Index

A

actors (dipy.viz.horizon.tab.base.HorizonTab property) (dipy.viz.horizon.tab.cluster.ClustersTab property) (dipy.viz.horizon.tab.peak.PeaksTab property) (dipy.viz.horizon.tab.roi.ROIsTab property) (dipy.viz.horizon.tab.slice.SlicesTab property) (dipy.viz.horizon.tab.surface.SurfaceTab property) (dipy.viz.horizon.visualizer.peak.PeaksVisualizer property) (dipy.viz.horizon.visualizer.surface.SurfaceVisualizer property) ad() (dipy.reconst.dti.TensorFit method) adaptive_soft_matching() (in module dipy.denoise.adaptive_soft_matching) adc() (dipy.reconst.dti.TensorFit method) Add (class in dipy.nn.torch.evac) add() (dipy.segment.clustering.TreeCluster method) add_cluster() (dipy.segment.clustering.ClusterMap method) add_cluster_actors() (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer method) add_default_args_to_docstring() (in module dipy.workflows.base) add_description() (dipy.workflows.base.IntrospectiveArgumentParser method) add_edge() (dipy.core.graph.Graph method) add_epilogue() (dipy.workflows.base.IntrospectiveArgumentParser method) add_node() (dipy.core.graph.Graph method) add_noise() (in module dipy.sims.phantom) (in module dipy.sims.voxel) add_sub_flow_args() (dipy.workflows.base.IntrospectiveArgumentParser method) add_workflow() (dipy.workflows.base.IntrospectiveArgumentParser method) afb3D() (in module dipy.core.wavelet) afb3D_A() (in module dipy.core.wavelet) affine (dipy.io.stateful_tractogram.StatefulTractogram property) Affine matrix Affine transformation affine() (in module dipy.align._public) affine_registration() (in module dipy.align._public) AffineInvalidValuesError (class in dipy.align.imaffine) AffineInversionError (class in dipy.align.imaffine) AffineMap (class in dipy.align.imaffine)

AffineRegistration (class in dipy.align.imaffine) afq_profile() (in module dipy.stats.analysis) ak() (dipy.reconst.dki.DiffusionKurtosisFit method) akc() (dipy.reconst.dki.DiffusionKurtosisFit method) all_paths() (dipy.core.graph.Graph method) all_shm_coeff (dipy.reconst.mcsd.MSDeconvFit property) all_tensor_evecs() (in module dipy.sims.voxel) allocate() (dipy.align.imwarp.DiffeomorphicMap method) amplitude_lobe() (dipy.reconst.bingham.BinghamMetrics method) anatomical_measures() (in module dipy.stats.analysis) angular_basis_EAP_opt() (in module dipy.reconst.qtdmri) angular_basis_opt() (in module dipy.reconst.qtdmri) angular_similarity() (in module dipy.core.sphere_stats) anisotropic_power() (in module dipy.reconst.shm) apparent_diffusion_coef() (in module dipy.reconst.dti) apparent_kurtosis_coef() (in module dipy.reconst.dki) applymask() (in module dipy.segment.mask) ApplyTransformFlow (class in dipy.workflows.align) arbitrarypoint() (in module dipy.tracking.metrics) are_compatible() (dipy.io.stateful_tractogram.StatefulTractogram static method) assign() (dipy.segment.clustering.Cluster method) (dipy.segment.clustering.ClusterCentroid method) assignment_map() (in module dipy.stats.analysis) auto_attr() (in module dipy.core.onetime) auto_response_msmt() (in module dipy.reconst.mcsd) auto_response_ssst() (in module dipy.reconst.csdeconv) average_bundle_length() (in module dipy.align.streamwarp) awf (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) awf_from_msk() (in module dipy.reconst.msdki) axial_diffusivity() (in module dipy.reconst.dti) axial_kurtosis() (in module dipy.reconst.dki) Axis angle axonal_diffusivity (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) axonal_water_fraction() (in module dipy.reconst.dki_micro) AxSymShResponse (class in dipy.reconst.csdeconv)

B

b0_threshold_empty_gradient_message() (in module dipy.core.gradients) b0_threshold_update_slicing_message() (in module dipy.core.gradients) b0s_mask() (dipy.core.gradients.GradientTable method) b_mat() (in module dipy.reconst.mapmri) b_mat_isotropic() (in module dipy.reconst.mapmri) ba_analysis() (in module dipy.segment.bundles) basename_without_extension() (in module dipy.workflows.multi_io) basis() (dipy.reconst.csdeconv.AxSymShResponse method) BiasFieldCorrectionFlow (class in dipy.workflows.nn) bingham_fiber_density() (in module dipy.reconst.bingham) bingham_fiber_spread() (in module dipy.reconst.bingham) bingham_to_sf() (in module dipy.reconst.bingham) BinghamMetrics (class in dipy.reconst.bingham) binomialfloat() (in module dipy.reconst.mapmri) Block (class in dipy.nn.tf.evac) (class in dipy.nn.torch.evac) bootstrap_data_array() (in module dipy.reconst.shm) bootstrap_data_voxel() (in module dipy.reconst.shm) bootstrap_tracking() (in module dipy.tracking.tracker) bounding_box() (in module dipy.segment.mask) btens_to_params() (in module dipy.core.gradients) buan_bundle_profiles() (in module dipy.workflows.stats) build() (dipy.viz.horizon.tab.base.HorizonTab method) (dipy.viz.horizon.tab.cluster.ClustersTab method) (dipy.viz.horizon.tab.peak.PeaksTab method) (dipy.viz.horizon.tab.roi.ROIsTab method) (dipy.viz.horizon.tab.slice.SlicesTab method) (dipy.viz.horizon.tab.surface.SurfaceTab method)

build_checkbox() (in module dipy.viz.horizon.tab.base) build_label() (in module dipy.viz.horizon.tab.base) (in module dipy.viz.panel) build_radio_button() (in module dipy.viz.horizon.tab.base) build_scene() (dipy.viz.horizon.app.Horizon method) build_show() (dipy.viz.horizon.app.Horizon method) build_slider() (in module dipy.viz.horizon.tab.base) build_switcher() (in module dipy.viz.horizon.tab.base) Bunch (class in dipy.align) bundle_adjacency() (in module dipy.segment.bundles) bundle_min_distance() (in module dipy.align.streamlinear) bundle_min_distance_asymmetric_fast() (in module dipy.align.streamlinear) bundle_min_distance_fast() (in module dipy.align.streamlinear) bundle_shape_profile() (in module dipy.viz.plotting) bundle_shape_similarity() (in module dipy.segment.bundles) bundle_sum_distance() (in module dipy.align.streamlinear) BundleAnalysisTractometryFlow (class in dipy.workflows.stats) BundleMinDistanceAsymmetricMetric (class in dipy.align.streamlinear) BundleMinDistanceMatrixMetric (class in dipy.align.streamlinear) BundleMinDistanceMetric (class in dipy.align.streamlinear) BundleShapeAnalysis (class in dipy.workflows.stats) BundleSumDistanceMatrixMetric (class in dipy.align.streamlinear) bundlewarp() (in module dipy.align.streamwarp) bundlewarp_shape_analysis() (in module dipy.align.streamwarp) bundlewarp_vector_filed() (in module dipy.align.streamwarp) BundleWarpFlow (class in dipy.workflows.align) bvals() (dipy.core.gradients.GradientTable method) bvecs() (dipy.core.gradients.GradientTable method) bytes() (in module dipy.tracking.metrics)

C

c_c() (dipy.reconst.qti.QtiFit method) c_m() (dipy.reconst.qti.QtiFit method) c_md() (dipy.reconst.qti.QtiFit method) c_mu() (dipy.reconst.qti.QtiFit method) Cache (class in dipy.reconst.cache) cache_clear() (dipy.reconst.cache.Cache method) cache_get() (dipy.reconst.cache.Cache method) cache_set() (dipy.reconst.cache.Cache method) calc_signal() (dipy.tracking.life.LifeSignalMaker method) calculate_max_order() (in module dipy.reconst.shm) call() (dipy.nn.tf.deepn4.DecoderBlock method) (dipy.nn.tf.deepn4.EncoderBlock method) (dipy.nn.tf.evac.Block method) (dipy.nn.tf.evac.ChannelSum method) (dipy.nn.tf.synb0.DecoderBlock method) (dipy.nn.tf.synb0.EncoderBlock method) CallableArray (class in dipy.reconst.multi_voxel) callaghan_perpendicular() (in module dipy.sims.voxel) carlson_rd() (in module dipy.reconst.dki) carlson_rf() (in module dipy.reconst.dki) cart2sphere() (in module dipy.core.geometry) cart_distance() (in module dipy.core.geometry) CCMetric (class in dipy.align.metrics) center_of_mass() (in module dipy.align._public) (in module dipy.tracking.metrics) center_streamlines() (in module dipy.tracking.streamline) centroid_actors (dipy.viz.horizon.tab.cluster.ClustersTab property) (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) centroids (dipy.segment.clustering.ClusterMapCentroid property) change_volume() (dipy.viz.horizon.visualizer.slice.SlicesVisualizer method) ChannelSum (class in dipy.nn.tf.evac) (class in dipy.nn.torch.evac) check_dimensions() (in module dipy.workflows.align) check_img_dtype() (in module dipy.viz.horizon.util) check_img_shapes() (in module dipy.viz.horizon.util) check_md5() (in module dipy.data.fetcher) check_multi_b() (in module dipy.core.gradients) check_peak_size() (in module dipy.viz.horizon.util) check_range() (in module dipy.segment.bundles) children() (dipy.core.graph.Graph method) cholesky_to_lower_triangular() (in module dipy.reconst.fwdti) circumradius() (in module dipy.core.geometry) classify() (dipy.segment.tissue.TissueClassifierHMRF method) ClassifyTissueFlow (class in dipy.workflows.segment) clean_cc_mask() (in module dipy.segment.mask) clear() (dipy.segment.clustering.ClusterMap method) close() (dipy.io.dpy.Dpy method) closestpeak_tracking() (in module dipy.tracking.tracker) cls_fit_dki() (in module dipy.reconst.dki) Cluster (class in dipy.segment.clustering) cluster() (dipy.segment.clustering.Clustering method) (dipy.segment.clustering.QuickBundles method) (dipy.segment.clustering.QuickBundlesX method) cluster_actors (dipy.viz.horizon.tab.cluster.ClustersTab property) (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) cluster_bundle() (in module dipy.segment.bundles) cluster_confidence() (in module dipy.tracking.streamline) ClusterCentroid (class in dipy.segment.clustering) Clustering (class in dipy.segment.clustering) ClusterMap (class in dipy.segment.clustering) ClusterMapCentroid (class in dipy.segment.clustering) clusters (dipy.segment.clustering.ClusterMap property) clusters_sizes() (dipy.segment.clustering.ClusterMap method) ClustersTab (class in dipy.viz.horizon.tab.cluster) ClustersVisualizer (class in dipy.viz.horizon.visualizer.cluster) Cnn1DDenoiser (class in dipy.nn.tf.cnn_1d_denoising) coeff_of_determination() (in module dipy.reconst.cross_validation) color_fa() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti)

combined_odf_iso() (dipy.reconst.rumba.RumbaFit method) CombinedWorkflow (class in dipy.workflows.combined_workflow) common_start() (in module dipy.workflows.multi_io) compare_maps() (in module dipy.viz.plotting) compare_orientation_sets() (in module dipy.core.sphere_stats) compare_qti_maps() (in module dipy.viz.plotting) compile() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) compose_matrix() (in module dipy.core.geometry) compose_matrix44() (in module dipy.align.streamlinear) compose_transformations() (in module dipy.core.geometry) compute_backward() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) compute_bounding_box() (dipy.io.stateful_tractogram.StatefulTractogram method) compute_demons_step() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) compute_directional_average() (in module dipy.segment.tissue) compute_forward() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) compute_gauss_newton_step() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) compute_inversion_error() (dipy.align.imwarp.DiffeomorphicMap method) compute_num_samples() (in module dipy.denoise.localpca) compute_patch_size() (in module dipy.denoise.localpca) compute_suggested_patch_radius() (in module dipy.denoise.localpca) concatenate_inputs() (in module dipy.workflows.multi_io) ConcatenateTractogramFlow (class in dipy.workflows.io) connect_output_paths() (in module dipy.workflows.multi_io) connectivity_matrix() (in module dipy.tracking.utils) ConstrainedSDTModel (class in dipy.reconst.csdeconv) ConstrainedSphericalDeconvModel (class in dipy.reconst.csdeconv) convert_sh_descoteaux_tournier() (in module dipy.reconst.shm) convert_sh_from_legacy() (in module dipy.reconst.shm) convert_sh_to_full_basis() (in module dipy.reconst.shm) convert_sh_to_legacy() (in module dipy.reconst.shm) convert_tensors() (in module dipy.reconst.utils) ConvertSHFlow (class in dipy.workflows.io) ConvertTensorsFlow (class in dipy.workflows.io) ConvertTractogramFlow (class in dipy.workflows.io) copyfileobj_withprogress() (in module dipy.data.fetcher) CorrelationTensorFit (class in dipy.reconst.cti) CorrelationTensorModel (class in dipy.reconst.cti) count_sketch() (in module dipy.stats.sketching) create_directories() (dipy.workflows.multi_io.IOIterator method) create_nifti_header() (in module dipy.io.utils) create_outputs() (dipy.workflows.multi_io.IOIterator method) create_patch_radius_arr() (in module dipy.denoise.localpca) create_qspace() (in module dipy.reconst.dsi) create_qtable() (in module dipy.reconst.dsi) create_rspace() (in module dipy.reconst.mapmri) (in module dipy.reconst.shore) create_rt_space_grid() (in module dipy.reconst.qtdmri) create_tractogram_header() (in module dipy.io.utils) create_unit_hemisphere() (in module dipy.core.subdivide_octahedron) create_unit_sphere() (in module dipy.core.subdivide_octahedron) crop() (in module dipy.segment.mask) cross_section (dipy.viz.horizon.visualizer.peak.PeakActor property) CsaOdfModel (class in dipy.reconst.shm) csdeconv() (in module dipy.reconst.csdeconv) cshift3D() (in module dipy.core.wavelet) ct (dipy.reconst.cti.CorrelationTensorFit property) cti_design_matrix() (in module dipy.reconst.utils) cti_prediction() (in module dipy.reconst.cti) cvx_fit() (dipy.reconst.ivim.IvimModelVP method) cvxpy_1x21_to_6x6() (in module dipy.reconst.qti) cvxpy_1x6_to_3x3() (in module dipy.reconst.qti) cylinders_and_ball_soderman() (in module dipy.sims.voxel)

D

D (dipy.reconst.ivim.IvimFit property) d_sq() (dipy.reconst.qti.QtiFit method) D_star (dipy.reconst.ivim.IvimFit property) dam_classifier() (in module dipy.segment.tissue) data_per_point (dipy.io.stateful_tractogram.StatefulTractogram property) data_per_streamline (dipy.io.stateful_tractogram.StatefulTractogram property) data_shape (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) DataError (class in dipy.data) decfa() (in module dipy.io.utils) decfa_to_float() (in module dipy.io.utils) decoder_block() (dipy.nn.torch.deepn4.UNet3D method) DecoderBlock (class in dipy.nn.tf.deepn4) (class in dipy.nn.tf.synb0) decompose_matrix() (in module dipy.core.geometry) decompose_matrix44() (in module dipy.align.streamlinear) decompose_tensor() (in module dipy.reconst.dti) dedent_lines() (in module dipy.workflows.docstring_parser) DeepN4 (class in dipy.nn.tf.deepn4) (class in dipy.nn.torch.deepn4) deform_streamlines() (in module dipy.tracking.streamline) DeformableRegistration (class in dipy.align.cpd) del_node() (dipy.core.graph.Graph method) del_node_and_edges() (dipy.core.graph.Graph method) delta() (in module dipy.reconst.mapmri) DenseModel (class in dipy.nn.torch.histo_resdnn) density_map() (in module dipy.tracking.utils) design_matrix() (dipy.reconst.sfm.SparseFascicleModel method) (in module dipy.reconst.dti) (in module dipy.reconst.msdki) (in module dipy.reconst.qti) design_matrix_spatial() (in module dipy.reconst.qtdmri) detect_corresponding_tracks() (in module dipy.tracking.learning) detect_corresponding_tracks_plus() (in module dipy.tracking.learning) determinant() (in module dipy.reconst.dti) deterministic_tracking() (in module dipy.tracking.tracker) deviatoric() (in module dipy.reconst.dti) diff2eigenvectors() (in module dipy.sims.phantom) DiffeomorphicMap (class in dipy.align.imwarp) DiffeomorphicRegistration (class in dipy.align.imwarp) diffusion_components() (in module dipy.reconst.dki_micro) DiffusionKurtosisFit (class in dipy.reconst.dki) DiffusionKurtosisModel (class in dipy.reconst.dki) DiffusionSpectrumDeconvFit (class in dipy.reconst.dsi) DiffusionSpectrumDeconvModel (class in dipy.reconst.dsi) DiffusionSpectrumFit (class in dipy.reconst.dsi) DiffusionSpectrumModel (class in dipy.reconst.dsi) dimensionality_problem_message() (in module dipy.denoise.localpca) dimensions (dipy.io.stateful_tractogram.StatefulTractogram property) dipy module dipy.align module dipy.align._public module dipy.align.cpd module dipy.align.imaffine module dipy.align.imwarp module dipy.align.metrics module dipy.align.reslice module dipy.align.scalespace module dipy.align.streamlinear module dipy.align.streamwarp module dipy.core module dipy.core.geometry module dipy.core.gradients module dipy.core.graph module dipy.core.histeq module dipy.core.ndindex module dipy.core.onetime module dipy.core.optimize module dipy.core.profile module dipy.core.rng module dipy.core.sphere module dipy.core.sphere_stats module dipy.core.subdivide_octahedron module dipy.core.wavelet module dipy.data module dipy.data.fetcher module dipy.denoise module dipy.denoise.adaptive_soft_matching module dipy.denoise.gibbs module dipy.denoise.localpca module dipy.denoise.nlmeans module dipy.denoise.noise_estimate module dipy.denoise.non_local_means module dipy.denoise.patch2self module dipy.direction module dipy.direction.peaks module dipy.io module dipy.io.dpy module dipy.io.gradients module dipy.io.image module dipy.io.peaks module dipy.io.pickles module dipy.io.stateful_tractogram module dipy.io.streamline module dipy.io.surface module dipy.io.utils module dipy.io.vtk module dipy.nn module dipy.nn.tf module dipy.nn.tf.cnn_1d_denoising module dipy.nn.tf.deepn4 module dipy.nn.tf.evac module dipy.nn.tf.histo_resdnn module dipy.nn.tf.model module dipy.nn.tf.synb0 module dipy.nn.torch module dipy.nn.torch.deepn4 module dipy.nn.torch.evac module dipy.nn.torch.histo_resdnn module dipy.nn.utils module dipy.reconst module dipy.reconst.base module dipy.reconst.bingham module dipy.reconst.cache module dipy.reconst.cross_validation module dipy.reconst.csdeconv module dipy.reconst.cti module dipy.reconst.dki module dipy.reconst.dki_micro module dipy.reconst.dsi module dipy.reconst.dti module dipy.reconst.forecast module dipy.reconst.fwdti module dipy.reconst.gqi module

dipy.reconst.ivim module dipy.reconst.mapmri module dipy.reconst.mcsd module dipy.reconst.msdki module dipy.reconst.multi_voxel module dipy.reconst.odf module dipy.reconst.qtdmri module dipy.reconst.qti module dipy.reconst.rumba module dipy.reconst.sfm module dipy.reconst.shm module dipy.reconst.shore module dipy.reconst.utils module dipy.reconst.weights_method module dipy.segment module dipy.segment.bundles module dipy.segment.clustering module dipy.segment.fss module dipy.segment.mask module dipy.segment.metric module dipy.segment.threshold module dipy.segment.tissue module dipy.segment.utils module dipy.sims module dipy.sims.phantom module dipy.sims.voxel module dipy.stats module dipy.stats.analysis module dipy.stats.qc module dipy.stats.sketching module dipy.tracking module dipy.tracking._utils module dipy.tracking.learning module dipy.tracking.life module dipy.tracking.local_tracking module dipy.tracking.mesh module dipy.tracking.metrics module dipy.tracking.streamline module dipy.tracking.tracker module dipy.tracking.utils module dipy.version module dipy.viz module dipy.viz.gmem module dipy.viz.horizon module dipy.viz.horizon.app module dipy.viz.horizon.tab module dipy.viz.horizon.tab.base module dipy.viz.horizon.tab.cluster module dipy.viz.horizon.tab.peak module dipy.viz.horizon.tab.roi module dipy.viz.horizon.tab.slice module dipy.viz.horizon.tab.surface module dipy.viz.horizon.util module dipy.viz.horizon.visualizer module dipy.viz.horizon.visualizer.cluster module dipy.viz.horizon.visualizer.peak module dipy.viz.horizon.visualizer.slice module dipy.viz.horizon.visualizer.surface module dipy.viz.panel module dipy.viz.plotting module dipy.viz.projections module dipy.viz.regtools module dipy.viz.streamline module dipy.workflows module dipy.workflows.align module dipy.workflows.base module dipy.workflows.cli module dipy.workflows.combined_workflow module dipy.workflows.denoise module dipy.workflows.docstring_parser module dipy.workflows.flow_runner module dipy.workflows.io module dipy.workflows.mask module dipy.workflows.multi_io module dipy.workflows.nn module dipy.workflows.reconst module dipy.workflows.segment module dipy.workflows.stats module dipy.workflows.tracking module dipy.workflows.utils module dipy.workflows.viz module dipy.workflows.workflow module directional_diffusion() (in module dipy.reconst.dki) directional_diffusion_variance() (in module dipy.reconst.dki) directional_kurtosis() (in module dipy.reconst.dki) directions (dipy.reconst.dti.TensorFit property) disperse_charges() (in module dipy.core.sphere) disperse_charges_alt() (in module dipy.core.sphere) display_cross_section() (dipy.viz.horizon.visualizer.peak.PeakActor method) display_extent() (dipy.viz.horizon.visualizer.peak.PeakActor method) dist_to_corner() (in module dipy.core.geometry) distance() (dipy.align.imaffine.MutualInformationMetric method) (dipy.align.streamlinear.BundleMinDistanceAsymmetricMetric method) (dipy.align.streamlinear.BundleMinDistanceMatrixMetric method) (dipy.align.streamlinear.BundleMinDistanceMetric method) (dipy.align.streamlinear.BundleSumDistanceMatrixMetric method) (dipy.align.streamlinear.JointBundleMinDistanceMetric method) (dipy.align.streamlinear.StreamlineDistanceMetric method) distance_and_gradient() (dipy.align.imaffine.MutualInformationMetric method) dki_design_matrix() (in module dipy.reconst.utils) dki_prediction() (in module dipy.reconst.dki) dki_signal() (in module dipy.sims.voxel) dkimicro_prediction() (in module dipy.reconst.dki_micro) down() (dipy.core.graph.Graph method) down_short() (dipy.core.graph.Graph method) dpar (dipy.reconst.forecast.ForecastFit property) dperp (dipy.reconst.forecast.ForecastFit property) Dpy (class in dipy.io.dpy) draw_lattice_2d() (in module dipy.viz.regtools) dsi_deconv_voxels() (in module dipy.data) dsi_voxels() (in module dipy.data) dtd_covariance() (in module dipy.reconst.qti) dtype_dict (dipy.io.stateful_tractogram.StatefulTractogram property) dwt3D() (in module dipy.core.wavelet)

E

edges() (dipy.core.sphere.Sphere method) eig_from_lo_tri() (in module dipy.reconst.dti) eigenstats() (in module dipy.core.sphere_stats) elastic_crossvalidation() (in module dipy.reconst.qtdmri) elements (dipy.viz.horizon.tab.base.HorizonTab property) EMMetric (class in dipy.align.metrics) encoder_block() (dipy.nn.torch.deepn4.UNet3D method) EncoderBlock (class in dipy.nn.tf.deepn4) (class in dipy.nn.tf.synb0) endpoint() (in module dipy.tracking.metrics) eof() (dipy.workflows.docstring_parser.Reader method) equatorial_maximum() (in module dipy.reconst.gqi) equatorial_zone_vertices() (in module dipy.reconst.gqi) estimate_f_D_star() (dipy.reconst.ivim.IvimModelTRR method) estimate_linear_fit() (dipy.reconst.ivim.IvimModelTRR method) estimate_response() (in module dipy.reconst.csdeconv) estimate_sigma() (in module dipy.denoise.noise_estimate) Euclidean norm eudx_tracking() (in module dipy.tracking.tracker) Euler angles euler_characteristic_check() (in module dipy.core.sphere)

euler_matrix() (in module dipy.core.geometry) EVACPlus (class in dipy.nn.tf.evac) (class in dipy.nn.torch.evac) EVACPlusFlow (class in dipy.workflows.nn) evals (dipy.reconst.dti.TensorFit property) evaluate() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.tf.model.MultipleLayerPercepton method) (dipy.nn.tf.model.SingleLayerPerceptron method) evaluate_results() (dipy.segment.bundles.RecoBundles method) evecs (dipy.reconst.dti.TensorFit property) evolution (dipy.core.optimize.Optimizer property) expand_fields() (dipy.align.imwarp.DiffeomorphicMap method) expectation() (dipy.align.cpd.DeformableRegistration method) ExponentialIsotropicFit (class in dipy.reconst.sfm) ExponentialIsotropicModel (class in dipy.reconst.sfm) extract_b0() (in module dipy.core.gradients) extract_dwi_shell() (in module dipy.core.gradients) extract_example_tracts() (in module dipy.data.fetcher) ExtractB0Flow (class in dipy.workflows.io) ExtractShellFlow (class in dipy.workflows.io) ExtractVolumeFlow (class in dipy.workflows.io)

F

f (dipy.reconst.fwdti.FreeWaterTensorFit property) f_csf() (dipy.reconst.rumba.RumbaFit method) f_D_star_error() (in module dipy.reconst.ivim) f_D_star_prediction() (in module dipy.reconst.ivim) f_gm() (dipy.reconst.rumba.RumbaFit method) f_iso() (dipy.reconst.rumba.RumbaFit method) f_wm() (dipy.reconst.rumba.RumbaFit method) fa() (dipy.reconst.dti.TensorFit method) (dipy.reconst.qti.QtiFit method) fa_trace_to_lambdas() (in module dipy.reconst.csdeconv) faces() (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) faces_from_sphere_vertices() (in module dipy.core.sphere) FastStreamlineSearch (class in dipy.segment.fss) fd_lobe() (dipy.reconst.bingham.BinghamMetrics method) fd_voxel() (dipy.reconst.bingham.BinghamMetrics method) fetch_30_bundle_atlas_hcp842() (in module dipy.data.fetcher) fetch_bundle_atlas_hcp842() (in module dipy.data.fetcher) fetch_bundle_fa_hcp() (in module dipy.data.fetcher) fetch_bundle_warp_dataset() (in module dipy.data.fetcher) fetch_bundles_2_subjects() (in module dipy.data.fetcher) fetch_cenir_multib() (in module dipy.data.fetcher) fetch_cfin_multib() (in module dipy.data.fetcher) fetch_cti_rat1() (in module dipy.data.fetcher) fetch_data() (in module dipy.data.fetcher) fetch_deepn4_test() (in module dipy.data.fetcher) fetch_deepn4_tf_weights() (in module dipy.data.fetcher) fetch_deepn4_torch_weights() (in module dipy.data.fetcher) fetch_default_weights() (dipy.nn.tf.deepn4.DeepN4 method) (dipy.nn.tf.evac.EVACPlus method) (dipy.nn.tf.histo_resdnn.HistoResDNN method) (dipy.nn.tf.synb0.Synb0 method) (dipy.nn.torch.deepn4.DeepN4 method) (dipy.nn.torch.evac.EVACPlus method) (dipy.nn.torch.histo_resdnn.HistoResDNN method) fetch_DiB_217_lte_pte_ste() (in module dipy.data.fetcher) fetch_DiB_70_lte_pte_ste() (in module dipy.data.fetcher) fetch_disco1_dataset() (in module dipy.data.fetcher) fetch_disco2_dataset() (in module dipy.data.fetcher) fetch_disco3_dataset() (in module dipy.data.fetcher) fetch_disco_dataset() (in module dipy.data.fetcher) fetch_evac_test() (in module dipy.data.fetcher) fetch_evac_tf_weights() (in module dipy.data.fetcher) fetch_evac_torch_weights() (in module dipy.data.fetcher) fetch_file_formats() (in module dipy.data.fetcher) fetch_fury_surface() (in module dipy.data.fetcher) fetch_gold_standard_io() (in module dipy.data.fetcher) fetch_hbn() (in module dipy.data.fetcher) fetch_hcp() (in module dipy.data.fetcher) fetch_isbi2013_2shell() (in module dipy.data.fetcher) fetch_ivim() (in module dipy.data.fetcher) fetch_mni_template() (in module dipy.data.fetcher) fetch_ptt_minimal_dataset() (in module dipy.data.fetcher) fetch_qtdMRI_test_retest_2subjects() (in module dipy.data.fetcher) fetch_qte_lte_pte() (in module dipy.data.fetcher) fetch_resdnn_tf_weights() (in module dipy.data.fetcher) fetch_resdnn_torch_weights() (in module dipy.data.fetcher) fetch_scil_b0() (in module dipy.data.fetcher) fetch_sherbrooke_3shell() (in module dipy.data.fetcher) fetch_stanford_hardi() (in module dipy.data.fetcher) fetch_stanford_labels() (in module dipy.data.fetcher) fetch_stanford_pve_maps() (in module dipy.data.fetcher) fetch_stanford_t1() (in module dipy.data.fetcher) fetch_stanford_tracks() (in module dipy.data.fetcher) fetch_syn_data() (in module dipy.data.fetcher) fetch_synb0_test() (in module dipy.data.fetcher) fetch_synb0_weights() (in module dipy.data.fetcher) fetch_taiwan_ntu_dsi() (in module dipy.data.fetcher) fetch_target_tractogram_hcp() (in module dipy.data.fetcher) fetch_tissue_data() (in module dipy.data.fetcher) FetchFlow (class in dipy.workflows.io) FiberFit (class in dipy.tracking.life) FiberModel (class in dipy.tracking.life) fibonacci_sphere() (in module dipy.core.sphere)

file_existence_check() (dipy.workflows.multi_io.IOIterator method) file_name (dipy.viz.horizon.tab.slice.SlicesTab property) find_closest() (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) find_missing() (in module dipy.align.streamwarp) find_qspace_neighbors() (in module dipy.stats.qc) find_signal_means() (in module dipy.reconst.forecast) fit() (dipy.core.optimize.NonNegativeLeastSquares method) (dipy.core.optimize.SKLearnLinearSolver method) (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.tf.model.MultipleLayerPercepton method) (dipy.nn.tf.model.SingleLayerPerceptron method) (dipy.reconst.base.ReconstModel method) (dipy.reconst.csdeconv.ConstrainedSDTModel method) (dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel method) (dipy.reconst.cti.CorrelationTensorModel method) (dipy.reconst.dki.DiffusionKurtosisModel method) (dipy.reconst.dki_micro.KurtosisMicrostructureModel method) (dipy.reconst.dsi.DiffusionSpectrumDeconvModel method) (dipy.reconst.dsi.DiffusionSpectrumModel method) (dipy.reconst.dti.TensorModel method) (dipy.reconst.forecast.ForecastModel method) (dipy.reconst.fwdti.FreeWaterTensorModel method) (dipy.reconst.gqi.GeneralizedQSamplingModel method) (dipy.reconst.ivim.IvimModelTRR method) (dipy.reconst.ivim.IvimModelVP method) (dipy.reconst.mapmri.MapmriModel method) (dipy.reconst.mcsd.MultiShellDeconvModel method) (dipy.reconst.msdki.MeanDiffusionKurtosisModel method) (dipy.reconst.odf.OdfModel method) (dipy.reconst.qtdmri.QtdmriModel method) (dipy.reconst.qti.QtiModel method) (dipy.reconst.sfm.ExponentialIsotropicModel method) (dipy.reconst.sfm.IsotropicModel method) (dipy.reconst.sfm.SparseFascicleModel method) (dipy.reconst.shm.QballBaseModel method) (dipy.reconst.shore.ShoreModel method) (dipy.tracking.life.FiberModel method) fitted_signal() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) fopt (dipy.core.optimize.Optimizer property) forecast_error_func() (in module dipy.reconst.forecast) forecast_matrix() (in module dipy.reconst.forecast) ForecastFit (class in dipy.reconst.forecast) ForecastModel (class in dipy.reconst.forecast) forward() (dipy.nn.torch.deepn4.UNet3D method) (dipy.nn.torch.evac.Add method) (dipy.nn.torch.evac.Block method) (dipy.nn.torch.evac.ChannelSum method) (dipy.nn.torch.evac.Model method) (dipy.nn.torch.evac.MoveDimLayer method) (dipy.nn.torch.histo_resdnn.DenseModel method) forward_sdeconv_mat() (in module dipy.reconst.shm) forward_sdt_deconv_mat() (in module dipy.reconst.csdeconv) fractional_anisotropy() (dipy.reconst.forecast.ForecastFit method) (in module dipy.reconst.dti) free_iteration() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) FreeWaterTensorFit (class in dipy.reconst.fwdti) FreeWaterTensorModel (class in dipy.reconst.fwdti) frenet_serret() (in module dipy.tracking.metrics) from_21x1_to_6x6() (in module dipy.reconst.qti) from_3x3_to_6x1() (in module dipy.reconst.qti) from_6x1_to_3x3() (in module dipy.reconst.qti) from_6x6_to_21x1() (in module dipy.reconst.qti) from_lower_triangular() (in module dipy.reconst.dti) from_qte_to_cti() (in module dipy.reconst.cti) from_sft() (dipy.io.stateful_tractogram.StatefulTractogram static method) from_sphere() (dipy.core.sphere.HemiSphere class method) fs_lobe() (dipy.reconst.bingham.BinghamMetrics method) fs_voxel() (dipy.reconst.bingham.BinghamMetrics method) fwdti_prediction() (in module dipy.reconst.fwdti)

G

ga() (dipy.reconst.dti.TensorFit method) gaussian_kernel() (in module dipy.align.cpd) gaussian_parallel() (in module dipy.sims.voxel) gaussian_weights() (in module dipy.stats.analysis) gcv_cost_function() (in module dipy.reconst.mapmri) GCV_cost_function() (in module dipy.reconst.qtdmri) gen_dirac() (in module dipy.reconst.shm) gen_PSF() (in module dipy.reconst.dsi) generalized_crossvalidation() (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) generalized_crossvalidation_array() (in module dipy.reconst.mapmri) GeneralizedQSamplingFit (class in dipy.reconst.gqi) GeneralizedQSamplingModel (class in dipy.reconst.gqi) generate_bvecs() (in module dipy.core.gradients) generate_combinations() (in module dipy.tracking.metrics) generate_kernel() (in module dipy.reconst.rumba) generic_tracking() (in module dipy.tracking.tracker) genpca() (in module dipy.denoise.localpca) geodesic_anisotropy() (in module dipy.reconst.dti) get_3shell_gtab() (in module dipy.data) get_affine() (dipy.align.imaffine.AffineMap method) (dipy.align.scalespace.ScaleSpace method) get_affine_inv() (dipy.align.scalespace.ScaleSpace method) get_args_default() (in module dipy.workflows.base) get_backward_field() (dipy.align.imwarp.DiffeomorphicMap method) get_bundle_atlas_hcp842() (in module dipy.data.fetcher) get_bval_indices() (in module dipy.core.gradients) get_clusters() (dipy.segment.clustering.TreeClusterMap method) get_cmap() (in module dipy.data) get_data_per_point_keys() (dipy.io.stateful_tractogram.StatefulTractogram method) get_data_per_streamline_keys() (dipy.io.stateful_tractogram.StatefulTractogram method) get_direction_and_spacings() (in module dipy.align.imwarp) get_domain_shape() (dipy.align.scalespace.ScaleSpace method) get_energy() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) get_expand_factors() (dipy.align.scalespace.ScaleSpace method) get_fetcher_datanames() (dipy.workflows.io.FetchFlow static method) get_file_formats() (in module dipy.data.fetcher) get_fitted_ivim() (dipy.workflows.reconst.ReconstIvimFlow method) get_fitted_tensor() (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) get_flow_args() (dipy.workflows.base.IntrospectiveArgumentParser method) get_fnames() (in module dipy.data.fetcher) get_forward_field() (dipy.align.imwarp.DiffeomorphicMap method) get_gtab_taiwan_dsi() (in module dipy.data) get_image() (dipy.align.scalespace.ScaleSpace method) get_info() (in module dipy) get_io_iterator() (dipy.workflows.workflow.Workflow method) get_isbi2013_2shell_gtab() (in module dipy.data) get_large_clusters() (dipy.segment.clustering.ClusterMap method) get_level() (in module dipy.workflows.flow_runner) get_map() (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) get_metric_name() (dipy.workflows.stats.LinearMixedModelsFlow method) get_optionals() (dipy.workflows.combined_workflow.CombinedWorkflow method) get_reference_info() (in module dipy.io.utils) get_registration_parameters() (dipy.align.cpd.DeformableRegistration method) get_scaling() (dipy.align.scalespace.ScaleSpace method) get_short_name() (dipy.workflows.align.BundleWarpFlow class method) (dipy.workflows.align.ResliceFlow class method) (dipy.workflows.align.SlrWithQbxFlow class method) (dipy.workflows.denoise.GibbsRingingFlow class method) (dipy.workflows.denoise.LPCAFlow class method) (dipy.workflows.denoise.MPPCAFlow class method) (dipy.workflows.denoise.NLMeansFlow class method) (dipy.workflows.denoise.Patch2SelfFlow class method) (dipy.workflows.io.ConcatenateTractogramFlow class method) (dipy.workflows.io.ConvertSHFlow class method) (dipy.workflows.io.ConvertTensorsFlow class method) (dipy.workflows.io.ConvertTractogramFlow class method) (dipy.workflows.io.ExtractB0Flow class method) (dipy.workflows.io.ExtractShellFlow class method) (dipy.workflows.io.ExtractVolumeFlow class method) (dipy.workflows.io.FetchFlow class method) (dipy.workflows.io.IoInfoFlow class method) (dipy.workflows.io.MathFlow class method) (dipy.workflows.io.NiftisToPamFlow class method) (dipy.workflows.io.PamToNiftisFlow class method) (dipy.workflows.io.SplitFlow class method) (dipy.workflows.io.TensorToPamFlow class method) (dipy.workflows.mask.MaskFlow class method) (dipy.workflows.nn.BiasFieldCorrectionFlow class method) (dipy.workflows.nn.EVACPlusFlow class method) (dipy.workflows.reconst.ReconstCSDFlow class method) (dipy.workflows.reconst.ReconstDkiFlow class method) (dipy.workflows.reconst.ReconstDsiFlow class method) (dipy.workflows.reconst.ReconstDtiFlow class method) (dipy.workflows.reconst.ReconstForecastFlow class method) (dipy.workflows.reconst.ReconstGQIFlow class method) (dipy.workflows.reconst.ReconstIvimFlow class method) (dipy.workflows.reconst.ReconstMAPMRIFlow class method) (dipy.workflows.reconst.ReconstQBallBaseFlow class method) (dipy.workflows.reconst.ReconstRUMBAFlow class method) (dipy.workflows.reconst.ReconstSDTFlow class method) (dipy.workflows.reconst.ReconstSFMFlow class method) (dipy.workflows.segment.ClassifyTissueFlow class method) (dipy.workflows.segment.LabelsBundlesFlow class method) (dipy.workflows.segment.MedianOtsuFlow class method) (dipy.workflows.segment.RecoBundlesFlow class method) (dipy.workflows.stats.BundleAnalysisTractometryFlow class method) (dipy.workflows.stats.BundleShapeAnalysis class method) (dipy.workflows.stats.LinearMixedModelsFlow class method) (dipy.workflows.stats.SNRinCCFlow class method) (dipy.workflows.tracking.LocalFiberTrackingPAMFlow class method) (dipy.workflows.tracking.PFTrackingPAMFlow class method) (dipy.workflows.viz.HorizonFlow class method) (dipy.workflows.workflow.Workflow class method)

get_sigmas() (dipy.align.scalespace.ScaleSpace method) get_sim_voxels() (in module dipy.data) get_simplified_transform() (dipy.align.imwarp.DiffeomorphicMap method) get_skeleton() (in module dipy.data) get_small_clusters() (dipy.segment.clustering.ClusterMap method) get_spacing() (dipy.align.scalespace.ScaleSpace method) get_sphere() (in module dipy.data) get_streamlines_copy() (dipy.io.stateful_tractogram.StatefulTractogram method) get_sub_runs() (dipy.workflows.combined_workflow.CombinedWorkflow method) (dipy.workflows.workflow.Workflow method) get_target_tractogram_hcp() (in module dipy.data.fetcher) get_two_hcp842_bundles() (in module dipy.data.fetcher) get_unique_pairs() (in module dipy.align.streamlinear) gfa() (dipy.reconst.shm.SphHarmFit method) (in module dipy.reconst.odf) gibbs_removal() (in module dipy.denoise.gibbs) GibbsRingingFlow (class in dipy.workflows.denoise) Gimbal lock global_opacity (dipy.viz.horizon.visualizer.peak.PeakActor property) GlobalHorizon (class in dipy.viz.gmem) grad_tensor() (in module dipy.tracking.life) gradient() (dipy.align.imaffine.MutualInformationMetric method) (in module dipy.tracking.life) gradient_strength() (dipy.core.gradients.GradientTable method) gradient_table() (in module dipy.core.gradients) gradient_table_from_bvals_bvecs() (in module dipy.core.gradients) gradient_table_from_gradient_strength_bvecs() (in module dipy.core.gradients) gradient_table_from_qvals_bvecs() (in module dipy.core.gradients) GradientTable (class in dipy.core.gradients) Graph (class in dipy.core.graph) groupwise_slr() (in module dipy.align.streamlinear)

H

H() (in module dipy.reconst.qtdmri) half_to_full_qspace() (in module dipy.reconst.dsi) handle_text_overflows() (dipy.viz.horizon.tab.base.TabManager method) handle_vol_idx() (in module dipy.workflows.utils) hanning_filter() (in module dipy.reconst.dsi) hat() (in module dipy.reconst.shm) HemiSphere (class in dipy.core.sphere) high_ranges (dipy.viz.horizon.visualizer.peak.PeakActor property) hindered_ad (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) hindered_evals (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property)

hindered_rd (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) histeq() (in module dipy.core.histeq) HistoResDNN (class in dipy.nn.tf.histo_resdnn) (class in dipy.nn.torch.histo_resdnn) Homogeneous coordinates Horizon (class in dipy.viz.horizon.app) horizon() (in module dipy.viz.horizon.app) HorizonFlow (class in dipy.workflows.viz) HorizonTab (class in dipy.viz.horizon.tab.base) HorizonUIElement (class in dipy.viz.horizon.tab.base)

I

Identity (class in dipy.segment.clustering) idwt3D() (in module dipy.core.wavelet) image_mosaic() (in module dipy.viz.plotting) ImageRegistrationFlow (class in dipy.workflows.align) info (dipy.core.gradients.GradientTable property) init_model() (dipy.nn.torch.evac.EVACPlus method) (in module dipy.nn.tf.evac) initialize_iteration() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) initialize_sigma2() (in module dipy.align.cpd) inside_sphere() (in module dipy.tracking.metrics) inside_sphere_points() (in module dipy.tracking.metrics) intensities_range (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) interpret_matrix() (dipy.align.imwarp.DiffeomorphicMap method) intersect_sphere() (in module dipy.tracking.metrics) IntrospectiveArgumentParser (class in dipy.workflows.base) inverse() (dipy.align.imwarp.DiffeomorphicMap method) io_iterator() (in module dipy.workflows.multi_io) IoInfoFlow (class in dipy.workflows.io) IOIterator (class in dipy.workflows.multi_io) is_bbox_in_vox_valid() (dipy.io.stateful_tractogram.StatefulTractogram method)

is_empty() (dipy.workflows.docstring_parser.Reader method) is_header_compatible() (in module dipy.io.utils) is_hemispherical() (in module dipy.core.geometry) is_leaf (dipy.segment.clustering.TreeCluster property) is_range (dipy.viz.horizon.visualizer.peak.PeakActor property) is_reference_info_valid() (in module dipy.io.utils) iso (dipy.reconst.mcsd.MultiShellResponse property) isotropic() (in module dipy.reconst.dti) isotropic_scale_factor() (in module dipy.reconst.mapmri) IsotropicFit (class in dipy.reconst.sfm) IsotropicModel (class in dipy.reconst.sfm) IsotropicScaleSpace (class in dipy.align.scalespace) iter_fit_tensor() (in module dipy.reconst.dti) iter_preorder() (dipy.segment.clustering.TreeClusterMap method) iterate() (dipy.align.cpd.DeformableRegistration method) iterative_fit() (dipy.reconst.dki.DiffusionKurtosisModel method) iterative_fit_tensor() (in module dipy.reconst.dti) ivim_mix_cost_one() (dipy.reconst.ivim.IvimModelVP method) ivim_model_selector() (in module dipy.reconst.ivim) ivim_prediction() (in module dipy.reconst.ivim) IvimFit (class in dipy.reconst.ivim) IvimModelTRR (class in dipy.reconst.ivim) IvimModelVP (class in dipy.reconst.ivim)

J

JointBundleMinDistanceMetric (class in dipy.align.streamlinear)

JointStreamlineRegistrationMap (class in dipy.align.streamlinear)

K

k2odi() (in module dipy.reconst.bingham) K_aniso (dipy.reconst.cti.CorrelationTensorFit property) k_bulk() (dipy.reconst.qti.QtiFit method) K_iso (dipy.reconst.cti.CorrelationTensorFit property) K_micro (dipy.reconst.cti.CorrelationTensorFit property) k_mu() (dipy.reconst.qti.QtiFit method) k_shear() (dipy.reconst.qti.QtiFit method) K_total() (dipy.reconst.cti.CorrelationTensorFit method) kappa1_lobe() (dipy.reconst.bingham.BinghamMetrics method) kappa2_lobe() (dipy.reconst.bingham.BinghamMetrics method)

kappa_total_lobe() (dipy.reconst.bingham.BinghamMetrics method) kfa (dipy.reconst.dki.DiffusionKurtosisFit property) kfold_xval() (in module dipy.reconst.cross_validation) kmax() (dipy.reconst.dki.DiffusionKurtosisFit method) kt (dipy.reconst.dki.DiffusionKurtosisFit property) kurtosis_element() (in module dipy.sims.voxel) kurtosis_fractional_anisotropy() (in module dipy.reconst.dki) kurtosis_maximum() (in module dipy.reconst.dki) KurtosisMicrostructuralFit (class in dipy.reconst.dki_micro) KurtosisMicrostructureModel (class in dipy.reconst.dki_micro)

L

l1_crossvalidation() (in module dipy.reconst.qtdmri) l_shore() (in module dipy.reconst.shore) LabelsBundlesFlow (class in dipy.workflows.segment) lambert_equal_area_projection_cart() (in module dipy.core.geometry) lambert_equal_area_projection_polar() (in module dipy.core.geometry) lazy_index() (in module dipy.reconst.shm) lb_forecast() (in module dipy.reconst.forecast) lcr_matrix() (in module dipy.reconst.shm) LEcuyer() (in module dipy.core.rng) length() (in module dipy.tracking.metrics) (in module dipy.tracking.utils) lengths (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) LifeSignalMaker (class in dipy.tracking.life) Linear transformation linearity() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) LinearMixedModelsFlow (class in dipy.workflows.stats) linewidth (dipy.viz.horizon.visualizer.peak.PeakActor property) load_dpy() (in module dipy.io.streamline) load_fib() (in module dipy.io.streamline) load_generator() (in module dipy.io.streamline) load_gifti() (in module dipy.io.surface) load_model_weights() (dipy.nn.tf.deepn4.DeepN4 method) (dipy.nn.tf.evac.EVACPlus method) (dipy.nn.tf.histo_resdnn.HistoResDNN method) (dipy.nn.tf.synb0.Synb0 method) (dipy.nn.torch.deepn4.DeepN4 method) (dipy.nn.torch.evac.EVACPlus method) (dipy.nn.torch.histo_resdnn.HistoResDNN method) load_module() (dipy.workflows.io.FetchFlow static method) load_nifti() (in module dipy.io.image)

load_nifti_data() (in module dipy.io.image) load_pam() (in module dipy.io.peaks) load_peaks() (in module dipy.io.peaks) load_pial() (in module dipy.io.surface) load_pickle() (in module dipy.io.pickles) load_polydata() (in module dipy.io.vtk) load_resample() (dipy.nn.tf.deepn4.DeepN4 method) (dipy.nn.torch.deepn4.DeepN4 method) load_sdp_constraints() (in module dipy.data) load_tck() (in module dipy.io.streamline) load_tractogram() (in module dipy.io.streamline) load_trk() (in module dipy.io.streamline) load_trx() (in module dipy.io.streamline) load_vtk() (in module dipy.io.streamline) load_vtk_streamlines() (in module dipy.io.vtk) load_vtp() (in module dipy.io.streamline) load_weights() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) loads_compat() (in module dipy.data) LocalFiberTrackingPAMFlow (class in dipy.workflows.tracking) localpca() (in module dipy.denoise.localpca) LocalTracking (class in dipy.tracking.local_tracking) longest_track_bundle() (in module dipy.tracking.metrics) low_ranges (dipy.viz.horizon.visualizer.peak.PeakActor property) low_rank_eigen() (in module dipy.align.cpd) lower_triangular() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) lower_triangular_to_cholesky() (in module dipy.reconst.fwdti) lowrankQS() (in module dipy.align.cpd) LPCAFlow (class in dipy.workflows.denoise) LR_deconv() (in module dipy.reconst.dsi) ls_fit_cti() (in module dipy.reconst.cti) ls_fit_dki() (in module dipy.reconst.dki)

M

magn() (in module dipy.tracking.metrics) make5d() (in module dipy.io.utils) manage_output_overwrite() (dipy.workflows.workflow.Workflow method) map_laplace_s() (in module dipy.reconst.mapmri) map_laplace_t() (in module dipy.reconst.mapmri) map_laplace_u() (in module dipy.reconst.mapmri) mapmri_coeff (dipy.reconst.mapmri.MapmriFit property) mapmri_index_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_index_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_K_mu_dependent() (in module dipy.reconst.mapmri) mapmri_isotropic_K_mu_independent() (in module dipy.reconst.mapmri) mapmri_isotropic_laplacian_reg_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_laplacian_reg_matrix_from_index_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_M_mu_dependent() (in module dipy.reconst.mapmri) mapmri_isotropic_M_mu_independent() (in module dipy.reconst.mapmri) mapmri_isotropic_odf_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_odf_sh_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_phi_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_psi_matrix() (in module dipy.reconst.mapmri) mapmri_isotropic_radial_pdf_basis() (in module dipy.reconst.mapmri) mapmri_isotropic_radial_signal_basis() (in module dipy.reconst.mapmri) mapmri_laplacian_reg_matrix() (in module dipy.reconst.mapmri) mapmri_mu (dipy.reconst.mapmri.MapmriFit property) mapmri_odf_matrix() (in module dipy.reconst.mapmri) mapmri_phi_1d() (in module dipy.reconst.mapmri) mapmri_phi_matrix() (in module dipy.reconst.mapmri) mapmri_psi_1d() (in module dipy.reconst.mapmri) mapmri_psi_matrix() (in module dipy.reconst.mapmri) mapmri_R (dipy.reconst.mapmri.MapmriFit property) mapmri_STU_reg_matrices() (in module dipy.reconst.mapmri) MapmriFit (class in dipy.reconst.mapmri) MapmriModel (class in dipy.reconst.mapmri) mask_for_response_msmt() (in module dipy.reconst.mcsd) mask_for_response_ssst() (in module dipy.reconst.csdeconv) mask_non_weighted_bvals() (in module dipy.core.gradients) MaskFlow (class in dipy.workflows.mask) MathFlow (class in dipy.workflows.io) matlab_life_results() (in module dipy.data) max (dipy.reconst.shm.CsaOdfModel attribute) max_angle_from_curvature() (in module dipy.tracking.utils) max_centers (dipy.viz.horizon.visualizer.peak.PeakActor property) maximization() (dipy.align.cpd.DeformableRegistration method) mbessel_ratio() (in module dipy.reconst.rumba) md() (dipy.reconst.dti.TensorFit method) (dipy.reconst.qti.QtiFit method) mdf() (in module dipy.segment.metric) mean_curvature() (in module dipy.tracking.metrics) mean_d_sq() (dipy.reconst.qti.QtiFit method) mean_diffusivity() (dipy.reconst.forecast.ForecastFit method) (in module dipy.reconst.dti) mean_euclidean_distance() (in module dipy.segment.metric) mean_kurtosis() (in module dipy.reconst.dki) mean_kurtosis_tensor() (in module dipy.reconst.dki) mean_manhattan_distance() (in module dipy.segment.metric) mean_orientation() (in module dipy.tracking.metrics) mean_signal_bvalue() (in module dipy.reconst.msdki) MeanDiffusionKurtosisFit (class in dipy.reconst.msdki) MeanDiffusionKurtosisModel (class in dipy.reconst.msdki) median_otsu() (in module dipy.segment.mask) MedianOtsuFlow (class in dipy.workflows.segment) message (dipy.core.optimize.Optimizer property) midpoint() (in module dipy.tracking.metrics) midpoint2point() (in module dipy.tracking.metrics) min (dipy.reconst.shm.CsaOdfModel attribute) min_centers (dipy.viz.horizon.visualizer.peak.PeakActor property) min_radius_curvature_from_angle() (in module dipy.tracking.utils) minmax_normalize() (in module dipy.reconst.odf) mirror() (dipy.core.sphere.HemiSphere method) mk() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.qti.QtiFit method) mkt() (dipy.reconst.dki.DiffusionKurtosisFit method) mode() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) Model (class in dipy.nn.torch.evac) module dipy dipy.align dipy.align._public dipy.align.cpd dipy.align.imaffine dipy.align.imwarp dipy.align.metrics dipy.align.reslice dipy.align.scalespace dipy.align.streamlinear dipy.align.streamwarp dipy.core dipy.core.geometry dipy.core.gradients dipy.core.graph dipy.core.histeq dipy.core.ndindex dipy.core.onetime dipy.core.optimize dipy.core.profile dipy.core.rng dipy.core.sphere dipy.core.sphere_stats dipy.core.subdivide_octahedron dipy.core.wavelet dipy.data dipy.data.fetcher dipy.denoise dipy.denoise.adaptive_soft_matching dipy.denoise.gibbs dipy.denoise.localpca dipy.denoise.nlmeans dipy.denoise.noise_estimate dipy.denoise.non_local_means dipy.denoise.patch2self dipy.direction dipy.direction.peaks dipy.io dipy.io.dpy dipy.io.gradients dipy.io.image dipy.io.peaks dipy.io.pickles dipy.io.stateful_tractogram dipy.io.streamline dipy.io.surface dipy.io.utils dipy.io.vtk dipy.nn dipy.nn.tf dipy.nn.tf.cnn_1d_denoising dipy.nn.tf.deepn4 dipy.nn.tf.evac dipy.nn.tf.histo_resdnn dipy.nn.tf.model dipy.nn.tf.synb0 dipy.nn.torch dipy.nn.torch.deepn4 dipy.nn.torch.evac dipy.nn.torch.histo_resdnn dipy.nn.utils dipy.reconst dipy.reconst.base dipy.reconst.bingham dipy.reconst.cache dipy.reconst.cross_validation dipy.reconst.csdeconv dipy.reconst.cti dipy.reconst.dki dipy.reconst.dki_micro dipy.reconst.dsi dipy.reconst.dti dipy.reconst.forecast dipy.reconst.fwdti dipy.reconst.gqi dipy.reconst.ivim dipy.reconst.mapmri dipy.reconst.mcsd dipy.reconst.msdki dipy.reconst.multi_voxel dipy.reconst.odf dipy.reconst.qtdmri dipy.reconst.qti dipy.reconst.rumba dipy.reconst.sfm dipy.reconst.shm dipy.reconst.shore dipy.reconst.utils dipy.reconst.weights_method dipy.segment dipy.segment.bundles dipy.segment.clustering dipy.segment.fss dipy.segment.mask dipy.segment.metric dipy.segment.threshold dipy.segment.tissue dipy.segment.utils dipy.sims dipy.sims.phantom dipy.sims.voxel dipy.stats dipy.stats.analysis dipy.stats.qc dipy.stats.sketching dipy.tracking dipy.tracking._utils dipy.tracking.learning dipy.tracking.life dipy.tracking.local_tracking dipy.tracking.mesh dipy.tracking.metrics dipy.tracking.streamline dipy.tracking.tracker dipy.tracking.utils dipy.version dipy.viz dipy.viz.gmem dipy.viz.horizon dipy.viz.horizon.app dipy.viz.horizon.tab dipy.viz.horizon.tab.base dipy.viz.horizon.tab.cluster dipy.viz.horizon.tab.peak dipy.viz.horizon.tab.roi dipy.viz.horizon.tab.slice dipy.viz.horizon.tab.surface dipy.viz.horizon.util dipy.viz.horizon.visualizer dipy.viz.horizon.visualizer.cluster dipy.viz.horizon.visualizer.peak dipy.viz.horizon.visualizer.slice dipy.viz.horizon.visualizer.surface dipy.viz.panel dipy.viz.plotting dipy.viz.projections dipy.viz.regtools dipy.viz.streamline dipy.workflows dipy.workflows.align dipy.workflows.base dipy.workflows.cli dipy.workflows.combined_workflow dipy.workflows.denoise dipy.workflows.docstring_parser dipy.workflows.flow_runner dipy.workflows.io dipy.workflows.mask dipy.workflows.multi_io dipy.workflows.nn dipy.workflows.reconst dipy.workflows.segment dipy.workflows.stats dipy.workflows.tracking dipy.workflows.utils dipy.workflows.viz dipy.workflows.workflow

motion_correction() (in module dipy.align._public) MotionCorrectionFlow (class in dipy.workflows.align) MoveDimLayer (class in dipy.nn.torch.evac) mppca() (in module dipy.denoise.localpca) MPPCAFlow (class in dipy.workflows.denoise) mrtrix_spherical_functions() (in module dipy.data) msd() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) msd_discrete() (dipy.reconst.dsi.DiffusionSpectrumFit method) MSDeconvFit (class in dipy.reconst.mcsd) msdki_prediction() (in module dipy.reconst.msdki) msk() (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) msk_from_awf() (in module dipy.reconst.msdki) mult_aff() (in module dipy.align.imwarp) multi_fit() (dipy.reconst.dki.DiffusionKurtosisModel method) multi_gaussian_k_from_c() (in module dipy.reconst.cti) multi_median() (in module dipy.segment.mask) multi_shell_fiber_response() (in module dipy.reconst.mcsd) multi_tensor() (in module dipy.sims.voxel) multi_tensor_dki() (in module dipy.sims.voxel) multi_tensor_msd() (in module dipy.sims.voxel) multi_tensor_odf() (in module dipy.sims.voxel) multi_tensor_pdf() (in module dipy.sims.voxel) multi_tensor_rtop() (in module dipy.sims.voxel) multi_tissue_basis() (in module dipy.reconst.mcsd) multi_voxel_fit() (in module dipy.reconst.multi_voxel) MultipleLayerPercepton (class in dipy.nn.tf.model) MultiShellDeconvModel (class in dipy.reconst.mcsd) MultiShellResponse (class in dipy.reconst.mcsd) MultiVoxelFit (class in dipy.reconst.multi_voxel) MutualInformationMetric (class in dipy.align.imaffine)

N

n_shore() (in module dipy.reconst.shore) name (dipy.viz.horizon.tab.base.HorizonTab property) (dipy.viz.horizon.tab.cluster.ClustersTab property) (dipy.viz.horizon.tab.peak.PeaksTab property) (dipy.viz.horizon.tab.roi.ROIsTab property) (dipy.viz.horizon.tab.slice.SlicesTab property) (dipy.viz.horizon.tab.surface.SurfaceTab property) nbytes() (in module dipy.tracking.streamline) ndbincount() (in module dipy.tracking.utils) ndindex() (in module dipy.core.ndindex) near_roi() (in module dipy.tracking.utils) nearest_from_matrix_col() (in module dipy.segment.fss) nearest_from_matrix_row() (in module dipy.segment.fss) nearest_pos_semi_def() (in module dipy.core.geometry) neighboring_dwi_correlation() (in module dipy.stats.qc) nfev (dipy.core.optimize.Optimizer property) ng() (dipy.reconst.mapmri.MapmriFit method) ng_parallel() (dipy.reconst.mapmri.MapmriFit method) ng_perpendicular() (dipy.reconst.mapmri.MapmriFit method) NIFTI (dipy.io.stateful_tractogram.Origin attribute) nifti1_symmat() (in module dipy.io.utils)

niftis_to_pam() (in module dipy.io.peaks) NiftisToPamFlow (class in dipy.workflows.io) nit (dipy.core.optimize.Optimizer property) nlls_cost() (dipy.reconst.ivim.IvimModelVP method) nlls_fit_tensor() (in module dipy.reconst.dti) nlmeans() (in module dipy.denoise.nlmeans) NLMeansFlow (class in dipy.workflows.denoise) nls_fit_tensor() (in module dipy.reconst.fwdti) nls_iter() (in module dipy.reconst.fwdti) non_local_means() (in module dipy.denoise.non_local_means) none_or_dtype() (in module dipy.workflows.base) NonNegativeLeastSquares (class in dipy.core.optimize) norm() (in module dipy.reconst.dti) norm_of_laplacian_signal() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) normalize() (in module dipy.nn.utils) normalize_data() (in module dipy.reconst.shm) normalize_qa() (in module dipy.reconst.gqi) normalized_vector() (in module dipy.core.geometry) npa() (in module dipy.reconst.gqi) NumpyDocString (class in dipy.workflows.docstring_parser)

O

obj (dipy.viz.horizon.tab.base.HorizonUIElement attribute) odf() (dipy.reconst.bingham.BinghamMetrics method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.forecast.ForecastFit method) (dipy.reconst.gqi.GeneralizedQSamplingFit method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.odf.OdfFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.rumba.RumbaFit method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.shm.SphHarmFit method) (dipy.reconst.shore.ShoreFit method) odf_deconv() (in module dipy.reconst.csdeconv) odf_sh() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) odf_sh_to_sharp() (in module dipy.reconst.csdeconv) odf_sum() (in module dipy.reconst.gqi) OdfFit (class in dipy.reconst.odf) OdfModel (class in dipy.reconst.odf) odi1_lobe() (dipy.reconst.bingham.BinghamMetrics method) odi1_voxel() (dipy.reconst.bingham.BinghamMetrics method) odi2_lobe() (dipy.reconst.bingham.BinghamMetrics method) odi2_voxel() (dipy.reconst.bingham.BinghamMetrics method) odi2k() (in module dipy.reconst.bingham) odi_total_lobe() (dipy.reconst.bingham.BinghamMetrics method)

odi_total_voxel() (dipy.reconst.bingham.BinghamMetrics method) ols_fit_tensor() (in module dipy.reconst.dti) on_sphere() (dipy.reconst.csdeconv.AxSymShResponse method) on_tab_selected() (dipy.viz.horizon.tab.base.HorizonTab method) (dipy.viz.horizon.tab.peak.PeaksTab method) (dipy.viz.horizon.tab.slice.SlicesTab method) OneTimeProperty (class in dipy.core.onetime) OpdtModel (class in dipy.reconst.shm) optimize() (dipy.align.imaffine.AffineRegistration method) (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) (dipy.align.streamlinear.StreamlineLinearRegistration method) Optimizer (class in dipy.core.optimize) optional_parameters (dipy.workflows.base.IntrospectiveArgumentParser property) orbital_phantom() (in module dipy.sims.phantom) order_from_ncoef() (in module dipy.reconst.shm) orient_by_rois() (in module dipy.tracking.streamline) orient_by_streamline() (in module dipy.tracking.streamline) orientation_from_string() (in module dipy.core.gradients) orientation_to_string() (in module dipy.core.gradients) Origin (class in dipy.io.stateful_tractogram) origin (dipy.io.stateful_tractogram.StatefulTractogram property) ornt_mapping() (in module dipy.core.gradients) otsu() (in module dipy.segment.threshold) output_parameters (dipy.workflows.base.IntrospectiveArgumentParser property) overlay_images() (in module dipy.viz.regtools) overlay_slices() (in module dipy.viz.regtools)

P

pad() (dipy.nn.tf.deepn4.DeepN4 method) (dipy.nn.torch.deepn4.DeepN4 method) pad_crop() (in module dipy.nn.utils) pam_to_niftis() (in module dipy.io.peaks) PamToNiftisFlow (class in dipy.workflows.io) params_to_btens() (in module dipy.core.gradients) params_to_cti_params() (in module dipy.reconst.cti) params_to_dki_params() (in module dipy.reconst.dki) parents() (dipy.core.graph.Graph method) part1_reg_matrix_tau() (in module dipy.reconst.qtdmri) part23_iso_reg_matrix_q() (in module dipy.reconst.qtdmri) part23_reg_matrix_q() (in module dipy.reconst.qtdmri) part23_reg_matrix_tau() (in module dipy.reconst.qtdmri) part4_iso_reg_matrix_q() (in module dipy.reconst.qtdmri) part4_reg_matrix_q() (in module dipy.reconst.qtdmri) part4_reg_matrix_tau() (in module dipy.reconst.qtdmri) ParticleFilteringTracking (class in dipy.tracking.local_tracking) patch2self() (in module dipy.denoise.patch2self) Patch2SelfFlow (class in dipy.workflows.denoise) patch_maximum() (in module dipy.reconst.gqi) patch_sum() (in module dipy.reconst.gqi) patch_vertices() (in module dipy.reconst.gqi) path_length() (in module dipy.tracking.utils) pdf() (dipy.reconst.dsi.DiffusionSpectrumDeconvFit method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) pdf_grid() (dipy.reconst.shore.ShoreFit method) pdf_interp_coords() (in module dipy.reconst.dsi) pdf_odf() (in module dipy.reconst.dsi) peak() (in module dipy.viz.horizon.visualizer.peak) peak_directions_nl() (in module dipy.direction.peaks) peak_values() (in module dipy.stats.analysis) PeakActor (class in dipy.viz.horizon.visualizer.peak) peaks_from_model() (in module dipy.direction.peaks) peaks_from_positions() (in module dipy.direction.peaks) peaks_to_niftis() (in module dipy.io.peaks) PeaksAndMetrics (class in dipy.direction.peaks) PeaksTab (class in dipy.viz.horizon.tab.peak) PeaksVisualizer (class in dipy.viz.horizon.visualizer.peak) peek() (dipy.workflows.docstring_parser.Reader method) perfusion_fraction (dipy.reconst.ivim.IvimFit property) permutationinverse() (in module dipy.core.wavelet) perpendicular_directions() (in module dipy.core.geometry) pft_tracking() (in module dipy.tracking.tracker) PFTrackingPAMFlow (class in dipy.workflows.tracking) phi() (dipy.reconst.ivim.IvimModelVP method) piesno() (in module dipy.denoise.noise_estimate) planarity() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) plot_2d_diffeomorphic_map() (in module dipy.viz.regtools) plot_slices() (in module dipy.viz.regtools) polar_zone_vertices() (in module dipy.reconst.gqi)

position (dipy.viz.horizon.tab.base.HorizonUIElement attribute) positional_parameters (dipy.workflows.base.IntrospectiveArgumentParser property) PositiveDefiniteLeastSquares (class in dipy.core.optimize) predict() (dipy.core.optimize.SKLearnLinearSolver method) (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.tf.deepn4.DeepN4 method) (dipy.nn.tf.evac.EVACPlus method) (dipy.nn.tf.histo_resdnn.HistoResDNN method) (dipy.nn.tf.model.MultipleLayerPercepton method) (dipy.nn.tf.model.SingleLayerPerceptron method) (dipy.nn.tf.synb0.Synb0 method) (dipy.nn.torch.deepn4.DeepN4 method) (dipy.nn.torch.evac.EVACPlus method) (dipy.nn.torch.histo_resdnn.HistoResDNN method) (dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel method) (dipy.reconst.cti.CorrelationTensorFit method) (dipy.reconst.cti.CorrelationTensorModel method) (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki.DiffusionKurtosisModel method) (dipy.reconst.dki_micro.KurtosisMicrostructuralFit method) (dipy.reconst.dki_micro.KurtosisMicrostructureModel method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.dti.TensorModel method) (dipy.reconst.forecast.ForecastFit method) (dipy.reconst.fwdti.FreeWaterTensorFit method) (dipy.reconst.fwdti.FreeWaterTensorModel method) (dipy.reconst.ivim.IvimFit method) (dipy.reconst.ivim.IvimModelTRR method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.mcsd.MultiShellDeconvModel method) (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) (dipy.reconst.msdki.MeanDiffusionKurtosisModel method) (dipy.reconst.multi_voxel.MultiVoxelFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.qti.QtiFit method) (dipy.reconst.qti.QtiModel method) (dipy.reconst.rumba.RumbaFit method) (dipy.reconst.sfm.ExponentialIsotropicFit method) (dipy.reconst.sfm.IsotropicFit method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.shm.SphHarmFit method) (dipy.tracking.life.FiberFit method) prepare_img() (in module dipy.nn.tf.evac) (in module dipy.nn.torch.evac) principal_components() (in module dipy.tracking.metrics) print_level() (dipy.align.scalespace.ScaleSpace method) print_stats() (dipy.core.profile.Profiler method) print_summary() (dipy.core.optimize.Optimizer method) probabilistic_tracking() (in module dipy.tracking.tracker) Profiler (class in dipy.core.profile) progressive_slr() (in module dipy.align.streamlinear) project_hemisph_bvecs() (in module dipy.reconst.dsi) psi_l() (in module dipy.reconst.forecast) ptt_tracking() (in module dipy.tracking.tracker)

Q

QballBaseModel (class in dipy.reconst.shm) QballModel (class in dipy.reconst.shm) qbx_and_merge() (in module dipy.segment.clustering) qiv() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) QpFitter (class in dipy.reconst.mcsd) qtdmri_anisotropic_scaling() (in module dipy.reconst.qtdmri) qtdmri_eap_matrix() (in module dipy.reconst.qtdmri) qtdmri_index_matrix() (in module dipy.reconst.qtdmri) qtdmri_isotropic_eap_matrix() (in module dipy.reconst.qtdmri) qtdmri_isotropic_index_matrix() (in module dipy.reconst.qtdmri) qtdmri_isotropic_laplacian_reg_matrix() (in module dipy.reconst.qtdmri) qtdmri_isotropic_scaling() (in module dipy.reconst.qtdmri) qtdmri_isotropic_signal_matrix() (in module dipy.reconst.qtdmri) qtdmri_isotropic_to_mapmri_matrix() (in module dipy.reconst.qtdmri) qtdmri_laplacian_reg_matrix() (in module dipy.reconst.qtdmri) qtdmri_mapmri_isotropic_normalization() (in module dipy.reconst.qtdmri)

qtdmri_mapmri_normalization() (in module dipy.reconst.qtdmri) qtdmri_number_of_coefficients() (in module dipy.reconst.qtdmri) qtdmri_signal_matrix() (in module dipy.reconst.qtdmri) qtdmri_temporal_normalization() (in module dipy.reconst.qtdmri) qtdmri_to_mapmri_coef() (dipy.reconst.qtdmri.QtdmriFit method) qtdmri_to_mapmri_matrix() (in module dipy.reconst.qtdmri) QtdmriFit (class in dipy.reconst.qtdmri) QtdmriModel (class in dipy.reconst.qtdmri) qti_signal() (in module dipy.reconst.qti) QtiFit (class in dipy.reconst.qti) QtiModel (class in dipy.reconst.qti) quadratic_form (dipy.reconst.dti.TensorFit property) quantize_evecs() (in module dipy.reconst.dti) Quaternion QuickBundles (class in dipy.segment.clustering) QuickBundlesX (class in dipy.segment.clustering) qvals() (dipy.core.gradients.GradientTable method)

R

radial_basis_EAP_opt() (in module dipy.reconst.qtdmri) radial_basis_opt() (in module dipy.reconst.qtdmri) radial_diffusivity() (in module dipy.reconst.dti) radial_kurtosis() (in module dipy.reconst.dki) radial_tensor_kurtosis() (in module dipy.reconst.dki) radius_search() (dipy.segment.fss.FastStreamlineSearch method) random_coordinates_from_surface() (in module dipy.tracking.mesh) random_seeds_from_mask() (in module dipy.tracking.utils) random_uniform_on_sphere() (in module dipy.core.sphere_stats) RASMM (dipy.io.stateful_tractogram.Space attribute) rd() (dipy.reconst.dti.TensorFit method) read() (dipy.workflows.docstring_parser.Reader method) read_bundles_2_subjects() (in module dipy.data.fetcher) read_bvals_bvecs() (in module dipy.io.gradients) read_cenir_multib() (in module dipy.data.fetcher) read_cfin_dwi() (in module dipy.data.fetcher) read_cfin_t1() (in module dipy.data.fetcher) read_DiB_217_lte_pte_ste() (in module dipy.data.fetcher) read_DiB_70_lte_pte_ste() (in module dipy.data.fetcher) read_five_af_bundles() (in module dipy.data.fetcher) read_img_arr_or_path() (in module dipy.io.utils) read_isbi2013_2shell() (in module dipy.data.fetcher) read_ivim() (in module dipy.data.fetcher) read_mapping() (in module dipy.align._public) read_mni_template() (in module dipy.data.fetcher) read_qtdMRI_test_retest_2subjects() (in module dipy.data.fetcher) read_qte_lte_pte() (in module dipy.data.fetcher) read_scil_b0() (in module dipy.data.fetcher) read_sherbrooke_3shell() (in module dipy.data.fetcher) read_siemens_scil_b0() (in module dipy.data.fetcher) read_stanford_hardi() (in module dipy.data.fetcher) read_stanford_labels() (in module dipy.data.fetcher) read_stanford_pve_maps() (in module dipy.data.fetcher) read_stanford_t1() (in module dipy.data.fetcher) read_syn_data() (in module dipy.data.fetcher) read_taiwan_ntu_dsi() (in module dipy.data.fetcher) read_tissue_data() (in module dipy.data.fetcher) read_to_condition() (dipy.workflows.docstring_parser.Reader method) read_to_next_empty_line() (dipy.workflows.docstring_parser.Reader method) read_to_next_unindented_line() (dipy.workflows.docstring_parser.Reader method) read_track() (dipy.io.dpy.Dpy method) read_tracks() (dipy.io.dpy.Dpy method) read_tracksi() (dipy.io.dpy.Dpy method) Reader (class in dipy.workflows.docstring_parser) real_sh_descoteaux() (in module dipy.reconst.shm) real_sh_descoteaux_from_index() (in module dipy.reconst.shm) real_sh_tournier() (in module dipy.reconst.shm) real_sh_tournier_from_index() (in module dipy.reconst.shm) real_sph_harm() (in module dipy.reconst.shm) real_sym_sh_basis() (in module dipy.reconst.shm) real_sym_sh_mrtrix() (in module dipy.reconst.shm) recluster_tractograms() (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer method) RecoBundles (class in dipy.segment.bundles) RecoBundlesFlow (class in dipy.workflows.segment) recognize() (dipy.segment.bundles.RecoBundles method) ReconstCSDFlow (class in dipy.workflows.reconst) ReconstDkiFlow (class in dipy.workflows.reconst) ReconstDsiFlow (class in dipy.workflows.reconst) ReconstDtiFlow (class in dipy.workflows.reconst) ReconstFit (class in dipy.reconst.base) ReconstForecastFlow (class in dipy.workflows.reconst) ReconstGQIFlow (class in dipy.workflows.reconst) ReconstIvimFlow (class in dipy.workflows.reconst) ReconstMAPMRIFlow (class in dipy.workflows.reconst) ReconstModel (class in dipy.reconst.base) ReconstQBallBaseFlow (class in dipy.workflows.reconst) ReconstRUMBAFlow (class in dipy.workflows.reconst) ReconstSDTFlow (class in dipy.workflows.reconst) ReconstSFMFlow (class in dipy.workflows.reconst) recover_img() (in module dipy.nn.utils) recursive_response() (in module dipy.reconst.csdeconv) reduce_labels() (in module dipy.tracking.utils) reduce_rois() (in module dipy.tracking.utils) refdata (dipy.segment.clustering.ClusterMap property) (dipy.segment.clustering.TreeClusterMap property) refine() (dipy.segment.bundles.RecoBundles method) Reflection register() (dipy.align.cpd.DeformableRegistration method) register_dwi_series() (in module dipy.align._public) register_dwi_to_template() (in module dipy.align._public) register_picker_callback() (dipy.viz.horizon.visualizer.slice.SlicesVisualizer method) register_series() (in module dipy.align._public) relist_streamlines() (in module dipy.tracking.streamline) remove_cluster() (dipy.segment.clustering.ClusterMap method) remove_clusters_by_size() (in module dipy.align.streamlinear) remove_holes_and_islands() (in module dipy.segment.utils) remove_invalid_streamlines() (dipy.io.stateful_tractogram.StatefulTractogram method) reorient_bvecs() (in module dipy.core.gradients) reorient_on_axis() (in module dipy.core.gradients) reorient_vectors() (in module dipy.core.gradients) reposition() (dipy.viz.horizon.tab.base.TabManager method) resample() (in module dipy.align._public) reset() (dipy.core.onetime.ResetMixin method) (dipy.workflows.docstring_parser.Reader method)

ResetMixin (class in dipy.core.onetime) reshape_peaks_for_visualization() (in module dipy.direction.peaks) ResidualBootstrapWrapper (class in dipy.reconst.shm) reslice() (in module dipy.align.reslice) ResliceFlow (class in dipy.workflows.align) response_from_mask_msmt() (in module dipy.reconst.mcsd) response_from_mask_ssst() (in module dipy.reconst.csdeconv) restore_fit_tensor() (in module dipy.reconst.dti) restricted_evals (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) return_indices() (dipy.segment.clustering.TreeCluster method) rgb (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) rho_matrix() (in module dipy.reconst.forecast) rigid() (in module dipy.align._public) rigid_isoscaling() (in module dipy.align._public) rigid_scaling() (in module dipy.align._public) rk() (dipy.reconst.dki.DiffusionKurtosisFit method) robust_fit_tensor_nlls() (in module dipy.reconst.dti) robust_fit_tensor_wls() (in module dipy.reconst.dti) rodrigues_axis_rotation() (in module dipy.core.geometry) ROIsTab (class in dipy.viz.horizon.tab.roi) Rotation matrix Rotation vector round_bvals() (in module dipy.core.gradients) rtap() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) rtk() (dipy.reconst.dki.DiffusionKurtosisFit method) rtop() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) rtop_pdf() (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.shore.ShoreFit method) rtop_signal() (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.shore.ShoreFit method) rtpp() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) rumba_deconv() (in module dipy.reconst.rumba) rumba_deconv_global() (in module dipy.reconst.rumba) RumbaFit (class in dipy.reconst.rumba) RumbaSDModel (class in dipy.reconst.rumba) run() (dipy.workflows.align.ApplyTransformFlow method) (dipy.workflows.align.BundleWarpFlow method) (dipy.workflows.align.ImageRegistrationFlow method) (dipy.workflows.align.MotionCorrectionFlow method) (dipy.workflows.align.ResliceFlow method) (dipy.workflows.align.SlrWithQbxFlow method) (dipy.workflows.align.SynRegistrationFlow method) (dipy.workflows.denoise.GibbsRingingFlow method) (dipy.workflows.denoise.LPCAFlow method) (dipy.workflows.denoise.MPPCAFlow method) (dipy.workflows.denoise.NLMeansFlow method) (dipy.workflows.denoise.Patch2SelfFlow method) (dipy.workflows.io.ConcatenateTractogramFlow method) (dipy.workflows.io.ConvertSHFlow method) (dipy.workflows.io.ConvertTensorsFlow method) (dipy.workflows.io.ConvertTractogramFlow method) (dipy.workflows.io.ExtractB0Flow method) (dipy.workflows.io.ExtractShellFlow method) (dipy.workflows.io.ExtractVolumeFlow method) (dipy.workflows.io.FetchFlow method) (dipy.workflows.io.IoInfoFlow method) (dipy.workflows.io.MathFlow method) (dipy.workflows.io.NiftisToPamFlow method) (dipy.workflows.io.PamToNiftisFlow method) (dipy.workflows.io.SplitFlow method) (dipy.workflows.io.TensorToPamFlow method) (dipy.workflows.mask.MaskFlow method) (dipy.workflows.nn.BiasFieldCorrectionFlow method) (dipy.workflows.nn.EVACPlusFlow method) (dipy.workflows.reconst.ReconstCSDFlow method) (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDsiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) (dipy.workflows.reconst.ReconstForecastFlow method) (dipy.workflows.reconst.ReconstGQIFlow method) (dipy.workflows.reconst.ReconstIvimFlow method) (dipy.workflows.reconst.ReconstMAPMRIFlow method) (dipy.workflows.reconst.ReconstQBallBaseFlow method) (dipy.workflows.reconst.ReconstRUMBAFlow method) (dipy.workflows.reconst.ReconstSDTFlow method) (dipy.workflows.reconst.ReconstSFMFlow method) (dipy.workflows.segment.ClassifyTissueFlow method) (dipy.workflows.segment.LabelsBundlesFlow method) (dipy.workflows.segment.MedianOtsuFlow method) (dipy.workflows.segment.RecoBundlesFlow method) (dipy.workflows.stats.BundleAnalysisTractometryFlow method) (dipy.workflows.stats.BundleShapeAnalysis method) (dipy.workflows.stats.LinearMixedModelsFlow method) (dipy.workflows.stats.SNRinCCFlow method) (dipy.workflows.tracking.LocalFiberTrackingPAMFlow method) (dipy.workflows.tracking.PFTrackingPAMFlow method) (dipy.workflows.viz.HorizonFlow method) (dipy.workflows.workflow.Workflow method) (in module dipy.workflows.cli) run_flow() (in module dipy.workflows.flow_runner) run_sub_flow() (dipy.workflows.combined_workflow.CombinedWorkflow method)

S

S0_hat (dipy.reconst.dti.TensorFit property) (dipy.reconst.msdki.MeanDiffusionKurtosisFit property) S0_hat() (dipy.reconst.qti.QtiFit method) S0_predicted (dipy.reconst.ivim.IvimFit property) sampling_matrix() (dipy.reconst.shm.SphHarmModel method) save_buan_profiles_hdf5() (in module dipy.io.utils) save_dpy() (in module dipy.io.streamline) save_fib() (in module dipy.io.streamline) save_generator() (in module dipy.io.streamline) save_lmm_plot() (dipy.workflows.stats.LinearMixedModelsFlow method) save_nifti() (in module dipy.io.image) save_pam() (in module dipy.io.peaks) save_peaks() (in module dipy.io.peaks) save_pickle() (in module dipy.io.pickles) save_polydata() (in module dipy.io.vtk) save_qa_metric() (in module dipy.io.image) save_tck() (in module dipy.io.streamline) save_tractogram() (in module dipy.io.streamline) save_trk() (in module dipy.io.streamline) save_trx() (in module dipy.io.streamline) save_vtk() (in module dipy.io.streamline) save_vtk_streamlines() (in module dipy.io.vtk) save_vtp() (in module dipy.io.streamline) save_weights() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) ScaleSpace (class in dipy.align.scalespace) seeds_directions_pairs() (in module dipy.tracking.utils) seeds_from_mask() (in module dipy.tracking.utils) seeds_from_surface_coordinates() (in module dipy.tracking.mesh) seek_next_non_empty_line() (dipy.workflows.docstring_parser.Reader method) segment_from_cfa() (in module dipy.segment.mask) select_by_rois() (in module dipy.tracking.streamline) select_random_set_of_streamlines() (in module dipy.tracking.streamline) selected_slices (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) selected_value (dipy.viz.horizon.tab.base.HorizonUIElement attribute) set_affine() (dipy.align.imaffine.AffineMap method) set_inputs() (dipy.workflows.multi_io.IOIterator method) set_level_iters() (dipy.align.imwarp.DiffeomorphicRegistration method) set_levels_above() (dipy.align.metrics.SimilarityMetric method) set_levels_below() (dipy.align.metrics.SimilarityMetric method) set_moving_image() (dipy.align.metrics.SimilarityMetric method) set_out_dir() (dipy.workflows.multi_io.IOIterator method) set_out_fnames() (dipy.workflows.multi_io.IOIterator method) set_output_keys() (dipy.workflows.multi_io.IOIterator method) set_static_image() (dipy.align.metrics.SimilarityMetric method) set_sub_flows_optionals() (dipy.workflows.combined_workflow.CombinedWorkflow method) setup() (dipy.align.imaffine.MutualInformationMetric method) (dipy.align.streamlinear.BundleMinDistanceMatrixMetric method) (dipy.align.streamlinear.BundleMinDistanceMetric method) (dipy.align.streamlinear.JointBundleMinDistanceMetric method) (dipy.align.streamlinear.StreamlineDistanceMetric method) (dipy.tracking.life.FiberModel method) sf_to_bingham() (in module dipy.reconst.bingham) sf_to_sh() (in module dipy.reconst.shm) sfb3D() (in module dipy.core.wavelet) sfb3D_A() (in module dipy.core.wavelet) sfm_design_matrix() (in module dipy.reconst.sfm) sh_coeff (dipy.reconst.forecast.ForecastFit property) sh_to_bingham() (in module dipy.reconst.bingham) sh_to_rh() (in module dipy.reconst.shm) sh_to_sf() (in module dipy.reconst.shm) sh_to_sf_matrix() (in module dipy.reconst.shm) shallow_copy() (dipy.align.imwarp.DiffeomorphicMap method) shape (dipy.reconst.dti.TensorFit property) (dipy.reconst.ivim.IvimFit property) (dipy.reconst.multi_voxel.MultiVoxelFit property) (dipy.reconst.shm.SphHarmFit property) Shear matrix shm_coeff (dipy.reconst.mcsd.MSDeconvFit property) (dipy.reconst.shm.SphHarmFit property) shore_coeff (dipy.reconst.shore.ShoreFit property) shore_indices() (in module dipy.reconst.shore) shore_matrix() (in module dipy.reconst.shore) shore_matrix_odf() (in module dipy.reconst.shore) shore_matrix_pdf() (in module dipy.reconst.shore) shore_order() (in module dipy.reconst.shore) ShoreFit (class in dipy.reconst.shore) ShoreModel (class in dipy.reconst.shore) shortest_path() (dipy.core.graph.Graph method) show_argument() (dipy.workflows.base.IntrospectiveArgumentParser method) show_bundles() (in module dipy.viz.streamline) show_ellipsis() (in module dipy.viz.horizon.util)

SimilarityMetric (class in dipy.align.metrics) simple_cutoff() (in module dipy.reconst.weights_method) simple_plot() (in module dipy.viz.regtools) single_tensor() (in module dipy.sims.voxel) single_tensor_msd() (in module dipy.sims.voxel) single_tensor_odf() (in module dipy.sims.voxel) single_tensor_pdf() (in module dipy.sims.voxel) single_tensor_rtop() (in module dipy.sims.voxel) SingleLayerPerceptron (class in dipy.nn.tf.model) size (dipy.viz.horizon.tab.base.HorizonUIElement attribute) size() (dipy.segment.clustering.ClusterMap method) sizes (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) SKLearnLinearSolver (class in dipy.core.optimize) slash_to_under() (in module dipy.workflows.multi_io) slice_actors (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) slicer_panel() (in module dipy.viz.panel) SlicesTab (class in dipy.viz.horizon.tab.slice) SlicesVisualizer (class in dipy.viz.horizon.visualizer.slice) slr_with_qbx() (in module dipy.align.streamlinear) SlrWithQbxFlow (class in dipy.workflows.align) smooth_pinv() (in module dipy.reconst.shm) smt2di() (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) smt2f() (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) smt2uFA() (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) SNRinCCFlow (class in dipy.workflows.stats) solve() (dipy.core.optimize.PositiveDefiniteLeastSquares method) solve_qp() (in module dipy.reconst.mcsd) Space (class in dipy.io.stateful_tractogram) space (dipy.io.stateful_tractogram.StatefulTractogram property) space_attributes (dipy.io.stateful_tractogram.StatefulTractogram property) sparse_nnls() (in module dipy.core.optimize) SparseFascicleFit (class in dipy.reconst.sfm) SparseFascicleModel (class in dipy.reconst.sfm) sparsity_abs() (dipy.reconst.qtdmri.QtdmriFit method) sparsity_density() (dipy.reconst.qtdmri.QtdmriFit method) spdot() (in module dipy.core.optimize) sph2latlon() (in module dipy.core.geometry) sph_harm_ind_list() (in module dipy.reconst.shm) sph_project() (in module dipy.viz.projections) Sphere (class in dipy.core.sphere) sphere2cart() (in module dipy.core.geometry) sphere_distance() (in module dipy.core.geometry) spherical_harmonics() (in module dipy.reconst.shm) sphericity() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) SphHarmFit (class in dipy.reconst.shm) SphHarmModel (class in dipy.reconst.shm) spline() (in module dipy.tracking.metrics) split_cti_params() (in module dipy.reconst.cti) split_dki_param() (in module dipy.reconst.dki) split_name_with_gz() (in module dipy.io.utils) SplitFlow (class in dipy.workflows.io) squared_radial_component() (in module dipy.reconst.gqi) SSDMetric (class in dipy.align.metrics) startpoint() (in module dipy.tracking.metrics) StatefulTractogram (class in dipy.io.stateful_tractogram) sticks_and_ball() (in module dipy.sims.voxel) stoc_search_cost() (dipy.reconst.ivim.IvimModelVP method) streamline_gradients() (in module dipy.tracking.life) streamline_near_roi() (in module dipy.tracking.utils) streamline_registration() (in module dipy.align._public) streamline_signal() (dipy.tracking.life.LifeSignalMaker method) (in module dipy.tracking.life) streamline_tensors() (in module dipy.tracking.life) StreamlineDistanceMetric (class in dipy.align.streamlinear) StreamlineLinearRegistration (class in dipy.align.streamlinear) StreamlineRegistrationMap (class in dipy.align.streamlinear) streamlines (dipy.io.stateful_tractogram.StatefulTractogram property) subdivide() (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) subsegment() (in module dipy.tracking.utils) summary() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.tf.model.MultipleLayerPercepton method) (dipy.nn.tf.model.SingleLayerPerceptron method) SurfaceTab (class in dipy.viz.horizon.tab.surface) SurfaceVisualizer (class in dipy.viz.horizon.visualizer.surface) SymmetricDiffeomorphicRegistration (class in dipy.align.imwarp) syn_registration() (in module dipy.align._public) Synb0 (class in dipy.nn.tf.synb0) synchronize_slices() (dipy.viz.horizon.tab.base.TabManager method) synchronize_volumes() (dipy.viz.horizon.tab.base.TabManager method) SynRegistrationFlow (class in dipy.workflows.align)

T

tab_id (dipy.viz.horizon.tab.base.HorizonTab property) tab_ui (dipy.viz.horizon.tab.base.TabManager property) TabManager (class in dipy.viz.horizon.tab.base) target() (in module dipy.tracking.utils) target_line_based() (in module dipy.tracking.utils) tau() (dipy.core.gradients.GradientTable method) temporal_basis() (in module dipy.reconst.qtdmri) tensor_prediction() (in module dipy.reconst.dti) tensor_to_pam() (in module dipy.io.peaks) TensorFit (class in dipy.reconst.dti) TensorModel (class in dipy.reconst.dti) TensorToPamFlow (class in dipy.workflows.io) threshold_propagator() (in module dipy.reconst.dsi) TissueClassifierHMRF (class in dipy.segment.tissue) to_bids_description() (in module dipy.data.fetcher) to_center() (dipy.io.stateful_tractogram.StatefulTractogram method) to_corner() (dipy.io.stateful_tractogram.StatefulTractogram method) to_origin() (dipy.io.stateful_tractogram.StatefulTractogram method) to_rasmm() (dipy.io.stateful_tractogram.StatefulTractogram method) to_space() (dipy.io.stateful_tractogram.StatefulTractogram method) to_vox() (dipy.io.stateful_tractogram.StatefulTractogram method) to_voxmm() (dipy.io.stateful_tractogram.StatefulTractogram method) tortuosity (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) tortuosity() (in module dipy.reconst.dki_micro) trace() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti)

TRACKVIS (dipy.io.stateful_tractogram.Origin attribute) tractogram_clusters (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) train_test_split() (dipy.nn.tf.cnn_1d_denoising.Cnn1DDenoiser method) transform() (dipy.align.imaffine.AffineMap method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.align.streamlinear.JointStreamlineRegistrationMap method) (dipy.align.streamlinear.StreamlineRegistrationMap method) transform_centers_of_mass() (in module dipy.align.imaffine) transform_geometric_centers() (in module dipy.align.imaffine) transform_img() (in module dipy.nn.utils) transform_inverse() (dipy.align.imaffine.AffineMap method) (dipy.align.imwarp.DiffeomorphicMap method) transform_origins() (in module dipy.align.imaffine) transform_point_cloud() (dipy.align.cpd.DeformableRegistration method) transform_points() (dipy.align.imwarp.DiffeomorphicMap method) transform_points_inverse() (dipy.align.imwarp.DiffeomorphicMap method) transform_streamlines() (in module dipy.tracking.streamline) transform_tracking_output() (in module dipy.tracking.utils) translation() (in module dipy.align._public) traverse_postorder() (dipy.segment.clustering.TreeClusterMap method) TreeCluster (class in dipy.segment.clustering) TreeClusterMap (class in dipy.segment.clustering) triangles_area() (in module dipy.tracking.mesh) triple_odf_maxima() (in module dipy.reconst.gqi) two_cingulum_bundles() (in module dipy.data) two_eyes_cutoff() (in module dipy.reconst.weights_method)

U

ufa() (dipy.reconst.qti.QtiFit method) UNet3D (class in dipy.nn.torch.deepn4) UNet3D() (in module dipy.nn.tf.deepn4) (in module dipy.nn.tf.synb0) unique_bvals_magnitude() (in module dipy.core.gradients) unique_bvals_tolerance() (in module dipy.core.gradients) unique_edges() (in module dipy.core.sphere) unique_rows() (in module dipy.tracking.utils) unique_sets() (in module dipy.core.sphere) Unit vector unlist_streamlines() (in module dipy.tracking.streamline) unnormalize() (in module dipy.nn.utils) unpack_image() (in module dipy.viz.horizon.util) unpack_surface() (in module dipy.viz.horizon.util) up() (dipy.core.graph.Graph method) up_short() (dipy.core.graph.Graph method)

update() (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) (dipy.segment.clustering.ClusterCentroid method) update_argument() (dipy.workflows.base.IntrospectiveArgumentParser method) update_flat_outputs() (dipy.workflows.workflow.Workflow method) update_slices() (dipy.viz.horizon.tab.peak.PeaksTab method) (dipy.viz.horizon.tab.slice.SlicesTab method) update_transform() (dipy.align.cpd.DeformableRegistration method) update_variance() (dipy.align.cpd.DeformableRegistration method) update_volume() (dipy.viz.horizon.tab.slice.SlicesTab method) upper_bound_by_percent() (in module dipy.segment.threshold) upper_bound_by_rate() (in module dipy.segment.threshold) upper_hemi_map() (in module dipy.reconst.gqi) use_moving_image_dynamics() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) use_static_image_dynamics() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method)

V

v_cycle_2d() (in module dipy.align.metrics) v_cycle_3d() (in module dipy.align.metrics) v_iso() (dipy.reconst.qti.QtiFit method) v_md() (dipy.reconst.qti.QtiFit method) v_shear() (dipy.reconst.qti.QtiFit method) values_from_volume() (in module dipy.tracking.streamline) vec2vec_rotmat() (in module dipy.core.geometry) vector_cosine() (in module dipy.core.geometry) vector_norm() (in module dipy.core.geometry) version() (dipy.io.dpy.Dpy method) vertices() (dipy.core.sphere.Sphere method) vertices_to_triangles_values() (in module dipy.tracking.mesh) visibility (dipy.viz.horizon.tab.base.HorizonUIElement attribute)

visualise_gradient_table_G_Delta_rainbow() (in module dipy.reconst.qtdmri) viz_displacement_mag() (in module dipy.viz.streamline) viz_two_bundles() (in module dipy.viz.streamline) viz_vector_field() (in module dipy.viz.streamline) vol_denoise() (in module dipy.denoise.patch2self) volume_fractions (dipy.reconst.mcsd.MSDeconvFit property) volume_max (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) volume_min (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) VOX (dipy.io.stateful_tractogram.Space attribute) voxel2streamline() (in module dipy.tracking.life) voxel_order (dipy.io.stateful_tractogram.StatefulTractogram property) voxel_sizes (dipy.io.stateful_tractogram.StatefulTractogram property) VOXMM (dipy.io.stateful_tractogram.Space attribute)

W

warp_endomorphism() (dipy.align.imwarp.DiffeomorphicMap method) Wcons() (in module dipy.reconst.dki) weighted_voxel_metric() (in module dipy.reconst.bingham) weights_method_nlls_m_est() (in module dipy.reconst.weights_method) weights_method_wls_m_est() (in module dipy.reconst.weights_method) WichmannHill1982() (in module dipy.core.rng) WichmannHill2006() (in module dipy.core.rng) winding() (in module dipy.tracking.metrics) wls_fit_msdki() (in module dipy.reconst.msdki)

wls_fit_tensor() (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) wls_iter() (in module dipy.reconst.fwdti) Workflow (class in dipy.workflows.workflow) write_mapping() (in module dipy.align._public) write_track() (dipy.io.dpy.Dpy method) write_tracks() (dipy.io.dpy.Dpy method) Wrotate() (in module dipy.reconst.dki) Wrotate_element() (in module dipy.reconst.dki)

X

x (dipy.core.sphere.Sphere property) x_and_f_to_x_f() (dipy.reconst.ivim.IvimModelVP method)

x_f_to_x_and_f() (dipy.reconst.ivim.IvimModelVP method) xopt (dipy.core.optimize.Optimizer property)

Y

y (dipy.core.sphere.Sphere property)

Z

z (dipy.core.sphere.Sphere property)