower_triangular
- decompose_tensor
- design_matrix
- from_lower_triangular
- fwdti_prediction
- lower_triangular
- lower_triangular_to_cholesky
- multi_voxel_fit
- ndindex
- nls_fit_tensor
- nls_iter
- vec_val_vect
- wls_fit_tensor
- wls_iter
CacheGeneralizedQSamplingFitGeneralizedQSamplingModelOdfFitOdfModel- equatorial_maximum
- equatorial_zone_vertices
- gfa
- local_maxima
- multi_voxel_fit
- normalize_qa
- npa
- odf_sum
- patch_maximum
- patch_sum
- patch_vertices
- polar_zone_vertices
- remove_similar_vertices
- squared_radial_component
- triple_odf_maxima
- upper_hemi_map
IvimFitIvimModelTRRIvimModelVPReconstModel- IvimModel
- differential_evolution
- f_D_star_error
- f_D_star_prediction
- ivim_model_selector
- ivim_prediction
- least_squares
- multi_voxel_fit
- optional_package
CacheMapmriFitMapmriModelOptimizerReconstFitReconstModel- b_mat
- b_mat_isotropic
- binomialfloat
- cart2sphere
- create_rspace
- delta
- factorial2
- gcv_cost_function
- generalized_crossvalidation
- generalized_crossvalidation_array
- genlaguerre
- gradient_table
- hermite
- isotropic_scale_factor
- map_laplace_s
- map_laplace_t
- map_laplace_u
- mapmri_STU_reg_matrices
- mapmri_index_matrix
- mapmri_isotropic_K_mu_dependent
- mapmri_isotropic_K_mu_independent
- mapmri_isotropic_M_mu_dependent
- mapmri_isotropic_M_mu_independent
- mapmri_isotropic_index_matrix
- mapmri_isotropic_laplacian_reg_matrix
- mapmri_isotropic_laplacian_reg_matrix_from_index_matrix
- mapmri_isotropic_odf_matrix
- mapmri_isotropic_odf_sh_matrix
- mapmri_isotropic_phi_matrix
- mapmri_isotropic_psi_matrix
- mapmri_isotropic_radial_pdf_basis
- mapmri_isotropic_radial_signal_basis
- mapmri_laplacian_reg_matrix
- mapmri_odf_matrix
- mapmri_phi_1d
- mapmri_phi_matrix
- mapmri_psi_1d
- mapmri_psi_matrix
- mfactorial
- multi_voxel_fit
- optional_package
- real_sph_harm
- sfactorial
- sph_harm_ind_list
- warn
MSDeconvFitMultiShellDeconvModelMultiShellResponseQpFitter- multi_tissue_basis
- multi_voxel_fit
- optional_package
- solve_qp
MeanDiffusionKurtosisFitMeanDiffusionKurtosisModelReconstModel- auto_attr
- check_multi_b
- design_matrix
- mean_signal_bvalue
- msdki_prediction
- ndindex
- round_bvals
- unique_bvals
- wls_fit_msdki
CallableArrayMultiVoxelFitReconstFit- as_strided
- multi_voxel_fit
- ndindex
OdfFitOdfModelReconstFitReconstModel- gfa
- minmax_normalize
CacheQtdmriFitQtdmriModel- GCV_cost_function
- H
- angular_basis_EAP_opt
- angular_basis_opt
- cart2sphere
- create_rt_space_grid
- design_matrix_spatial
- elastic_crossvalidation
- factorial
- factorial2
- fmin_l_bfgs_b
- generalized_crossvalidation
- genlaguerre
- gradient_table_from_gradient_strength_bvecs
- l1_crossvalidation
- multi_voxel_fit
- optional_package
- part1_reg_matrix_tau
- part23_iso_reg_matrix_q
- part23_reg_matrix_q
- part23_reg_matrix_tau
- part4_iso_reg_matrix_q
- part4_reg_matrix_q
- part4_reg_matrix_tau
- qtdmri_anisotropic_scaling
- qtdmri_eap_matrix
- qtdmri_eap_matrix_
- qtdmri_index_matrix
- qtdmri_isotropic_eap_matrix
- qtdmri_isotropic_eap_matrix_
- qtdmri_isotropic_index_matrix
- qtdmri_isotropic_laplacian_reg_matrix
- qtdmri_isotropic_scaling
- qtdmri_isotropic_signal_matrix
- qtdmri_isotropic_signal_matrix_
- qtdmri_isotropic_to_mapmri_matrix
- qtdmri_laplacian_reg_matrix
- qtdmri_mapmri_isotropic_normalization
- qtdmri_mapmri_normalization
- qtdmri_number_of_coefficients
- qtdmri_signal_matrix
- qtdmri_signal_matrix_
- qtdmri_temporal_normalization
- qtdmri_to_mapmri_matrix
- radial_basis_EAP_opt
- radial_basis_opt
- real_sph_harm
- temporal_basis
- visualise_gradient_table_G_Delta_rainbow
- warn
CacheExponentialIsotropicFitExponentialIsotropicModelIsotropicFitIsotropicModelReconstFitReconstModelSparseFascicleFitSparseFascicleModel- auto_attr
- nanmean
- optional_package
- sfm_design_matrix
CacheCsaOdfModelLooseVersionOdfFitOdfModelOpdtModelQballBaseModelQballModelResidualBootstrapWrapperSphHarmFitSphHarmModel- anisotropic_power
- auto_attr
- bootstrap_data_array
- bootstrap_data_voxel
- calculate_max_order
- cart2sphere
- concatenate
- diag
- diff
- dot
- empty
- eye
- forward_sdeconv_mat
- gen_dirac
- hat
- lazy_index
- lcr_matrix
- lpn
- normalize_data
- order_from_ncoef
- pinv
- randint
- real_sph_harm
- real_sym_sh_basis
- real_sym_sh_mrtrix
- sf_to_sh
- sh_to_rh
- sh_to_sf
- sh_to_sf_matrix
- smooth_pinv
- sph_harm_ind_list
- spherical_harmonics
- svd
- unique
CacheShoreFitShoreModel- cart2sphere
- create_rspace
- factorial
- genlaguerre
- l_shore
- multi_voxel_fit
- n_shore
- optional_package
- real_sph_harm
- shore_indices
- shore_matrix
- shore_matrix_odf
- shore_matrix_pdf
- shore_order
- warn
- dki_design_matrix
- Module:
segment- Module:
segment.benchmarks - Module:
segment.benchmarks.bench_quickbundles - Module:
segment.bundles - Module:
segment.clustering - Module:
segment.mask - Module:
segment.metric - Module:
segment.threshold - Module:
segment.tissueMDFpyMetricQB_NewStreamlines- assert_array_equal
- assert_arrays_equal
- assert_equal
- bench_quickbundles
- get_fnames
- load_tractogram
- measure
- set_number_of_points
BundleMinDistanceAsymmetricMetricBundleMinDistanceMetricBundleSumDistanceMatrixMetricRecoBundlesStreamlineLinearRegistrationStreamlineschain- apply_affine
- bundle_adjacency
- bundles_distances_mam
- bundles_distances_mdf
- check_range
- length
- nbytes
- qbx_and_merge
- select_random_set_of_streamlines
- set_number_of_points
- time
ABCMetaAveragePointwiseEuclideanMetricClusterClusterCentroidClusterMapClusterMapCentroidClusteringIdentityMetricMinimumAverageDirectFlipMetricQuickBundlesQuickBundlesXResampleFeatureTreeClusterTreeClusterMap- abstractmethod
- nbytes
- qbx_and_merge
- set_number_of_points
- time
- applymask
- binary_dilation
- bounding_box
- clean_cc_mask
- color_fa
- crop
- fractional_anisotropy
- generate_binary_structure
- median_filter
- median_otsu
- multi_median
- otsu
- segment_from_cfa
- warn
ArcLengthFeatureAveragePointwiseEuclideanMetricCenterOfMassFeatureCosineMetricEuclideanMetricFeatureIdentityFeatureMetricMidpointFeatureMinimumAverageDirectFlipMetricResampleFeatureSumPointwiseEuclideanMetricVectorOfEndpointsFeature- dist
- distance_matrix
- mdf
- otsu
- upper_bound_by_percent
- upper_bound_by_rate
ConstantObservationModelIteratedConditionalModesTissueClassifierHMRF- add_noise
- Module:
sims- Module:
sims.phantom - Module:
sims.voxel- add_noise
- diff2eigenvectors
- get_fnames
- gradient_table
- orbital_phantom
- single_tensor
- vec2vec_rotmat
- add_noise
- all_tensor_evecs
- callaghan_perpendicular
- cylinders_and_ball_soderman
- dki_design_matrix
- dki_signal
- dot
- gaussian_parallel
- kurtosis_element
- multi_tensor
- multi_tensor_dki
- multi_tensor_msd
- multi_tensor_odf
- multi_tensor_pdf
- multi_tensor_rtop
- single_tensor
- single_tensor_msd
- single_tensor_odf
- single_tensor_pdf
- single_tensor_rtop
- sphere2cart
- sticks_and_ball
- vec2vec_rotmat
- Module:
stats- Module:
stats.analysisAveragePointwiseEuclideanMetricQuickBundlesStreamlinescKDTree- afq_profile
- bundle_analysis
- dti_measures
- gaussian_weights
- load_nifti
- load_peaks
- load_tractogram
- mahalanobis
- map_coordinates
- optional_package
- orient_by_streamline
- peak_values
- set_number_of_points
- transform_streamlines
- values_from_volume
- Module:
tracking- Module:
tracking._utils - Module:
tracking.benchmarks - Module:
tracking.benchmarks.bench_streamline - Module:
tracking.learning - Module:
tracking.life - Module:
tracking.local_tracking - Module:
tracking.metrics - Module:
tracking.streamline - Module:
tracking.utils- Important Notes
Streamlines- bench
- test
- warn
Streamlines- assert_array_almost_equal
- assert_array_equal
- bench_compress_streamlines
- bench_length
- bench_set_number_of_points
- compress_streamlines
- compress_streamlines_python
- generate_streamlines
- get_fnames
- length
- length_python
- load_tractogram
- measure
- set_number_of_points
- set_number_of_points_python
- setup
- detect_corresponding_tracks
- detect_corresponding_tracks_plus
FiberFitFiberModelLifeSignalMakerReconstFitReconstModel- grad_tensor
- gradient
- streamline_gradients
- streamline_signal
- streamline_tensors
- transform_streamlines
- unique_rows
- voxel2streamline
AnatomicalStoppingCriterionLocalTrackingParticleFilteringTrackingStreamlineStatus- local_tracker
- pft_tracker
- arbitrarypoint
- bytes
- center_of_mass
- downsample
- endpoint
- frenet_serret
- generate_combinations
- inside_sphere
- inside_sphere_points
- intersect_sphere
- length
- longest_track_bundle
- magn
- mean_curvature
- mean_orientation
- midpoint
- midpoint2point
- principal_components
- splev
- spline
- splprep
- startpoint
- winding
Streamlines- apply_affine
- bundles_distances_mdf
- cdist
- center_streamlines
- cluster_confidence
- compress_streamlines
- deepcopy
- deform_streamlines
- dist_to_corner
- interpolate_scalar_3d
- interpolate_vector_3d
- length
- nbytes
- orient_by_rois
- orient_by_streamline
- relist_streamlines
- select_by_rois
- select_random_set_of_streamlines
- set_number_of_points
- transform_streamlines
- unlist_streamlines
- values_from_volume
- warn
defaultdict- apply_affine
- asarray
- cdist
- connectivity_matrix
- density_map
- dist_to_corner
- empty
- length
- minimum_at
- ndbincount
- near_roi
- path_length
- random_seeds_from_mask
- ravel_multi_index
- reduce_labels
- reduce_rois
- seeds_from_mask
- streamline_near_roi
- subsegment
- target
- target_line_based
- transform_tracking_output
- unique_rows
- warn
- wraps
- Module:
viz- Module:
viz.app - Module:
viz.gmem - Module:
viz.panel - Module:
viz.projections - Module:
viz.regtools- fetch_viz_icons
- optional_package
- read_viz_icons
EventCounterHorizonSpaceStatefulTractogramStreamlines- apply_shader
- build_label
- distinguishable_colormap
- horizon
- length
- optional_package
- qbx_and_merge
- save_tractogram
- setup_module
- slicer_panel
GlobalHorizon- build_label
- optional_package
- setup_module
- slicer_panel
- doctest_skip_parser
- optional_package
- setup_module
- sph_project
- draw_lattice_2d
- optional_package
- overlay_images
- overlay_slices
- plot_2d_diffeomorphic_map
- plot_slices
- setup_module
- simple_plot
- Module:
workflows- Module:
workflows.align - Module:
workflows.base - 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.reconst - Module:
workflows.segment - Module:
workflows.stats - Module:
workflows.tracking - Module:
workflows.viz - Module:
workflows.workflowAffineMapAffineRegistrationAffineTransform3DApplyTransformFlowCCMetricDiffeomorphicMapEMMetricImageRegistrationFlowMutualInformationMetricResliceFlowRigidTransform3DSSDMetricSlrWithQbxFlowSymmetricDiffeomorphicRegistrationSynRegistrationFlowTranslationTransform3DWorkflow- check_dimensions
- load_nifti
- reslice
- save_nifti
- save_qa_metric
- slr_with_qbx
- transform_centers_of_mass
- transform_streamlines
IntrospectiveArgumentParserNumpyDocString- get_args_default
CombinedWorkflowWorkflowNLMeansFlowWorkflow- estimate_sigma
- load_nifti
- nlmeans
- save_nifti
NumpyDocStringReader- dedent_lines
- warn
IntrospectiveArgumentParser- get_level
- run_flow
FetchFlowIoInfoFlowWorkflow- getfullargspec
- getmembers
- isfunction
- load_nifti
MaskFlowWorkflow- load_nifti
- save_nifti
IOIterator- basename_without_extension
- common_start
- concatenate_inputs
- connect_output_paths
- get_args_default
- glob
- io_iterator
- io_iterator_
- slash_to_under
ConstrainedSphericalDeconvModelCsaOdfModelDiffusionKurtosisModelReconstCSAFlowReconstCSDFlowReconstDkiFlowReconstDtiFlowReconstIvimFlowReconstMAPMRIFlowTensorModelWorkflow- IvimModel
- auto_response
- axial_diffusivity
- color_fa
- fractional_anisotropy
- geodesic_anisotropy
- get_mode
- gradient_table
- literal_eval
- load_nifti
- lower_triangular
- mean_diffusivity
- nifti1_symmat
- peaks_from_model
- peaks_to_niftis
- radial_diffusivity
- read_bvals_bvecs
- save_nifti
- save_peaks
- split_dki_param
- warn
LabelsBundlesFlowMedianOtsuFlowRecoBundlesRecoBundlesFlowWorkflow- load_nifti
- median_otsu
- save_nifti
- time
BundleAnalysisPopulationFlowLinearMixedModelsFlowSNRinCCFlowTensorModelWorkflow- binary_dilation
- bounding_box
- bundle_analysis
- gradient_table
- load_nifti
- median_otsu
- optional_package
- read_bvals_bvecs
- save_nifti
- segment_from_cfa
- simple_plot
BinaryStoppingCriterionClosestPeakDirectionGetterCmcStoppingCriterionDeterministicMaximumDirectionGetterLocalFiberTrackingPAMFlowLocalTrackingPFTrackingPAMFlowParticleFilteringTrackingProbabilisticDirectionGetterSpaceStatefulTractogramThresholdStoppingCriterionWorkflow- load_nifti
- load_peaks
- save_tractogram
DpyHorizonFlowWorkflow- horizon
- load_nifti
- load_peaks
- pjoin
Workflow- io_iterator_
- Module: