Index

_

__init__() (dipy.align.Bunch method) (dipy.align.cpd.DeformableRegistration method) (dipy.align.imaffine.AffineInvalidValuesError method) (dipy.align.imaffine.AffineInversionError method) (dipy.align.imaffine.AffineMap method) (dipy.align.imaffine.AffineRegistration method) (dipy.align.imaffine.MutualInformationMetric method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.parzenhist.ParzenJointHistogram method) (dipy.align.scalespace.IsotropicScaleSpace method) (dipy.align.scalespace.ScaleSpace 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.JointStreamlineRegistrationMap method) (dipy.align.streamlinear.StreamlineDistanceMetric method) (dipy.align.streamlinear.StreamlineLinearRegistration method) (dipy.align.streamlinear.StreamlineRegistrationMap method) (dipy.align.transforms.AffineTransform2D method) (dipy.align.transforms.AffineTransform3D method) (dipy.align.transforms.RigidIsoScalingTransform2D method) (dipy.align.transforms.RigidIsoScalingTransform3D method) (dipy.align.transforms.RigidScalingTransform2D method) (dipy.align.transforms.RigidScalingTransform3D method) (dipy.align.transforms.RigidTransform2D method) (dipy.align.transforms.RigidTransform3D method) (dipy.align.transforms.RotationTransform2D method) (dipy.align.transforms.RotationTransform3D method) (dipy.align.transforms.ScalingTransform2D method) (dipy.align.transforms.ScalingTransform3D method) (dipy.align.transforms.Transform method) (dipy.align.transforms.TranslationTransform2D method) (dipy.align.transforms.TranslationTransform3D method) (dipy.core.gradients.GradientTable method) (dipy.core.graph.Graph method) (dipy.core.interpolation.Interpolator method) (dipy.core.interpolation.NearestNeighborInterpolator method) (dipy.core.interpolation.OutsideImage method) (dipy.core.interpolation.TriLinearInterpolator method) (dipy.core.onetime.OneTimeProperty method) (dipy.core.onetime.ResetMixin method) (dipy.core.optimize.NonNegativeLeastSquares method) (dipy.core.optimize.Optimizer method) (dipy.core.optimize.PositiveDefiniteLeastSquares method) (dipy.core.optimize.SKLearnLinearSolver method) (dipy.core.profile.Profiler method) (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.data.DataError method) (dipy.denoise.enhancement_kernel.EnhancementKernel method) (dipy.denoise.enhancement_kernel.HemiSphere method) (dipy.denoise.enhancement_kernel.Sphere method) (dipy.direction.bootstrap_direction_getter.BootDirectionGetter method) (dipy.direction.closest_peak_direction_getter.BaseDirectionGetter method) (dipy.direction.closest_peak_direction_getter.BasePmfDirectionGetter method) (dipy.direction.closest_peak_direction_getter.ClosestPeakDirectionGetter method) (dipy.direction.closest_peak_direction_getter.PmfGenDirectionGetter method) (dipy.direction.peaks.PeaksAndMetrics method) (dipy.direction.pmf.PmfGen method) (dipy.direction.pmf.SHCoeffPmfGen method) (dipy.direction.pmf.SimplePmfGen method) (dipy.direction.probabilistic_direction_getter.DeterministicMaximumDirectionGetter method) (dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter method) (dipy.direction.ptt_direction_getter.PTTDirectionGetter method) (dipy.io.dpy.Dpy method) (dipy.io.stateful_tractogram.Origin method) (dipy.io.stateful_tractogram.Space method) (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.deepn4.DecoderBlock method) (dipy.nn.deepn4.DeepN4 method) (dipy.nn.deepn4.EncoderBlock method) (dipy.nn.evac.Block method) (dipy.nn.evac.ChannelSum method) (dipy.nn.evac.EVACPlus method) (dipy.nn.histo_resdnn.HistoResDNN method) (dipy.nn.model.MultipleLayerPercepton method) (dipy.nn.model.SingleLayerPerceptron method) (dipy.nn.synb0.DecoderBlock method) (dipy.nn.synb0.EncoderBlock method) (dipy.nn.synb0.Synb0 method) (dipy.reconst.base.ReconstFit method) (dipy.reconst.base.ReconstModel method) (dipy.reconst.cache.Cache method) (dipy.reconst.csdeconv.AxSymShResponse method) (dipy.reconst.csdeconv.ConstrainedSDTModel 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.dsi.DiffusionSpectrumDeconvFit method) (dipy.reconst.dsi.DiffusionSpectrumDeconvModel method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.dsi.DiffusionSpectrumModel method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.dti.TensorModel method) (dipy.reconst.eudx_direction_getter.EuDXDirectionGetter method) (dipy.reconst.forecast.ForecastFit method) (dipy.reconst.forecast.ForecastModel method) (dipy.reconst.fwdti.FreeWaterTensorFit method) (dipy.reconst.fwdti.FreeWaterTensorModel method) (dipy.reconst.gqi.GeneralizedQSamplingFit method) (dipy.reconst.gqi.GeneralizedQSamplingModel method) (dipy.reconst.ivim.IvimFit method) (dipy.reconst.ivim.IvimModelTRR method) (dipy.reconst.ivim.IvimModelVP method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.mapmri.MapmriModel method) (dipy.reconst.mcsd.MSDeconvFit method) (dipy.reconst.mcsd.MultiShellDeconvModel method) (dipy.reconst.mcsd.MultiShellResponse method) (dipy.reconst.mcsd.QpFitter method) (dipy.reconst.msdki.MeanDiffusionKurtosisFit method) (dipy.reconst.msdki.MeanDiffusionKurtosisModel method) (dipy.reconst.multi_voxel.CallableArray method) (dipy.reconst.multi_voxel.MultiVoxelFit method) (dipy.reconst.odf.OdfFit method) (dipy.reconst.odf.OdfModel method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.qtdmri.QtdmriModel method) (dipy.reconst.qti.QtiFit method) (dipy.reconst.qti.QtiModel method) (dipy.reconst.rumba.RumbaFit method) (dipy.reconst.rumba.RumbaSDModel method) (dipy.reconst.sfm.ExponentialIsotropicFit method) (dipy.reconst.sfm.ExponentialIsotropicModel method) (dipy.reconst.sfm.IsotropicFit method) (dipy.reconst.sfm.IsotropicModel method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.sfm.SparseFascicleModel method) (dipy.reconst.shm.CsaOdfModel method) (dipy.reconst.shm.OpdtModel method) (dipy.reconst.shm.QballBaseModel method) (dipy.reconst.shm.QballModel method) (dipy.reconst.shm.ResidualBootstrapWrapper method) (dipy.reconst.shm.SphHarmFit method) (dipy.reconst.shm.SphHarmModel method) (dipy.reconst.shore.ShoreFit method) (dipy.reconst.shore.ShoreModel method) (dipy.segment.bundles.RecoBundles method) (dipy.segment.clustering.Cluster method) (dipy.segment.clustering.ClusterCentroid method) (dipy.segment.clustering.Clustering method) (dipy.segment.clustering.ClusterMap method) (dipy.segment.clustering.ClusterMapCentroid method) (dipy.segment.clustering.Identity method) (dipy.segment.clustering.QuickBundles method) (dipy.segment.clustering.QuickBundlesX method) (dipy.segment.clustering.TreeCluster method) (dipy.segment.clustering.TreeClusterMap method) (dipy.segment.clustering_algorithms.ClusterCentroid method) (dipy.segment.clustering_algorithms.ClusterMapCentroid method) (dipy.segment.clusteringspeed.ClusterCentroid method) (dipy.segment.clusteringspeed.ClusterMapCentroid method) (dipy.segment.clusteringspeed.Clusters method) (dipy.segment.clusteringspeed.ClustersCentroid method) (dipy.segment.clusteringspeed.QuickBundles method) (dipy.segment.clusteringspeed.QuickBundlesX method) (dipy.segment.clusteringspeed.TreeCluster method) (dipy.segment.clusteringspeed.TreeClusterMap method) (dipy.segment.featurespeed.ArcLengthFeature method) (dipy.segment.featurespeed.CenterOfMassFeature method) (dipy.segment.featurespeed.CythonFeature method) (dipy.segment.featurespeed.Feature method) (dipy.segment.featurespeed.IdentityFeature method) (dipy.segment.featurespeed.MidpointFeature method) (dipy.segment.featurespeed.ResampleFeature method) (dipy.segment.featurespeed.VectorOfEndpointsFeature method) (dipy.segment.fss.FastStreamlineSearch method) (dipy.segment.metricspeed.AveragePointwiseEuclideanMetric method) (dipy.segment.metricspeed.CosineMetric method) (dipy.segment.metricspeed.CythonMetric method) (dipy.segment.metricspeed.Metric method) (dipy.segment.metricspeed.MinimumAverageDirectFlipMetric method) (dipy.segment.metricspeed.SumPointwiseEuclideanMetric method) (dipy.segment.mrf.ConstantObservationModel method) (dipy.segment.mrf.IteratedConditionalModes method) (dipy.segment.tissue.TissueClassifierHMRF method) (dipy.tracking.direction_getter.DirectionGetter method) (dipy.tracking.fbcmeasures.FBCMeasures method) (dipy.tracking.fbcmeasures.interp1d method) (dipy.tracking.fbcmeasures.KDTree method) (dipy.tracking.life.FiberFit method) (dipy.tracking.life.FiberModel method) (dipy.tracking.life.LifeSignalMaker method) (dipy.tracking.local_tracking.LocalTracking method) (dipy.tracking.local_tracking.ParticleFilteringTracking method) (dipy.tracking.stopping_criterion.ActStoppingCriterion method) (dipy.tracking.stopping_criterion.AnatomicalStoppingCriterion method) (dipy.tracking.stopping_criterion.BinaryStoppingCriterion method) (dipy.tracking.stopping_criterion.CmcStoppingCriterion method) (dipy.tracking.stopping_criterion.StoppingCriterion method) (dipy.tracking.stopping_criterion.StreamlineStatus method) (dipy.tracking.stopping_criterion.ThresholdStoppingCriterion method) (dipy.viz.gmem.GlobalHorizon method) (dipy.viz.horizon.app.Horizon method) (dipy.viz.horizon.tab.base.HorizonTab method) (dipy.viz.horizon.tab.base.HorizonUIElement method) (dipy.viz.horizon.tab.base.TabManager 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) (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer method) (dipy.viz.horizon.visualizer.peak.PeakActor method) (dipy.viz.horizon.visualizer.peak.PeaksVisualizer method) (dipy.viz.horizon.visualizer.slice.SlicesVisualizer method) (dipy.viz.horizon.visualizer.surface.SurfaceVisualizer method) (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.base.IntrospectiveArgumentParser method) (dipy.workflows.combined_workflow.CombinedWorkflow 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.docstring_parser.NumpyDocString method) (dipy.workflows.docstring_parser.Reader method) (dipy.workflows.io.ConcatenateTractogramFlow method) (dipy.workflows.io.ConvertSHFlow method) (dipy.workflows.io.ConvertTensorsFlow method) (dipy.workflows.io.ConvertTractogramFlow method) (dipy.workflows.io.FetchFlow method) (dipy.workflows.io.IoInfoFlow method) (dipy.workflows.io.SplitFlow method) (dipy.workflows.mask.MaskFlow method) (dipy.workflows.multi_io.IOIterator method) (dipy.workflows.nn.EVACPlusFlow method) (dipy.workflows.reconst.ReconstCSAFlow method) (dipy.workflows.reconst.ReconstCSDFlow method) (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDsiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) (dipy.workflows.reconst.ReconstIvimFlow method) (dipy.workflows.reconst.ReconstMAPMRIFlow method) (dipy.workflows.reconst.ReconstRUMBAFlow 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)

_lt_cols() (in module dipy.reconst.dti) _lt_indices() (in module dipy.reconst.dti) _lt_rows() (in module dipy.reconst.dti) _METHOD_DICT() (in module dipy.align._public) _transform_method() (in module dipy.align.imaffine) _TUPLE2AXES() (in module dipy.core.geometry)

A

actors (dipy.viz.horizon.tab.peak.PeaksTab 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) ActStoppingCriterion (class in dipy.tracking.stopping_criterion) ad() (dipy.reconst.dti.TensorFit method) adaptive_soft_matching() (in module dipy.denoise.adaptive_soft_matching) adc() (dipy.reconst.dti.TensorFit method) add() (dipy.segment.clustering.TreeCluster method) (dipy.segment.clusteringspeed.TreeCluster method) add_3vecs() (in module dipy.tracking.distances) add_cluster() (dipy.segment.clustering.ClusterMap method) add_cluster_actors() (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer method) 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_padding_reflection() (in module dipy.denoise.denspeed) add_sub_flow_args() (dipy.workflows.base.IntrospectiveArgumentParser method) add_workflow() (dipy.workflows.base.IntrospectiveArgumentParser method) adj_to_countarrs() (in module dipy.reconst.recspeed) 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) AffineTransform2D (class in dipy.align.transforms) AffineTransform3D (class in dipy.align.transforms) 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) anatomical_measures() (in module dipy.stats.analysis) AnatomicalStoppingCriterion (class in dipy.tracking.stopping_criterion) ang_thr (dipy.reconst.eudx_direction_getter.EuDXDirectionGetter attribute) 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) approx_polygon_track() (in module dipy.tracking.distances) approximate_mdl_trajectory() (in module dipy.tracking.distances) arbitrarypoint() (in module dipy.tracking.metrics) ArcLengthFeature (class in dipy.segment.featurespeed) are_compatible() (dipy.io.stateful_tractogram.StatefulTractogram static method) (dipy.segment.metricspeed.CythonMetric method) (dipy.segment.metricspeed.Metric method) argmax_from_adj() (in module dipy.reconst.recspeed) argmax_from_countarrs() (in module dipy.reconst.recspeed) assign() (dipy.segment.clustering.Cluster method) (dipy.segment.clustering.ClusterCentroid method) (dipy.segment.clustering_algorithms.ClusterCentroid method) (dipy.segment.clusteringspeed.ClusterCentroid method) assignment_map() (in module dipy.stats.analysis) auto_attr() (in module dipy.core.onetime) auto_response() (in module dipy.reconst.csdeconv) auto_response_msmt() (in module dipy.reconst.mcsd) auto_response_ssst() (in module dipy.reconst.csdeconv) average_bundle_length() (in module dipy.align.streamwarp) AveragePointwiseEuclideanMetric (class in dipy.segment.metricspeed) 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) BaseDirectionGetter (class in dipy.direction.closest_peak_direction_getter) basename_without_extension() (in module dipy.workflows.multi_io) BasePmfDirectionGetter (class in dipy.direction.closest_peak_direction_getter) basis() (dipy.reconst.csdeconv.AxSymShResponse method) bin_index() (dipy.align.parzenhist.ParzenJointHistogram method) bin_normalize_moving() (dipy.align.parzenhist.ParzenJointHistogram method) bin_normalize_static() (dipy.align.parzenhist.ParzenJointHistogram method) BinaryStoppingCriterion (class in dipy.tracking.stopping_criterion) binomialfloat() (in module dipy.reconst.mapmri) Block (class in dipy.nn.evac) BootDirectionGetter (class in dipy.direction.bootstrap_direction_getter) bootstrap_data_array() (in module dipy.reconst.shm) bootstrap_data_voxel() (in module dipy.reconst.shm) 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_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) bundles_distances_mam() (in module dipy.tracking.distances) bundles_distances_mdf() (in module dipy.tracking.distances) 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.deepn4.DecoderBlock method) (dipy.nn.deepn4.EncoderBlock method) (dipy.nn.evac.Block method) (dipy.nn.evac.ChannelSum method) (dipy.nn.synb0.DecoderBlock method) (dipy.nn.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) ceil() (in module dipy.denoise.enhancement_kernel) center_of_mass() (in module dipy.align._public) (in module dipy.tracking.metrics) center_streamlines() (in module dipy.tracking.streamline) CenterOfMassFeature (class in dipy.segment.featurespeed) centroid_actors (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) centroids (dipy.segment.clustering.ClusterMapCentroid property) (dipy.segment.clustering_algorithms.ClusterMapCentroid property) (dipy.segment.clusteringspeed.ClusterMapCentroid property) change_volume() (dipy.viz.horizon.visualizer.slice.SlicesVisualizer method) ChannelSum (class in dipy.nn.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_point() (dipy.tracking.stopping_criterion.StoppingCriterion method) check_range() (in module dipy.segment.bundles) children (dipy.tracking.fbcmeasures.KDTree.innernode property) (dipy.tracking.fbcmeasures.KDTree.leafnode property) 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) clean_cc_mask() (in module dipy.segment.mask) clear() (dipy.segment.clustering.ClusterMap method) close() (dipy.io.dpy.Dpy method) ClosestPeakDirectionGetter (class in dipy.direction.closest_peak_direction_getter) 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.visualizer.cluster.ClustersVisualizer property) cluster_bundle() (in module dipy.segment.bundles) cluster_confidence() (in module dipy.tracking.streamline) ClusterCentroid (class in dipy.segment.clustering) (class in dipy.segment.clustering_algorithms) (class in dipy.segment.clusteringspeed) Clustering (class in dipy.segment.clustering) ClusterMap (class in dipy.segment.clustering) ClusterMapCentroid (class in dipy.segment.clustering) (class in dipy.segment.clustering_algorithms) (class in dipy.segment.clusteringspeed) Clusters (class in dipy.segment.clusteringspeed) clusters (dipy.segment.clustering.ClusterMap property) clusters_centroid2clustermap_centroid() (in module dipy.segment.clustering_algorithms) clusters_sizes() (dipy.segment.clustering.ClusterMap method) ClustersCentroid (class in dipy.segment.clusteringspeed) ClustersTab (class in dipy.viz.horizon.tab.cluster) ClustersVisualizer (class in dipy.viz.horizon.visualizer.cluster) CmcStoppingCriterion (class in dipy.tracking.stopping_criterion) Cnn1DDenoiser (class in dipy.nn.cnn_1d_denoising) coeff_of_determination() (in module dipy.reconst.cross_validation) color_double_slider() (in module dipy.viz.horizon.tab.base) color_fa() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) color_single_slider() (in module dipy.viz.horizon.tab.base) 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.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) compose_vector_fields_2d() (in module dipy.align.vector_fields)

compose_vector_fields_3d() (in module dipy.align.vector_fields) compress_streamlines() (in module dipy.tracking.streamlinespeed) 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_cc_backward_step_2d() (in module dipy.align.crosscorr) compute_cc_backward_step_3d() (in module dipy.align.crosscorr) compute_cc_forward_step_2d() (in module dipy.align.crosscorr) compute_cc_forward_step_3d() (in module dipy.align.crosscorr) compute_demons_step() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) compute_em_demons_step_2d() (in module dipy.align.expectmax) compute_em_demons_step_3d() (in module dipy.align.expectmax) compute_energy_ssd_2d() (in module dipy.align.sumsqdiff) compute_energy_ssd_3d() (in module dipy.align.sumsqdiff) 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_masked_class_stats_2d() (in module dipy.align.expectmax) compute_masked_class_stats_3d() (in module dipy.align.expectmax) compute_num_samples() (in module dipy.denoise.localpca) compute_parzen_mi() (in module dipy.align.parzenhist) compute_patch_size() (in module dipy.denoise.localpca) compute_residual_displacement_field_ssd_2d() (in module dipy.align.sumsqdiff) compute_residual_displacement_field_ssd_3d() (in module dipy.align.sumsqdiff) compute_rfbc() (in module dipy.tracking.fbcmeasures) compute_ssd_demons_step_2d() (in module dipy.align.sumsqdiff) compute_ssd_demons_step_3d() (in module dipy.align.sumsqdiff) 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) ConstantObservationModel (class in dipy.segment.mrf) 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) convolve() (in module dipy.denoise.shift_twist_convolution) convolve_sf() (in module dipy.denoise.shift_twist_convolution) copyfileobj_withprogress() (in module dipy.data.fetcher) correct_minor_errors() (in module dipy.nn.utils) CorrelationTensorFit (class in dipy.reconst.cti) CorrelationTensorModel (class in dipy.reconst.cti) correspond_indices() (in module dipy.denoise.denspeed) CosineMetric (class in dipy.segment.metricspeed) count_neighbors() (dipy.tracking.fbcmeasures.KDTree method) create_circle() (in module dipy.align.vector_fields) create_directories() (dipy.workflows.multi_io.IOIterator method) create_harmonic_fields_2d() (in module dipy.align.vector_fields) create_harmonic_fields_3d() (in module dipy.align.vector_fields) 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_random_displacement_2d() (in module dipy.align.vector_fields) create_random_displacement_3d() (in module dipy.align.vector_fields) create_rspace() (in module dipy.reconst.mapmri) (in module dipy.reconst.shore) create_rt_space_grid() (in module dipy.reconst.qtdmri) create_sphere() (in module dipy.align.vector_fields) 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) cubic_spline() (in module dipy.align.parzenhist) cubic_spline_derivative() (in module dipy.align.parzenhist) cut_plane() (in module dipy.tracking.distances) 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) CythonFeature (class in dipy.segment.featurespeed) CythonMetric (class in dipy.segment.metricspeed)

D

D (dipy.reconst.ivim.IvimFit property) d_sq() (dipy.reconst.qti.QtiFit method) D_star (dipy.reconst.ivim.IvimFit property) DATA_DIR() (in module dipy.data) 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) DecoderBlock (class in dipy.nn.deepn4) (class in dipy.nn.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.deepn4) default_sphere() (in module dipy.data) 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) density_map() (in module dipy.tracking.utils) deprecated_params() (in module dipy.denoise.shift_twist_convolution) 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) determine_num_threads() (in module dipy.align.bundlemin) (in module dipy.denoise.denspeed) (in module dipy.denoise.shift_twist_convolution) (in module dipy.tracking.fbcmeasures) DeterministicMaximumDirectionGetter (class in dipy.direction.probabilistic_direction_getter) 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) diffusion_evals() (in module dipy.sims.voxel) 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.bundlemin module dipy.align.cpd module dipy.align.crosscorr module dipy.align.expectmax module dipy.align.imaffine module dipy.align.imwarp module dipy.align.metrics module dipy.align.parzenhist module dipy.align.reslice module dipy.align.scalespace module dipy.align.streamlinear module dipy.align.streamwarp module dipy.align.sumsqdiff module dipy.align.transforms module dipy.align.vector_fields module dipy.core module dipy.core.geometry module dipy.core.gradients module dipy.core.graph module dipy.core.histeq module dipy.core.interpolation 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.denspeed module dipy.denoise.enhancement_kernel module dipy.denoise.gibbs module dipy.denoise.localpca module dipy.denoise.nlmeans module dipy.denoise.nlmeans_block module dipy.denoise.noise_estimate module dipy.denoise.non_local_means module dipy.denoise.patch2self module dipy.denoise.pca_noise_estimate module dipy.denoise.shift_twist_convolution module dipy.direction module dipy.direction.bootstrap_direction_getter module dipy.direction.closest_peak_direction_getter module dipy.direction.peaks module dipy.direction.pmf module dipy.direction.probabilistic_direction_getter module dipy.direction.ptt_direction_getter 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.cnn_1d_denoising module dipy.nn.deepn4 module dipy.nn.evac module dipy.nn.histo_resdnn module dipy.nn.model module dipy.nn.synb0 module dipy.nn.utils module dipy.reconst module dipy.reconst.base 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.eudx_direction_getter 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.quick_squash module dipy.reconst.recspeed module dipy.reconst.rumba module dipy.reconst.sfm module dipy.reconst.shm module dipy.reconst.shore module dipy.reconst.utils module dipy.reconst.vec_val_sum module dipy.segment module dipy.segment.bundles module dipy.segment.clustering module dipy.segment.clustering_algorithms module dipy.segment.clusteringspeed module dipy.segment.cythonutils module dipy.segment.featurespeed module dipy.segment.fss module dipy.segment.mask module dipy.segment.metric module dipy.segment.metricspeed module dipy.segment.mrf module dipy.segment.threshold module dipy.segment.tissue module dipy.sims module dipy.sims.phantom module dipy.sims.voxel module dipy.stats module dipy.stats.analysis module dipy.tracking module dipy.tracking._utils module dipy.tracking.direction_getter module dipy.tracking.distances module dipy.tracking.fbcmeasures module dipy.tracking.learning module dipy.tracking.life module dipy.tracking.local_tracking module dipy.tracking.localtrack module dipy.tracking.mesh module dipy.tracking.metrics module dipy.tracking.propspeed module dipy.tracking.stopping_criterion module dipy.tracking.streamline module dipy.tracking.streamlinespeed module dipy.tracking.utils module dipy.tracking.vox2track 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.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) DirectionGetter (class in dipy.tracking.direction_getter) directions (dipy.reconst.dti.TensorFit property) disperse_charges() (in module dipy.core.sphere) (in module dipy.denoise.enhancement_kernel) 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() (dipy.segment.metricspeed.CythonMetric method) (dipy.segment.metricspeed.Metric method) (in module dipy.segment.metricspeed) 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) distance_matrix() (in module dipy.segment.metricspeed) distance_matrix_mdf() (in module dipy.align.bundlemin) 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) docstring_addendum (dipy.align.imaffine.AffineRegistration attribute) down() (dipy.core.graph.Graph method) down_short() (dipy.core.graph.Graph method) downsample() (in module dipy.tracking.metrics) downsample_displacement_field_2d() (in module dipy.align.vector_fields) downsample_displacement_field_3d() (in module dipy.align.vector_fields) downsample_scalar_field_2d() (in module dipy.align.vector_fields) downsample_scalar_field_3d() (in module dipy.align.vector_fields) 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 (dipy.tracking.fbcmeasures.interp1d attribute) DTYPE (in module dipy.segment.clustering_algorithms) (in module dipy.segment.clusteringspeed) dtype_dict (dipy.io.stateful_tractogram.StatefulTractogram property) dwt3D() (in module dipy.core.wavelet)

E

edges() (dipy.core.sphere.Sphere method) (dipy.denoise.enhancement_kernel.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) EncoderBlock (class in dipy.nn.deepn4) (class in dipy.nn.synb0) ENDPOINT (dipy.tracking.stopping_criterion.StreamlineStatus attribute) endpoint() (in module dipy.tracking.metrics) EnhancementKernel (class in dipy.denoise.enhancement_kernel) 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_both_directions() (in module dipy.tracking.propspeed) EuDXDirectionGetter (class in dipy.reconst.eudx_direction_getter)

Euler angles euler_characteristic_check() (in module dipy.core.sphere) euler_matrix() (in module dipy.core.geometry) EVACPlus (class in dipy.nn.evac) EVACPlusFlow (class in dipy.workflows.nn) evals (dipy.reconst.dti.TensorFit property) evaluate() (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.model.MultipleLayerPercepton method) (dipy.nn.model.SingleLayerPerceptron method) evaluate_aabb_checks() (in module dipy.segment.clusteringspeed) evaluate_kernel() (dipy.denoise.enhancement_kernel.EnhancementKernel 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() (dipy.segment.featurespeed.CythonFeature method) (dipy.segment.featurespeed.Feature method) (in module dipy.segment.featurespeed) extract_example_tracts() (in module dipy.data.fetcher)

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) (dipy.denoise.enhancement_kernel.HemiSphere method) (dipy.denoise.enhancement_kernel.Sphere method) faces_from_sphere_vertices() (in module dipy.core.sphere) FastStreamlineSearch (class in dipy.segment.fss) FBCMeasures (class in dipy.tracking.fbcmeasures) Feature (class in dipy.segment.featurespeed) feature (dipy.segment.metricspeed.Metric attribute) 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_weights() (in module dipy.data.fetcher) fetch_default_weights() (dipy.nn.deepn4.DeepN4 method) (dipy.nn.evac.EVACPlus method) (dipy.nn.histo_resdnn.HistoResDNN method) (dipy.nn.synb0.Synb0 method) fetch_DiB_217_lte_pte_ste() (in module dipy.data.fetcher) fetch_DiB_70_lte_pte_ste() (in module dipy.data.fetcher) fetch_evac_test() (in module dipy.data.fetcher) fetch_evac_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_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) fill_value (dipy.tracking.fbcmeasures.interp1d property) find_closest() (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.denoise.enhancement_kernel.HemiSphere method) (dipy.denoise.enhancement_kernel.Sphere method)

find_missing() (in module dipy.align.streamwarp) find_signal_means() (in module dipy.reconst.forecast) firdn() (in module dipy.denoise.nlmeans_block) fit() (dipy.core.optimize.NonNegativeLeastSquares method) (dipy.core.optimize.SKLearnLinearSolver method) (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.model.MultipleLayerPercepton method) (dipy.nn.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_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_data() (dipy.direction.bootstrap_direction_getter.BootDirectionGetter class method) from_lower_triangular() (in module dipy.reconst.dti) from_pmf() (dipy.direction.closest_peak_direction_getter.PmfGenDirectionGetter class method) from_pve() (dipy.tracking.stopping_criterion.AnatomicalStoppingCriterion class method) from_qte_to_cti() (in module dipy.reconst.cti) from_sft() (dipy.io.stateful_tractogram.StatefulTractogram static method) from_shcoeff() (dipy.direction.closest_peak_direction_getter.PmfGenDirectionGetter class method) from_sphere() (dipy.core.sphere.HemiSphere class method) (dipy.denoise.enhancement_kernel.HemiSphere class 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) generate_streamline() (dipy.direction.ptt_direction_getter.PTTDirectionGetter method) (dipy.tracking.direction_getter.DirectionGetter method) 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_cluster_map() (dipy.segment.clusteringspeed.QuickBundles method) get_clusters() (dipy.segment.clustering.TreeClusterMap method) (dipy.segment.clusteringspeed.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_dim() (dipy.align.transforms.Transform method) get_direction() (dipy.tracking.direction_getter.DirectionGetter 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_exclude() (dipy.tracking.stopping_criterion.AnatomicalStoppingCriterion 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_identity_parameters() (dipy.align.transforms.Transform method) get_image() (dipy.align.scalespace.ScaleSpace method) get_include() (dipy.tracking.stopping_criterion.AnatomicalStoppingCriterion 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_lookup_table() (dipy.denoise.enhancement_kernel.EnhancementKernel method) get_map() (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) get_metric_name() (dipy.workflows.stats.LinearMixedModelsFlow method) get_number_of_parameters() (dipy.align.transforms.Transform method) get_optionals() (dipy.workflows.combined_workflow.CombinedWorkflow method) get_orientations() (dipy.denoise.enhancement_kernel.EnhancementKernel method) get_pmf() (dipy.direction.bootstrap_direction_getter.BootDirectionGetter method) (dipy.direction.pmf.PmfGen method) get_pmf_no_boot() (dipy.direction.bootstrap_direction_getter.BootDirectionGetter method) get_pmf_value() (dipy.direction.pmf.PmfGen method) get_points_rfbc_thresholded() (dipy.tracking.fbcmeasures.FBCMeasures 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.FetchFlow class method) (dipy.workflows.io.IoInfoFlow class method) (dipy.workflows.io.SplitFlow class method) (dipy.workflows.mask.MaskFlow class method) (dipy.workflows.nn.EVACPlusFlow class method) (dipy.workflows.reconst.ReconstCSAFlow 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.ReconstIvimFlow class method) (dipy.workflows.reconst.ReconstMAPMRIFlow class method) (dipy.workflows.reconst.ReconstRUMBAFlow 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() (dipy.denoise.enhancement_kernel.EnhancementKernel method) (in module dipy.data) (in module dipy.denoise.enhancement_kernel) get_stats() (dipy.segment.clusteringspeed.QuickBundles method) (dipy.segment.clusteringspeed.QuickBundlesX method) 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_tree_cluster_map() (dipy.segment.clusteringspeed.QuickBundlesX method) get_two_hcp842_bundles() (in module dipy.data.fetcher) get_unique_pairs() (in module dipy.align.streamlinear) gettempdir() (in module dipy.denoise.enhancement_kernel) 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.align.vector_fields) (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) hanning_filter() (in module dipy.reconst.dsi) hat() (in module dipy.reconst.shm) hemi_icosahedron() (in module dipy.core.sphere) HemiSphere (class in dipy.core.sphere) (class in dipy.denoise.enhancement_kernel) 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.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

icm_ising() (dipy.segment.mrf.IteratedConditionalModes method) icosahedron_faces() (in module dipy.core.sphere) icosahedron_vertices() (in module dipy.core.sphere) Identity (class in dipy.segment.clustering) IdentityFeature (class in dipy.segment.featurespeed) idwt3D() (in module dipy.core.wavelet) idx (dipy.tracking.fbcmeasures.KDTree.leafnode property) ImageRegistrationFlow (class in dipy.workflows.align) infer_shape() (dipy.segment.featurespeed.CythonFeature method) (dipy.segment.featurespeed.Feature method) (in module dipy.segment.featurespeed) info (dipy.core.gradients.GradientTable property) init_model() (in module dipy.nn.evac) initial_direction() (dipy.direction.bootstrap_direction_getter.BootDirectionGetter method) (dipy.direction.closest_peak_direction_getter.BasePmfDirectionGetter method) (dipy.reconst.eudx_direction_getter.EuDXDirectionGetter method) (dipy.tracking.direction_getter.DirectionGetter method) initialize_iteration() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.align.metrics.SSDMetric method) initialize_maximum_likelihood() (dipy.segment.mrf.IteratedConditionalModes method) initialize_param_uniform() (dipy.segment.mrf.ConstantObservationModel method) initialize_sigma2() (in module dipy.align.cpd) inner_3vecs() (in module dipy.tracking.distances) insert() (dipy.segment.clusteringspeed.QuickBundlesX method) inside_sphere() (in module dipy.tracking.metrics) inside_sphere_points() (in module dipy.tracking.metrics) intensities_range (dipy.viz.horizon.visualizer.slice.SlicesVisualizer property) interp1d (class in dipy.tracking.fbcmeasures) interp_rbf() (in module dipy.core.interpolation) interpolate_scalar_2d() (in module dipy.core.interpolation) interpolate_scalar_3d() (in module dipy.core.interpolation) interpolate_scalar_nn_2d() (in module dipy.core.interpolation) interpolate_scalar_nn_3d() (in module dipy.core.interpolation) interpolate_vector_2d() (in module dipy.core.interpolation) interpolate_vector_3d() (in module dipy.core.interpolation) Interpolator (class in dipy.core.interpolation) interpret_matrix() (dipy.align.imwarp.DiffeomorphicMap method) intersect_segment_cylinder() (in module dipy.tracking.distances) intersect_sphere() (in module dipy.tracking.metrics)

IntrospectiveArgumentParser (class in dipy.workflows.base) INVALIDPOINT (dipy.tracking.stopping_criterion.StreamlineStatus attribute) inverse() (dipy.align.imwarp.DiffeomorphicMap method) invert_vector_field_fixed_point_2d() (in module dipy.align.vector_fields) invert_vector_field_fixed_point_3d() (in module dipy.align.vector_fields) io_iterator() (in module dipy.workflows.multi_io) 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_binary_image() (in module dipy.viz.horizon.util) 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) (dipy.segment.clusteringspeed.TreeCluster property) is_order_invariant (dipy.segment.featurespeed.Feature attribute) (dipy.segment.metricspeed.Metric attribute) (dipy.segment.metricspeed.MinimumAverageDirectFlipMetric attribute) is_range (dipy.viz.horizon.visualizer.peak.PeakActor property) is_reference_info_valid() (in module dipy.io.utils) is_valid_affine() (in module dipy.align.vector_fields) 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) (dipy.segment.clusteringspeed.TreeClusterMap method) iterate() (dipy.align.cpd.DeformableRegistration method) iterate_residual_displacement_field_ssd_2d() (in module dipy.align.sumsqdiff) iterate_residual_displacement_field_ssd_3d() (in module dipy.align.sumsqdiff) IteratedConditionalModes (class in dipy.segment.mrf) 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

jacobian() (dipy.align.transforms.Transform method)

JointBundleMinDistanceMetric (class in dipy.align.streamlinear) JointStreamlineRegistrationMap (class in dipy.align.streamlinear)

K

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) KDTree (class in dipy.tracking.fbcmeasures) KDTree.innernode (class in dipy.tracking.fbcmeasures) KDTree.leafnode (class in dipy.tracking.fbcmeasures)

KDTree.node (class in dipy.tracking.fbcmeasures) 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) larch_3merge() (in module dipy.tracking.distances) larch_3split() (in module dipy.tracking.distances) lazy_index() (in module dipy.reconst.shm) lb_forecast() (in module dipy.reconst.forecast) lcr_matrix() (in module dipy.reconst.shm) le_to_odf() (in module dipy.reconst.recspeed) LEcuyer() (in module dipy.core.rng) lee_angle_distance() (in module dipy.tracking.distances) lee_perpendicular_distance() (in module dipy.tracking.distances) length() (in module dipy.tracking.metrics) (in module dipy.tracking.streamlinespeed) (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.deepn4.DeepN4 method) (dipy.nn.evac.EVACPlus method) (dipy.nn.histo_resdnn.HistoResDNN method) (dipy.nn.synb0.Synb0 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_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.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.cnn_1d_denoising.Cnn1DDenoiser method) loads_compat() (in module dipy.data) local_maxima() (in module dipy.reconst.recspeed) local_skeleton_clustering() (in module dipy.tracking.distances) local_skeleton_clustering_3pts() (in module dipy.tracking.distances) local_tracker() (in module dipy.tracking.localtrack) LocalFiberTrackingPAMFlow (class in dipy.workflows.tracking) localpca() (in module dipy.denoise.localpca) LocalTracking (class in dipy.tracking.local_tracking) logger() (in module dipy.align.imwarp) (in module dipy.align.scalespace) (in module dipy.align.streamlinear) (in module dipy.core.gradients) (in module dipy.io.stateful_tractogram) (in module dipy.nn.deepn4) (in module dipy.nn.evac) (in module dipy.nn.histo_resdnn) (in module dipy.nn.synb0) (in module dipy.reconst.rumba) (in module dipy.segment.bundles) (in module dipy.segment.clustering) 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) mam_distances() (in module dipy.tracking.distances) manage_output_overwrite() (dipy.workflows.workflow.Workflow method) map_coordinates_trilinear_iso() (in module dipy.core.interpolation) 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) 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) Metric (class in dipy.segment.metricspeed) midpoint() (in module dipy.tracking.metrics) midpoint2point() (in module dipy.tracking.metrics) MidpointFeature (class in dipy.segment.featurespeed) min (dipy.reconst.shm.CsaOdfModel attribute) min_centers (dipy.viz.horizon.visualizer.peak.PeakActor property) min_moving_average() (in module dipy.tracking.fbcmeasures) min_radius_curvature_from_angle() (in module dipy.direction.ptt_direction_getter) (in module dipy.tracking.utils) minimum_closest_distance() (in module dipy.tracking.distances) MinimumAverageDirectFlipMetric (class in dipy.segment.metricspeed) minmax_normalize() (in module dipy.reconst.odf) mirror() (dipy.core.sphere.HemiSphere method) (dipy.denoise.enhancement_kernel.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) module dipy dipy.align dipy.align._public dipy.align.bundlemin dipy.align.cpd dipy.align.crosscorr dipy.align.expectmax dipy.align.imaffine dipy.align.imwarp dipy.align.metrics dipy.align.parzenhist dipy.align.reslice dipy.align.scalespace dipy.align.streamlinear dipy.align.streamwarp dipy.align.sumsqdiff dipy.align.transforms dipy.align.vector_fields dipy.core dipy.core.geometry dipy.core.gradients dipy.core.graph dipy.core.histeq dipy.core.interpolation 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.denspeed dipy.denoise.enhancement_kernel dipy.denoise.gibbs dipy.denoise.localpca dipy.denoise.nlmeans dipy.denoise.nlmeans_block dipy.denoise.noise_estimate dipy.denoise.non_local_means dipy.denoise.patch2self dipy.denoise.pca_noise_estimate dipy.denoise.shift_twist_convolution dipy.direction dipy.direction.bootstrap_direction_getter dipy.direction.closest_peak_direction_getter dipy.direction.peaks dipy.direction.pmf dipy.direction.probabilistic_direction_getter dipy.direction.ptt_direction_getter 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.cnn_1d_denoising dipy.nn.deepn4 dipy.nn.evac dipy.nn.histo_resdnn dipy.nn.model dipy.nn.synb0 dipy.nn.utils dipy.reconst dipy.reconst.base 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.eudx_direction_getter 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.quick_squash dipy.reconst.recspeed dipy.reconst.rumba dipy.reconst.sfm dipy.reconst.shm dipy.reconst.shore dipy.reconst.utils dipy.reconst.vec_val_sum dipy.segment dipy.segment.bundles dipy.segment.clustering dipy.segment.clustering_algorithms dipy.segment.clusteringspeed dipy.segment.cythonutils dipy.segment.featurespeed dipy.segment.fss dipy.segment.mask dipy.segment.metric dipy.segment.metricspeed dipy.segment.mrf dipy.segment.threshold dipy.segment.tissue dipy.sims dipy.sims.phantom dipy.sims.voxel dipy.stats dipy.stats.analysis dipy.tracking dipy.tracking._utils dipy.tracking.direction_getter dipy.tracking.distances dipy.tracking.fbcmeasures dipy.tracking.learning dipy.tracking.life dipy.tracking.local_tracking dipy.tracking.localtrack dipy.tracking.mesh dipy.tracking.metrics dipy.tracking.propspeed dipy.tracking.stopping_criterion dipy.tracking.streamline dipy.tracking.streamlinespeed dipy.tracking.utils dipy.tracking.vox2track 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.viz dipy.workflows.workflow

most_similar_track_mam() (in module dipy.tracking.distances) motion_correction() (in module dipy.align._public) MotionCorrectionFlow (class in dipy.workflows.align) 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) mul_3vec() (in module dipy.tracking.distances) mul_3vecs() (in module dipy.tracking.distances) 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.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) ndarray_offset() (in module dipy.tracking.propspeed) 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) nearestneighbor_interpolate() (in module dipy.core.interpolation) NearestNeighborInterpolator (class in dipy.core.interpolation) negloglikelihood() (dipy.segment.mrf.ConstantObservationModel method) 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) 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) nlmeans_3d() (in module dipy.denoise.denspeed) nlmeans_block() (in module dipy.denoise.nlmeans_block) 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_3vec() (in module dipy.tracking.distances) 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_3vec() (in module dipy.tracking.distances) 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) octahedron_faces() (in module dipy.core.sphere) octahedron_vertices() (in module dipy.core.sphere) odf() (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) 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) OutsideImage (class in dipy.core.interpolation) OUTSIDEIMAGE (dipy.tracking.stopping_criterion.StreamlineStatus attribute) overlay_images() (in module dipy.viz.regtools) overlay_slices() (in module dipy.viz.regtools)

P

pad() (dipy.nn.deepn4.DeepN4 method) param_to_matrix() (dipy.align.transforms.Transform method) 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) ParzenJointHistogram (class in dipy.align.parzenhist) 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) pca_noise_estimate() (in module dipy.denoise.pca_noise_estimate) 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() (in module dipy.direction.bootstrap_direction_getter) (in module dipy.direction.closest_peak_direction_getter) (in module dipy.direction.peaks) 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_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) (in module dipy.segment.clustering_algorithms) perfusion_fraction (dipy.reconst.ivim.IvimFit property) permutationinverse() (in module dipy.core.wavelet) perpendicular_directions() (in module dipy.core.geometry) pft_tracker() (in module dipy.tracking.localtrack) 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) PmfGen (class in dipy.direction.pmf) PmfGenDirectionGetter (class in dipy.direction.closest_peak_direction_getter) point_segment_sq_distance() (in module dipy.tracking.distances) point_track_sq_distance_check() (in module dipy.tracking.distances)

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) precompute_cc_factors_2d() (in module dipy.align.crosscorr) precompute_cc_factors_2d_test() (in module dipy.align.crosscorr) precompute_cc_factors_3d() (in module dipy.align.crosscorr) precompute_cc_factors_3d_test() (in module dipy.align.crosscorr) predict() (dipy.core.optimize.SKLearnLinearSolver method) (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.deepn4.DeepN4 method) (dipy.nn.evac.EVACPlus method) (dipy.nn.histo_resdnn.HistoResDNN method) (dipy.nn.model.MultipleLayerPercepton method) (dipy.nn.model.SingleLayerPerceptron method) (dipy.nn.synb0.Synb0 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.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) prob_image() (dipy.segment.mrf.ConstantObservationModel method) prob_neighborhood() (dipy.segment.mrf.IteratedConditionalModes method) ProbabilisticDirectionGetter (class in dipy.direction.probabilistic_direction_getter) proc_reco_args() (in module dipy.reconst.recspeed) 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) PTTDirectionGetter (class in dipy.direction.ptt_direction_getter) PYERROR (dipy.tracking.stopping_criterion.StreamlineStatus attribute)

Q

qa_thr (dipy.reconst.eudx_direction_getter.EuDXDirectionGetter attribute) 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_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_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_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_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) quantize_positive_2d() (in module dipy.align.expectmax) quantize_positive_3d() (in module dipy.align.expectmax) Quaternion query() (dipy.tracking.fbcmeasures.KDTree method) query_ball_point() (dipy.tracking.fbcmeasures.KDTree method) query_ball_tree() (dipy.tracking.fbcmeasures.KDTree method) query_pairs() (dipy.tracking.fbcmeasures.KDTree method) quick_squash() (in module dipy.reconst.quick_squash) QuickBundles (class in dipy.segment.clustering) (class in dipy.segment.clusteringspeed) quickbundles() (in module dipy.segment.clustering_algorithms) QuickBundlesX (class in dipy.segment.clustering) (class in dipy.segment.clusteringspeed) quickbundlesx() (in module dipy.segment.clustering_algorithms) 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) radius_search() (dipy.segment.fss.FastStreamlineSearch method) random() (in module dipy.direction.probabilistic_direction_getter) (in module dipy.tracking.localtrack) 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) ReconstCSAFlow (class in dipy.workflows.reconst) 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) ReconstIvimFlow (class in dipy.workflows.reconst) ReconstMAPMRIFlow (class in dipy.workflows.reconst) ReconstModel (class in dipy.reconst.base) ReconstRUMBAFlow (class in dipy.workflows.reconst) recover_img() (in module dipy.nn.utils) recursive_response() (in module dipy.reconst.csdeconv) reduce() (in module dipy.reconst.quick_squash) 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) (dipy.segment.clusteringspeed.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_elements() (dipy.viz.horizon.tab.base.HorizonTab method) register_picker_callback() (dipy.viz.horizon.visualizer.slice.SlicesVisualizer method) register_series() (in module dipy.align._public) RegistrationStages() (in module dipy.align.imwarp) relist_streamlines() (in module dipy.tracking.streamline) remove_cluster() (dipy.segment.clustering.ClusterMap method) remove_clusters_by_size() (in module dipy.align.streamlinear) remove_invalid_streamlines() (dipy.io.stateful_tractogram.StatefulTractogram method) remove_padding() (in module dipy.denoise.denspeed) remove_similar_vertices() (in module dipy.reconst.recspeed) reorient_bvecs() (in module dipy.core.gradients) reorient_on_axis() (in module dipy.core.gradients) reorient_vector_field_2d() (in module dipy.align.vector_fields) reorient_vector_field_3d() (in module dipy.align.vector_fields) reorient_vectors() (in module dipy.core.gradients)

reposition() (dipy.viz.horizon.tab.base.TabManager method) resample() (in module dipy.align._public) resample_displacement_field_2d() (in module dipy.align.vector_fields) resample_displacement_field_3d() (in module dipy.align.vector_fields) ResampleFeature (class in dipy.segment.featurespeed) 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() (in module dipy.reconst.csdeconv) 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) (dipy.segment.clusteringspeed.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) RigidIsoScalingTransform2D (class in dipy.align.transforms) RigidIsoScalingTransform3D (class in dipy.align.transforms) RigidScalingTransform2D (class in dipy.align.transforms) RigidScalingTransform3D (class in dipy.align.transforms) RigidTransform2D (class in dipy.align.transforms) RigidTransform3D (class in dipy.align.transforms) rk() (dipy.reconst.dki.DiffusionKurtosisFit method) rodrigues_axis_rotation() (in module dipy.core.geometry) ROIsTab (class in dipy.viz.horizon.tab.roi) Rotation matrix Rotation vector RotationTransform2D (class in dipy.align.transforms) RotationTransform3D (class in dipy.align.transforms) round_bvals() (in module dipy.core.gradients) rtap() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit 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.FetchFlow method) (dipy.workflows.io.IoInfoFlow method) (dipy.workflows.io.SplitFlow method) (dipy.workflows.mask.MaskFlow method) (dipy.workflows.nn.EVACPlusFlow method) (dipy.workflows.reconst.ReconstCSAFlow method) (dipy.workflows.reconst.ReconstCSDFlow method) (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDsiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) (dipy.workflows.reconst.ReconstIvimFlow method) (dipy.workflows.reconst.ReconstMAPMRIFlow method) (dipy.workflows.reconst.ReconstRUMBAFlow 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) sample_domain_regular() (in module dipy.align.parzenhist) 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_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.cnn_1d_denoising.Cnn1DDenoiser method) ScaleSpace (class in dipy.align.scalespace) ScalingTransform2D (class in dipy.align.transforms) ScalingTransform3D (class in dipy.align.transforms) search_descending() (in module dipy.reconst.recspeed) 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) seg_stats() (dipy.segment.mrf.ConstantObservationModel 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_logger_level() (in module dipy.nn.utils) set_moving_image() (dipy.align.metrics.SimilarityMetric method) set_number_of_points() (in module dipy.tracking.streamlinespeed) 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_sft_logger_level() (in module dipy.io.stateful_tractogram) 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.parzenhist.ParzenJointHistogram 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_sh() (in module dipy.denoise.shift_twist_convolution) (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_rh() (in module dipy.reconst.shm) sh_to_sf() (in module dipy.denoise.shift_twist_convolution) (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) SHCoeffPmfGen (class in dipy.direction.pmf) 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_plot() (in module dipy.viz.regtools) SimplePmfGen (class in dipy.direction.pmf) simplify_warp_function_2d() (in module dipy.align.vector_fields) simplify_warp_function_3d() (in module dipy.align.vector_fields) 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.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) small_sphere() (in module dipy.data) 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_2d_symmetric_positive_definite() (in module dipy.align.sumsqdiff) solve_3d_symmetric_positive_definite() (in module dipy.align.sumsqdiff) 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_distance_matrix() (dipy.tracking.fbcmeasures.KDTree method) sparse_gradient() (in module dipy.align.vector_fields) 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) (class in dipy.denoise.enhancement_kernel) 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 (dipy.tracking.fbcmeasures.KDTree.innernode property) split_cti_params() (in module dipy.reconst.cti) split_dim (dipy.tracking.fbcmeasures.KDTree.innernode property) 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) StoppingCriterion (class in dipy.tracking.stopping_criterion) streamline_gradients() (in module dipy.tracking.life) streamline_mapping() (in module dipy.tracking.vox2track) 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) Streamlines (in module dipy.tracking.streamlinespeed) StreamlineStatus (class in dipy.tracking.stopping_criterion) sub_3vecs() (in module dipy.tracking.distances) subdivide() (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.denoise.enhancement_kernel.HemiSphere method) (dipy.denoise.enhancement_kernel.Sphere method) subsegment() (in module dipy.tracking.utils) sum_on_blocks_1d() (in module dipy.reconst.recspeed) summary() (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method) (dipy.nn.model.MultipleLayerPercepton method) (dipy.nn.model.SingleLayerPerceptron method) SumPointwiseEuclideanMetric (class in dipy.segment.metricspeed) 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.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.peak.PeaksTab property) (dipy.viz.horizon.tab.slice.SlicesTab property) (dipy.viz.horizon.tab.surface.SurfaceTab 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) TensorFit (class in dipy.reconst.dti) TensorModel (class in dipy.reconst.dti) threshold_propagator() (in module dipy.reconst.dsi) ThresholdStoppingCriterion (class in dipy.tracking.stopping_criterion) 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) total_weight (dipy.reconst.eudx_direction_getter.EuDXDirectionGetter attribute) trace() (dipy.reconst.dti.TensorFit method) (in module dipy.reconst.dti) track_counts() (in module dipy.tracking.vox2track) track_dist_3pts() (in module dipy.tracking.distances) track_roi_intersection_check() (in module dipy.tracking.distances) TRACKPOINT (dipy.tracking.stopping_criterion.StreamlineStatus attribute) TRACKVIS (dipy.io.stateful_tractogram.Origin attribute) tractogram_clusters (dipy.viz.horizon.visualizer.cluster.ClustersVisualizer property) train_test_split() (dipy.nn.cnn_1d_denoising.Cnn1DDenoiser method)

Transform (class in dipy.align.transforms) transform() (dipy.align.imaffine.AffineMap method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.align.streamlinear.JointStreamlineRegistrationMap method) (dipy.align.streamlinear.StreamlineRegistrationMap method) transform_2d_affine() (in module dipy.align.vector_fields) transform_2d_affine_nn() (in module dipy.align.vector_fields) transform_3d_affine() (in module dipy.align.vector_fields) transform_3d_affine_nn() (in module dipy.align.vector_fields) 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) TranslationTransform2D (class in dipy.align.transforms) TranslationTransform3D (class in dipy.align.transforms) traverse_postorder() (dipy.segment.clustering.TreeClusterMap method) (dipy.segment.clusteringspeed.TreeClusterMap method) tree (dipy.tracking.fbcmeasures.KDTree property) TreeCluster (class in dipy.segment.clustering) (class in dipy.segment.clusteringspeed) TreeClusterMap (class in dipy.segment.clustering) (class in dipy.segment.clusteringspeed) triangles_area() (in module dipy.tracking.mesh) trilinear_interp() (in module dipy.core.interpolation) trilinear_interpolate4d() (in module dipy.core.interpolation) TriLinearInterpolator (class in dipy.core.interpolation) triple_odf_maxima() (in module dipy.reconst.gqi) two_cingulum_bundles() (in module dipy.data)

U

ufa() (dipy.reconst.qti.QtiFit method) UNet3D() (in module dipy.nn.deepn4) (in module dipy.nn.synb0) unique_bvals() (in module dipy.core.gradients) 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 unit_icosahedron() (in module dipy.core.sphere) unit_octahedron() (in module dipy.core.sphere) 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) (dipy.segment.clustering_algorithms.ClusterCentroid method) (dipy.segment.clusteringspeed.ClusterCentroid method)

update_argument() (dipy.workflows.base.IntrospectiveArgumentParser method) update_gradient_dense() (dipy.align.parzenhist.ParzenJointHistogram method) update_gradient_sparse() (dipy.align.parzenhist.ParzenJointHistogram method) update_param() (dipy.segment.mrf.ConstantObservationModel method) update_pdfs_dense() (dipy.align.parzenhist.ParzenJointHistogram method) update_pdfs_sparse() (dipy.align.parzenhist.ParzenJointHistogram 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) upfir() (in module dipy.denoise.nlmeans_block) 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) vec_val_vect() (in module dipy.reconst.vec_val_sum) vector_cosine() (in module dipy.core.geometry) vector_norm() (in module dipy.core.geometry) VectorOfEndpointsFeature (class in dipy.segment.featurespeed) VerbosityLevels() (in module dipy.align) version() (dipy.io.dpy.Dpy method) vertices() (dipy.core.sphere.Sphere method) (dipy.denoise.enhancement_kernel.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) 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

warn() (in module dipy.denoise.pca_noise_estimate) (in module dipy.tracking.distances) warp_2d() (in module dipy.align.vector_fields) warp_2d_nn() (in module dipy.align.vector_fields) warp_3d() (in module dipy.align.vector_fields) warp_3d_nn() (in module dipy.align.vector_fields) warp_coordinates_2d() (in module dipy.align.vector_fields) warp_coordinates_3d() (in module dipy.align.vector_fields) warp_endomorphism() (dipy.align.imwarp.DiffeomorphicMap method) Wcons() (in module dipy.reconst.dki) 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) (dipy.denoise.enhancement_kernel.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) (dipy.denoise.enhancement_kernel.Sphere property)

Z

z (dipy.core.sphere.Sphere property) (dipy.denoise.enhancement_kernel.Sphere property)