Index

_

__init__() (dipy.align.Bunch method) (dipy.align.imaffine.AffineInvalidValuesError method) (dipy.align.imaffine.AffineInversionError method) (dipy.align.imaffine.AffineMap method) (dipy.align.imaffine.AffineRegistration method) (dipy.align.imaffine.IsotropicScaleSpace method) (dipy.align.imaffine.MutualInformationMetric method) (dipy.align.imaffine.Optimizer method) (dipy.align.imaffine.ParzenJointHistogram method) (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.Bunch method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric 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.Optimizer method) (dipy.align.streamlinear.StreamlineDistanceMetric method) (dipy.align.streamlinear.StreamlineLinearRegistration method) (dipy.align.streamlinear.StreamlineRegistrationMap method) (dipy.core.gradients.GradientTable method) (dipy.core.gradients.HemiSphere method) (dipy.core.graph.Graph method) (dipy.core.onetime.OneTimeProperty method) (dipy.core.onetime.ResetMixin method) (dipy.core.optimize.NonNegativeLeastSquares method) (dipy.core.optimize.Optimizer method) (dipy.core.optimize.SKLearnLinearSolver method) (dipy.core.profile.Profiler method) (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.core.sphere_stats.permutations method) (dipy.core.subdivide_octahedron.HemiSphere method) (dipy.data.DataError method) (dipy.data.GradientTable method) (dipy.data.HemiSphere method) (dipy.data.Sphere method) (dipy.data.fetcher.FetcherError method) (dipy.direction.BootDirectionGetter method) (dipy.direction.ClosestPeakDirectionGetter method) (dipy.direction.DeterministicMaximumDirectionGetter method) (dipy.direction.EuDXDirectionGetter method) (dipy.direction.InTemporaryDirectory method) (dipy.direction.PeaksAndMetrics method) (dipy.direction.ProbabilisticDirectionGetter method) (dipy.direction.Sphere method) (dipy.direction.peaks.EuDXDirectionGetter method) (dipy.direction.peaks.InTemporaryDirectory method) (dipy.direction.peaks.PeaksAndMetrics method) (dipy.direction.peaks.Sphere method) (dipy.direction.peaks.repeat method) (dipy.direction.repeat method) (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.gradients.InTemporaryDirectory method) (dipy.io.peaks.PeaksAndMetrics method) (dipy.io.peaks.Sphere method) (dipy.io.stateful_tractogram.PerArrayDict method) (dipy.io.stateful_tractogram.PerArraySequenceDict method) (dipy.io.stateful_tractogram.Space method) (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.stateful_tractogram.Tractogram method) (dipy.io.stateful_tractogram.itemgetter method) (dipy.io.stateful_tractogram.product method) (dipy.io.streamline.Dpy method) (dipy.io.streamline.Space method) (dipy.io.streamline.StatefulTractogram method) (dipy.io.streamline.Tractogram method) (dipy.io.utils.Nifti1Image method) (dipy.reconst.base.ReconstFit method) (dipy.reconst.base.ReconstModel method) (dipy.reconst.benchmarks.bench_csd.ConstrainedSphericalDeconvModel method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) (dipy.reconst.cache.Cache method) (dipy.reconst.csdeconv.AxSymShResponse method) (dipy.reconst.csdeconv.ConstrainedSDTModel method) (dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel method) (dipy.reconst.csdeconv.SphHarmFit method) (dipy.reconst.csdeconv.SphHarmModel method) (dipy.reconst.csdeconv.TensorModel method) (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki.DiffusionKurtosisModel method) (dipy.reconst.dki.ReconstModel method) (dipy.reconst.dki.TensorFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisModel method) (dipy.reconst.dki_micro.KurtosisMicrostructuralFit method) (dipy.reconst.dki_micro.KurtosisMicrostructureModel method) (dipy.reconst.dsi.Cache method) (dipy.reconst.dsi.DiffusionSpectrumDeconvFit method) (dipy.reconst.dsi.DiffusionSpectrumDeconvModel method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.dsi.DiffusionSpectrumModel method) (dipy.reconst.dsi.OdfFit method) (dipy.reconst.dsi.OdfModel method) (dipy.reconst.dti.ReconstModel method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.dti.TensorModel method) (dipy.reconst.forecast.Cache method) (dipy.reconst.forecast.ForecastFit method) (dipy.reconst.forecast.ForecastModel method) (dipy.reconst.forecast.OdfFit method) (dipy.reconst.forecast.OdfModel method) (dipy.reconst.fwdti.FreeWaterTensorFit method) (dipy.reconst.fwdti.FreeWaterTensorModel method) (dipy.reconst.fwdti.ReconstModel method) (dipy.reconst.fwdti.TensorFit method) (dipy.reconst.gqi.Cache method) (dipy.reconst.gqi.GeneralizedQSamplingFit method) (dipy.reconst.gqi.GeneralizedQSamplingModel method) (dipy.reconst.gqi.OdfFit method) (dipy.reconst.gqi.OdfModel method) (dipy.reconst.ivim.IvimFit method) (dipy.reconst.ivim.IvimModelTRR method) (dipy.reconst.ivim.IvimModelVP method) (dipy.reconst.ivim.ReconstModel method) (dipy.reconst.mapmri.Cache method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.mapmri.MapmriModel method) (dipy.reconst.mapmri.Optimizer method) (dipy.reconst.mapmri.ReconstFit method) (dipy.reconst.mapmri.ReconstModel 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.msdki.ReconstModel method) (dipy.reconst.multi_voxel.CallableArray method) (dipy.reconst.multi_voxel.MultiVoxelFit method) (dipy.reconst.multi_voxel.ReconstFit method) (dipy.reconst.odf.OdfFit method) (dipy.reconst.odf.OdfModel method) (dipy.reconst.odf.ReconstFit method) (dipy.reconst.odf.ReconstModel method) (dipy.reconst.qtdmri.Cache method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.qtdmri.QtdmriModel method) (dipy.reconst.sfm.Cache method) (dipy.reconst.sfm.ExponentialIsotropicFit method) (dipy.reconst.sfm.ExponentialIsotropicModel method) (dipy.reconst.sfm.IsotropicFit method) (dipy.reconst.sfm.IsotropicModel method) (dipy.reconst.sfm.ReconstFit method) (dipy.reconst.sfm.ReconstModel method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.sfm.SparseFascicleModel method) (dipy.reconst.shm.Cache method) (dipy.reconst.shm.CsaOdfModel method) (dipy.reconst.shm.LooseVersion method) (dipy.reconst.shm.OdfFit method) (dipy.reconst.shm.OdfModel 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.Cache method) (dipy.reconst.shore.ShoreFit method) (dipy.reconst.shore.ShoreModel method) (dipy.segment.benchmarks.bench_quickbundles.MDFpy method) (dipy.segment.benchmarks.bench_quickbundles.Metric method) (dipy.segment.bundles.BundleMinDistanceAsymmetricMetric method) (dipy.segment.bundles.BundleMinDistanceMetric method) (dipy.segment.bundles.BundleSumDistanceMatrixMetric method) (dipy.segment.bundles.RecoBundles method) (dipy.segment.bundles.StreamlineLinearRegistration method) (dipy.segment.bundles.chain method) (dipy.segment.clustering.ABCMeta method) (dipy.segment.clustering.AveragePointwiseEuclideanMetric method) (dipy.segment.clustering.Cluster method) (dipy.segment.clustering.ClusterCentroid method) (dipy.segment.clustering.ClusterMap method) (dipy.segment.clustering.ClusterMapCentroid method) (dipy.segment.clustering.Clustering method) (dipy.segment.clustering.Identity method) (dipy.segment.clustering.Metric method) (dipy.segment.clustering.MinimumAverageDirectFlipMetric method) (dipy.segment.clustering.QuickBundles method) (dipy.segment.clustering.QuickBundlesX method) (dipy.segment.clustering.ResampleFeature method) (dipy.segment.clustering.TreeCluster method) (dipy.segment.clustering.TreeClusterMap method) (dipy.segment.metric.ArcLengthFeature method) (dipy.segment.metric.AveragePointwiseEuclideanMetric method) (dipy.segment.metric.CenterOfMassFeature method) (dipy.segment.metric.CosineMetric method) (dipy.segment.metric.Feature method) (dipy.segment.metric.IdentityFeature method) (dipy.segment.metric.Metric method) (dipy.segment.metric.MidpointFeature method) (dipy.segment.metric.MinimumAverageDirectFlipMetric method) (dipy.segment.metric.ResampleFeature method) (dipy.segment.metric.SumPointwiseEuclideanMetric method) (dipy.segment.metric.VectorOfEndpointsFeature method) (dipy.segment.tissue.ConstantObservationModel method) (dipy.segment.tissue.IteratedConditionalModes method) (dipy.segment.tissue.TissueClassifierHMRF method) (dipy.stats.analysis.AveragePointwiseEuclideanMetric method) (dipy.stats.analysis.QuickBundles method) (dipy.stats.analysis.cKDTree method) (dipy.tracking.life.FiberFit method) (dipy.tracking.life.FiberModel method) (dipy.tracking.life.LifeSignalMaker method) (dipy.tracking.life.ReconstFit method) (dipy.tracking.life.ReconstModel method) (dipy.tracking.local_tracking.AnatomicalStoppingCriterion method) (dipy.tracking.local_tracking.LocalTracking method) (dipy.tracking.local_tracking.ParticleFilteringTracking method) (dipy.tracking.local_tracking.StreamlineStatus method) (dipy.tracking.utils.defaultdict method) (dipy.viz.app.EventCounter method) (dipy.viz.app.Horizon method) (dipy.viz.app.Space method) (dipy.viz.app.StatefulTractogram method) (dipy.viz.gmem.GlobalHorizon method) (dipy.workflows.align.AffineMap method) (dipy.workflows.align.AffineRegistration method) (dipy.workflows.align.AffineTransform3D method) (dipy.workflows.align.ApplyTransformFlow method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.DiffeomorphicMap method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.ImageRegistrationFlow method) (dipy.workflows.align.MutualInformationMetric method) (dipy.workflows.align.ResliceFlow method) (dipy.workflows.align.RigidTransform3D method) (dipy.workflows.align.SSDMetric method) (dipy.workflows.align.SlrWithQbxFlow method) (dipy.workflows.align.SymmetricDiffeomorphicRegistration method) (dipy.workflows.align.SynRegistrationFlow method) (dipy.workflows.align.TranslationTransform3D method) (dipy.workflows.align.Workflow method) (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.base.NumpyDocString method) (dipy.workflows.combined_workflow.CombinedWorkflow method) (dipy.workflows.combined_workflow.Workflow method) (dipy.workflows.denoise.NLMeansFlow method) (dipy.workflows.denoise.Workflow method) (dipy.workflows.docstring_parser.NumpyDocString method) (dipy.workflows.docstring_parser.Reader method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) (dipy.workflows.io.FetchFlow method) (dipy.workflows.io.IoInfoFlow method) (dipy.workflows.io.Workflow method) (dipy.workflows.mask.MaskFlow method) (dipy.workflows.mask.Workflow method) (dipy.workflows.multi_io.IOIterator method) (dipy.workflows.reconst.ConstrainedSphericalDeconvModel method) (dipy.workflows.reconst.CsaOdfModel method) (dipy.workflows.reconst.DiffusionKurtosisModel method) (dipy.workflows.reconst.ReconstCSAFlow method) (dipy.workflows.reconst.ReconstCSDFlow method) (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) (dipy.workflows.reconst.ReconstIvimFlow method) (dipy.workflows.reconst.ReconstMAPMRIFlow method) (dipy.workflows.reconst.TensorModel method) (dipy.workflows.reconst.Workflow method) (dipy.workflows.segment.LabelsBundlesFlow method) (dipy.workflows.segment.MedianOtsuFlow method) (dipy.workflows.segment.RecoBundles method) (dipy.workflows.segment.RecoBundlesFlow method) (dipy.workflows.segment.Workflow method) (dipy.workflows.stats.BundleAnalysisPopulationFlow method) (dipy.workflows.stats.LinearMixedModelsFlow method) (dipy.workflows.stats.SNRinCCFlow method) (dipy.workflows.stats.TensorModel method) (dipy.workflows.stats.Workflow method) (dipy.workflows.tracking.BinaryStoppingCriterion method) (dipy.workflows.tracking.ClosestPeakDirectionGetter method) (dipy.workflows.tracking.CmcStoppingCriterion method) (dipy.workflows.tracking.DeterministicMaximumDirectionGetter method) (dipy.workflows.tracking.LocalFiberTrackingPAMFlow method) (dipy.workflows.tracking.LocalTracking method) (dipy.workflows.tracking.PFTrackingPAMFlow method) (dipy.workflows.tracking.ParticleFilteringTracking method) (dipy.workflows.tracking.ProbabilisticDirectionGetter method) (dipy.workflows.tracking.Space method) (dipy.workflows.tracking.StatefulTractogram method) (dipy.workflows.tracking.ThresholdStoppingCriterion method) (dipy.workflows.tracking.Workflow method) (dipy.workflows.viz.Dpy method) (dipy.workflows.viz.HorizonFlow method) (dipy.workflows.viz.Workflow method) (dipy.workflows.workflow.Workflow method)

A

ABCMeta (class in dipy.segment.clustering) abstractmethod() (in module dipy.segment.clustering) ad() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) adaptive_soft_matching() (in module dipy.denoise.adaptive_soft_matching) adc() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) add() (dipy.segment.clustering.TreeCluster method) add_actors() (dipy.viz.app.Horizon method) add_cluster() (dipy.segment.clustering.ClusterMap method) add_description() (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) add_edge() (dipy.core.graph.Graph method) add_epilogue() (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) add_node() (dipy.core.graph.Graph method) add_noise() (in module dipy.segment.tissue) (in module dipy.sims.phantom) (in module dipy.sims.voxel) add_sub_flow_args() (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) add_workflow() (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) afb3D() (in module dipy.core.wavelet) afb3D_A() (in module dipy.core.wavelet) Affine matrix Affine transformation affine() (dipy.workflows.align.ImageRegistrationFlow method) affine_to_rasmm() (dipy.io.stateful_tractogram.Tractogram property) (dipy.io.streamline.Tractogram property) affine_transform() (in module dipy.align.reslice) AffineInvalidValuesError (class in dipy.align.imaffine) AffineInversionError (class in dipy.align.imaffine) AffineMap (class in dipy.align.imaffine) (class in dipy.workflows.align) AffineRegistration (class in dipy.align.imaffine) (class in dipy.workflows.align) AffineTransform3D (class in dipy.workflows.align) afq_profile() (in module dipy.stats.analysis) ak() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) akc() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) all_paths() (dipy.core.graph.Graph method) all_tensor_evecs() (in module dipy.sims.voxel) allocate() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) AnatomicalStoppingCriterion (class in dipy.tracking.local_tracking) ang_thr (dipy.direction.EuDXDirectionGetter attribute) (dipy.direction.peaks.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) apply_affine() (dipy.io.stateful_tractogram.Tractogram method) (dipy.io.streamline.Tractogram method) (in module dipy.io.stateful_tractogram) (in module dipy.segment.bundles) (in module dipy.tracking.streamline) (in module dipy.tracking.utils) apply_shader() (in module dipy.viz.app) applymask() (in module dipy.segment.mask) ApplyTransformFlow (class in dipy.workflows.align) arbitrarypoint() (in module dipy.tracking.metrics) architecture() (in module dipy.core.rng) ArcLengthFeature (class in dipy.segment.metric) are_compatible() (dipy.segment.benchmarks.bench_quickbundles.MDFpy method) (dipy.segment.benchmarks.bench_quickbundles.Metric method) (dipy.segment.clustering.Metric method) (dipy.segment.metric.Metric method) as_native_array() (in module dipy.data) as_strided() (in module dipy.core.ndindex) (in module dipy.reconst.multi_voxel) asarray() (in module dipy.tracking.utils) assert_array_almost_equal() (in module dipy.tracking.benchmarks.bench_streamline) assert_array_equal() (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.tracking.benchmarks.bench_streamline) assert_arrays_equal() (in module dipy.segment.benchmarks.bench_quickbundles) assert_equal() (in module dipy.segment.benchmarks.bench_quickbundles) assign() (dipy.segment.clustering.Cluster method) (dipy.segment.clustering.ClusterCentroid method) auto_attr() (in module dipy.core.gradients) (in module dipy.core.onetime) (in module dipy.core.sphere) (in module dipy.reconst.cache) (in module dipy.reconst.dti) (in module dipy.reconst.msdki) (in module dipy.reconst.sfm) (in module dipy.reconst.shm) auto_response() (in module dipy.reconst.csdeconv) (in module dipy.workflows.reconst) AveragePointwiseEuclideanMetric (class in dipy.segment.clustering) (class in dipy.segment.metric) (class in dipy.stats.analysis) awf() (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) axial_diffusivity() (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.workflows.reconst) 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

b0s_mask() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) b_mat() (in module dipy.reconst.mapmri) b_mat_isotropic() (in module dipy.reconst.mapmri) basename_without_extension() (in module dipy.workflows.multi_io) basis() (dipy.reconst.csdeconv.AxSymShResponse method) bench() (in module dipy) (in module dipy.denoise) (in module dipy.reconst) (in module dipy.tracking) bench_bounding_box() (in module dipy.reconst.benchmarks.bench_bounding_box) bench_compress_streamlines() (in module dipy.tracking.benchmarks.bench_streamline) bench_csdeconv() (in module dipy.reconst.benchmarks.bench_csd) bench_length() (in module dipy.tracking.benchmarks.bench_streamline) bench_local_maxima() (in module dipy.reconst.benchmarks.bench_peaks) bench_quick_squash() (in module dipy.reconst.benchmarks.bench_squash) bench_quickbundles() (in module dipy.segment.benchmarks.bench_quickbundles) bench_set_number_of_points() (in module dipy.tracking.benchmarks.bench_streamline) bench_vec_val_vect() (in module dipy.reconst.benchmarks.bench_vec_val_sum) bin_index (dipy.align.imaffine.ParzenJointHistogram attribute) bin_normalize_moving (dipy.align.imaffine.ParzenJointHistogram attribute) bin_normalize_static (dipy.align.imaffine.ParzenJointHistogram attribute) binary_dilation() (in module dipy.segment.mask) (in module dipy.workflows.stats) BinaryStoppingCriterion (class in dipy.workflows.tracking) binomialfloat() (in module dipy.reconst.mapmri) bisect() (in module dipy.io.stateful_tractogram) BootDirectionGetter (class in dipy.direction) bootstrap_data_array() (in module dipy.reconst.shm) bootstrap_data_voxel() (in module dipy.reconst.shm) bounding_box() (in module dipy.reconst.benchmarks.bench_bounding_box) (in module dipy.segment.mask) (in module dipy.workflows.stats)

boxsize (dipy.stats.analysis.cKDTree attribute) build_label() (in module dipy.viz.app) (in module dipy.viz.panel) build_scene() (dipy.viz.app.Horizon method) build_show() (dipy.viz.app.Horizon method) Bunch (class in dipy.align) (class in dipy.align.imwarp) bundle_adjacency() (in module dipy.segment.bundles) bundle_analysis() (in module dipy.stats.analysis) (in module dipy.workflows.stats) 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_sum_distance() (in module dipy.align.streamlinear) BundleAnalysisPopulationFlow (class in dipy.workflows.stats) BundleMinDistanceAsymmetricMetric (class in dipy.align.streamlinear) (class in dipy.segment.bundles) BundleMinDistanceMatrixMetric (class in dipy.align.streamlinear) BundleMinDistanceMetric (class in dipy.align.streamlinear) (class in dipy.segment.bundles) bundles_distances_mam() (in module dipy.segment.bundles) bundles_distances_mdf() (in module dipy.segment.bundles) (in module dipy.tracking.streamline) BundleSumDistanceMatrixMetric (class in dipy.align.streamlinear) (class in dipy.segment.bundles) bvals() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) bvecs() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) bytes() (in module dipy.tracking.metrics)

C

Cache (class in dipy.reconst.cache) (class in dipy.reconst.dsi) (class in dipy.reconst.forecast) (class in dipy.reconst.gqi) (class in dipy.reconst.mapmri) (class in dipy.reconst.qtdmri) (class in dipy.reconst.sfm) (class in dipy.reconst.shm) (class in dipy.reconst.shore) cache_clear() (dipy.reconst.cache.Cache method) (dipy.reconst.dsi.Cache method) (dipy.reconst.forecast.Cache method) (dipy.reconst.gqi.Cache method) (dipy.reconst.mapmri.Cache method) (dipy.reconst.qtdmri.Cache method) (dipy.reconst.sfm.Cache method) (dipy.reconst.shm.Cache method) (dipy.reconst.shore.Cache method) cache_get() (dipy.reconst.cache.Cache method) (dipy.reconst.dsi.Cache method) (dipy.reconst.forecast.Cache method) (dipy.reconst.gqi.Cache method) (dipy.reconst.mapmri.Cache method) (dipy.reconst.qtdmri.Cache method) (dipy.reconst.sfm.Cache method) (dipy.reconst.shm.Cache method) (dipy.reconst.shore.Cache method) cache_set() (dipy.reconst.cache.Cache method) (dipy.reconst.dsi.Cache method) (dipy.reconst.forecast.Cache method) (dipy.reconst.gqi.Cache method) (dipy.reconst.mapmri.Cache method) (dipy.reconst.qtdmri.Cache method) (dipy.reconst.sfm.Cache method) (dipy.reconst.shm.Cache method) (dipy.reconst.shore.Cache method) calc_signal() (dipy.tracking.life.LifeSignalMaker method) calculate_max_order() (in module dipy.reconst.shm) 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) (in module dipy.core.sphere) (in module dipy.reconst.csdeconv) (in module dipy.reconst.dki) (in module dipy.reconst.forecast) (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) (in module dipy.reconst.shm) (in module dipy.reconst.shore) cart_distance() (in module dipy.core.geometry) CCMetric (class in dipy.align.metrics) (class in dipy.workflows.align) cdist() (in module dipy.tracking.streamline) (in module dipy.tracking.utils) center_of_mass() (dipy.workflows.align.ImageRegistrationFlow method) (in module dipy.tracking.metrics) center_streamlines() (in module dipy.align.streamlinear) (in module dipy.tracking.streamline) CenterOfMassFeature (class in dipy.segment.metric) centroids() (dipy.segment.clustering.ClusterMapCentroid property) chain (class in dipy.segment.bundles) check_counts() (dipy.viz.app.EventCounter method) check_dimensions() (in module dipy.workflows.align) check_md5() (in module dipy.data.fetcher) check_multi_b() (in module dipy.core.gradients) (in module dipy.reconst.dki) (in module dipy.reconst.fwdti) (in module dipy.reconst.msdki) check_range() (in module dipy.segment.bundles) children() (dipy.core.graph.Graph method) cholesky_to_lower_triangular() (in module dipy.reconst.fwdti) circumradius() (in module dipy.core.geometry) cKDTree (class in dipy.stats.analysis) classify() (dipy.segment.tissue.TissueClassifierHMRF method) clean_cc_mask() (in module dipy.segment.mask) clear() (dipy.segment.clustering.ClusterMap method) close() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) ClosestPeakDirectionGetter (class in dipy.direction) (class in dipy.workflows.tracking) Cluster (class in dipy.segment.clustering) cluster() (dipy.segment.clustering.Clustering method) (dipy.segment.clustering.QuickBundles method) (dipy.segment.clustering.QuickBundlesX method) (dipy.stats.analysis.QuickBundles method) cluster_confidence() (in module dipy.tracking.streamline) ClusterCentroid (class in dipy.segment.clustering) Clustering (class in dipy.segment.clustering) ClusterMap (class in dipy.segment.clustering)

ClusterMapCentroid (class in dipy.segment.clustering) clusters() (dipy.segment.clustering.ClusterMap property) clusters_sizes() (dipy.segment.clustering.ClusterMap method) CmcStoppingCriterion (class in dipy.workflows.tracking) coeff_of_determination() (in module dipy.reconst.cross_validation) color_fa() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dti) (in module dipy.segment.mask) (in module dipy.workflows.reconst) CombinedWorkflow (class in dipy.workflows.combined_workflow) common_start() (in module dipy.workflows.multi_io) compare_orientation_sets() (in module dipy.core.sphere_stats) component_re (dipy.reconst.shm.LooseVersion attribute) compose_matrix() (in module dipy.align.streamlinear) (in module dipy.core.geometry) compose_matrix44() (in module dipy.align.streamlinear) compose_transformations() (in module dipy.align.streamlinear) (in module dipy.core.geometry) compress_streamlines() (in module dipy.tracking.benchmarks.bench_streamline) (in module dipy.tracking.streamline) compress_streamlines_python() (in module dipy.tracking.benchmarks.bench_streamline) compute_backward() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) compute_bounding_box() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) compute_demons_step() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) compute_forward() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) compute_gauss_newton_step() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) compute_inversion_error() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) compute_parzen_mi() (in module dipy.align.imaffine) concatenate() (in module dipy.reconst.shm) concatenate_inputs() (in module dipy.workflows.multi_io) connect_output_paths() (in module dipy.workflows.multi_io) connectivity_matrix() (in module dipy.tracking.utils) ConstantObservationModel (class in dipy.segment.tissue) ConstrainedSDTModel (class in dipy.reconst.csdeconv) ConstrainedSphericalDeconvModel (class in dipy.reconst.benchmarks.bench_csd) (class in dipy.reconst.csdeconv) (class in dipy.workflows.reconst) convolve() (in module dipy.denoise.noise_estimate) copy() (dipy.io.stateful_tractogram.Tractogram method) (dipy.io.streamline.Tractogram method) (dipy.tracking.utils.defaultdict method) copyfileobj() (in module dipy.data.fetcher) copyfileobj_withprogress() (in module dipy.data.fetcher) CosineMetric (class in dipy.segment.metric) count() (dipy.viz.app.EventCounter method) count_neighbors() (dipy.stats.analysis.cKDTree method) cpu_count() (in module dipy.align.reslice) (in module dipy.direction) (in module dipy.direction.peaks) create_directories() (dipy.workflows.multi_io.IOIterator method) create_nifti_header() (in module dipy.io.utils) create_outputs() (dipy.workflows.multi_io.IOIterator method) create_qspace() (in module dipy.reconst.dsi) create_qtable() (in module dipy.reconst.dsi) create_rspace() (in module dipy.reconst.mapmri) (in module dipy.reconst.shore) create_rt_space_grid() (in module dipy.reconst.qtdmri) create_tractogram_header() (in module dipy.io.streamline) (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) CsaOdfModel (class in dipy.reconst.shm) (class in dipy.workflows.reconst) csdeconv() (in module dipy.reconst.csdeconv) (in module dipy.reconst.forecast) cshift3D() (in module dipy.core.wavelet) cvx_fit() (dipy.reconst.ivim.IvimModelVP method) cylinders_and_ball_soderman() (in module dipy.sims.voxel)

D

D() (dipy.reconst.ivim.IvimFit property) D_star() (dipy.reconst.ivim.IvimFit property) data (dipy.stats.analysis.cKDTree attribute) data_per_point() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.stateful_tractogram.Tractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.io.streamline.Tractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) data_per_streamline() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.stateful_tractogram.Tractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.io.streamline.Tractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) DataError (class in dipy.data) decfa() (in module dipy.io.utils) decfa_to_float() (in module dipy.io.utils) decompose_matrix() (in module dipy.align.streamlinear) (in module dipy.core.geometry) decompose_matrix44() (in module dipy.align.streamlinear) decompose_tensor() (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) dedent_lines() (in module dipy.workflows.docstring_parser) deepcopy() (in module dipy.io.stateful_tractogram) (in module dipy.io.streamline) (in module dipy.tracking.streamline) default_factory (dipy.tracking.utils.defaultdict attribute) defaultdict (class in dipy.tracking.utils) deform_streamlines() (in module dipy.tracking.streamline) 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) design_matrix() (dipy.reconst.sfm.SparseFascicleModel method) (in module dipy.reconst.dki) (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) (in module dipy.reconst.msdki) 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) detect_format() (in module dipy.io.streamline) (in module dipy.io.utils) determinant() (in module dipy.reconst.dti) DeterministicMaximumDirectionGetter (class in dipy.direction) (class in dipy.workflows.tracking) deviatoric() (in module dipy.reconst.dti) diag() (in module dipy.reconst.shm) diff() (in module dipy.reconst.shm) diff2eigenvectors() (in module dipy.sims.phantom) DiffeomorphicMap (class in dipy.align.imwarp) (class in dipy.workflows.align) DiffeomorphicRegistration (class in dipy.align.imwarp) differential_evolution() (in module dipy.reconst.ivim) diffusion_components() (in module dipy.reconst.dki_micro) DiffusionKurtosisFit (class in dipy.reconst.dki) (class in dipy.reconst.dki_micro) DiffusionKurtosisModel (class in dipy.reconst.dki) (class in dipy.reconst.dki_micro) (class in dipy.workflows.reconst) DiffusionSpectrumDeconvFit (class in dipy.reconst.dsi) DiffusionSpectrumDeconvModel (class in dipy.reconst.dsi) DiffusionSpectrumFit (class in dipy.reconst.dsi) DiffusionSpectrumModel (class in dipy.reconst.dsi) dipy (module) dipy.__config__ (module) dipy.align (module) dipy.align.imaffine (module) dipy.align.imwarp (module) dipy.align.metrics (module) dipy.align.reslice (module) dipy.align.scalespace (module) dipy.align.streamlinear (module) dipy.boots (module) dipy.core (module) dipy.core.geometry (module) dipy.core.gradients (module) dipy.core.graph (module) dipy.core.histeq (module) dipy.core.ndindex (module) dipy.core.onetime (module) dipy.core.optimize (module) dipy.core.profile (module) dipy.core.rng (module) dipy.core.sphere (module) dipy.core.sphere_stats (module) dipy.core.subdivide_octahedron (module) dipy.core.wavelet (module) dipy.data (module) dipy.data.fetcher (module) dipy.denoise (module) dipy.denoise.adaptive_soft_matching (module) dipy.denoise.gibbs (module) dipy.denoise.localpca (module) dipy.denoise.nlmeans (module) dipy.denoise.noise_estimate (module) dipy.denoise.non_local_means (module) dipy.direction (module) dipy.direction.peaks (module) dipy.io (module) dipy.io.bvectxt (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.utils (module) dipy.io.vtk (module) dipy.reconst (module) dipy.reconst.base (module) dipy.reconst.benchmarks (module) dipy.reconst.benchmarks.bench_bounding_box (module) dipy.reconst.benchmarks.bench_csd (module) dipy.reconst.benchmarks.bench_peaks (module) dipy.reconst.benchmarks.bench_squash (module) dipy.reconst.benchmarks.bench_vec_val_sum (module) dipy.reconst.cache (module) dipy.reconst.cross_validation (module)

dipy.reconst.csdeconv (module) dipy.reconst.dki (module) dipy.reconst.dki_micro (module) dipy.reconst.dsi (module) dipy.reconst.dti (module) dipy.reconst.forecast (module) dipy.reconst.fwdti (module) dipy.reconst.gqi (module) dipy.reconst.ivim (module) dipy.reconst.mapmri (module) dipy.reconst.mcsd (module) dipy.reconst.msdki (module) dipy.reconst.multi_voxel (module) dipy.reconst.odf (module) dipy.reconst.qtdmri (module) dipy.reconst.sfm (module) dipy.reconst.shm (module) dipy.reconst.shore (module) dipy.reconst.utils (module) dipy.segment (module) dipy.segment.benchmarks (module) dipy.segment.benchmarks.bench_quickbundles (module) dipy.segment.bundles (module) dipy.segment.clustering (module) dipy.segment.mask (module) dipy.segment.metric (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.benchmarks (module) dipy.tracking.benchmarks.bench_streamline (module) dipy.tracking.learning (module) dipy.tracking.life (module) dipy.tracking.local_tracking (module) dipy.tracking.metrics (module) dipy.tracking.streamline (module) dipy.tracking.utils (module) dipy.viz (module) dipy.viz.app (module) dipy.viz.gmem (module) dipy.viz.panel (module) dipy.viz.projections (module) dipy.viz.regtools (module) dipy.workflows (module) dipy.workflows.align (module) dipy.workflows.base (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.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) (in module dipy.reconst.dki_micro) directional_diffusion_variance() (in module dipy.reconst.dki) directional_kurtosis() (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) directions() (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) dirname() (in module dipy.data) disperse_charges() (in module dipy.core.gradients) (in module dipy.core.sphere) dist() (dipy.segment.benchmarks.bench_quickbundles.MDFpy method) (dipy.segment.benchmarks.bench_quickbundles.Metric method) (dipy.segment.clustering.Metric method) (dipy.segment.metric.Metric method) (in module dipy.segment.metric) dist_to_corner() (in module dipy.core.geometry) (in module dipy.tracking.streamline) (in module dipy.tracking.utils) 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.StreamlineDistanceMetric method) (dipy.segment.bundles.BundleMinDistanceAsymmetricMetric method) (dipy.segment.bundles.BundleMinDistanceMetric method) (dipy.segment.bundles.BundleSumDistanceMatrixMetric method) (dipy.workflows.align.MutualInformationMetric method) distance_and_gradient() (dipy.align.imaffine.MutualInformationMetric method) (dipy.workflows.align.MutualInformationMetric method) distance_matrix() (in module dipy.segment.metric) distance_matrix_mdf() (in module dipy.align.streamlinear) distinguishable_colormap() (in module dipy.viz.app) dki_design_matrix() (in module dipy.reconst.utils) (in module dipy.sims.voxel) 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) (dipy.workflows.align.AffineRegistration attribute) doctest_skip_parser() (in module dipy.viz.projections) dot() (in module dipy.reconst.shm) (in module dipy.sims.voxel) down() (dipy.core.graph.Graph method) down_short() (dipy.core.graph.Graph method) downsample() (in module dipy.tracking.metrics) dpar() (dipy.reconst.forecast.ForecastFit property) dperp() (dipy.reconst.forecast.ForecastFit property) Dpy (class in dipy.io) (class in dipy.io.dpy) (class in dipy.io.streamline) (class in dipy.workflows.viz) draw_lattice_2d() (in module dipy.viz.regtools) dsi_deconv_voxels() (in module dipy.data) dsi_voxels() (in module dipy.data) dti_design_matrix() (in module dipy.reconst.dki_micro) dti_measures() (in module dipy.stats.analysis) dwt3D() (in module dipy.core.wavelet)

E

edges() (dipy.core.sphere.Sphere method) (dipy.data.Sphere method) (dipy.direction.Sphere method) (dipy.direction.peaks.Sphere method) (dipy.io.peaks.Sphere method) eig_from_lo_tri() (in module dipy.reconst.dti) eigenstats() (in module dipy.core.sphere_stats) eigh() (in module dipy.denoise.localpca) elastic_crossvalidation() (in module dipy.reconst.qtdmri) EMMetric (class in dipy.align.metrics) (class in dipy.workflows.align) empty() (in module dipy.reconst.shm) (in module dipy.tracking.utils) ENDPOINT (dipy.tracking.local_tracking.StreamlineStatus attribute) endpoint() (in module dipy.tracking.metrics) eof() (dipy.workflows.docstring_parser.Reader method) equatorial_maximum() (in module dipy.reconst.gqi) equatorial_zone_vertices() (in module dipy.reconst.gqi) estimate_f_D_star() (dipy.reconst.ivim.IvimModelTRR method) estimate_linear_fit() (dipy.reconst.ivim.IvimModelTRR method) estimate_response() (in module dipy.reconst.csdeconv) estimate_sigma() (in module dipy.denoise.noise_estimate) (in module dipy.workflows.denoise) Euclidean norm EuclideanMetric (in module dipy.segment.metric) EuDXDirectionGetter (class in dipy.direction) (class in dipy.direction.peaks)

Euler angles euler_characteristic_check() (in module dipy.core.sphere) euler_matrix() (in module dipy.core.geometry) evals() (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) evaluate_results() (dipy.segment.bundles.RecoBundles method) (dipy.workflows.segment.RecoBundles method) evecs() (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) EventCounter (class in dipy.viz.app) evolution() (dipy.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.Optimizer property) expand_fields() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) ExponentialIsotropicFit (class in dipy.reconst.sfm) ExponentialIsotropicModel (class in dipy.reconst.sfm) extend() (dipy.io.stateful_tractogram.PerArrayDict method) (dipy.io.stateful_tractogram.Tractogram method) (dipy.io.streamline.Tractogram method) extract() (dipy.segment.metric.Feature method) eye() (in module dipy.reconst.shm)

F

f() (dipy.reconst.fwdti.FreeWaterTensorFit property) f_D_star_error() (in module dipy.reconst.ivim) f_D_star_prediction() (in module dipy.reconst.ivim) fa() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) fa_inferior() (in module dipy.reconst.csdeconv) fa_superior() (in module dipy.reconst.csdeconv) fa_trace_to_lambdas() (in module dipy.reconst.csdeconv) faces() (dipy.core.gradients.HemiSphere method) (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.core.subdivide_octahedron.HemiSphere method) (dipy.data.HemiSphere method) (dipy.data.Sphere method) (dipy.direction.Sphere method) (dipy.direction.peaks.Sphere method) (dipy.io.peaks.Sphere method) faces_from_sphere_vertices() (in module dipy.core.sphere) factorial() (in module dipy.reconst.qtdmri) (in module dipy.reconst.shore) factorial2() (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) Feature (class in dipy.segment.metric) feature (dipy.segment.benchmarks.bench_quickbundles.Metric attribute) (dipy.segment.clustering.Metric attribute) (dipy.segment.metric.Metric attribute) fetch_bundle_atlas_hcp842() (in module dipy.data) (in module dipy.data.fetcher) fetch_bundle_fa_hcp() (in module dipy.data) (in module dipy.data.fetcher) fetch_bundles_2_subjects() (in module dipy.data) (in module dipy.data.fetcher) fetch_cenir_multib() (in module dipy.data) (in module dipy.data.fetcher) fetch_cfin_multib() (in module dipy.data) (in module dipy.data.fetcher) fetch_data() (in module dipy.data.fetcher) fetch_file_formats() (in module dipy.data.fetcher) fetch_gold_standard_io() (in module dipy.data) (in module dipy.data.fetcher) fetch_isbi2013_2shell() (in module dipy.data) (in module dipy.data.fetcher) fetch_ivim() (in module dipy.data) (in module dipy.data.fetcher) fetch_mni_template() (in module dipy.data) (in module dipy.data.fetcher) fetch_qtdMRI_test_retest_2subjects() (in module dipy.data.fetcher) fetch_scil_b0() (in module dipy.data) (in module dipy.data.fetcher) fetch_sherbrooke_3shell() (in module dipy.data) (in module dipy.data.fetcher) fetch_stanford_hardi() (in module dipy.data) (in module dipy.data.fetcher) fetch_stanford_labels() (in module dipy.data) (in module dipy.data.fetcher) fetch_stanford_pve_maps() (in module dipy.data) (in module dipy.data.fetcher) fetch_stanford_t1() (in module dipy.data) (in module dipy.data.fetcher) fetch_syn_data() (in module dipy.data) (in module dipy.data.fetcher) fetch_taiwan_ntu_dsi() (in module dipy.data) (in module dipy.data.fetcher) fetch_target_tractogram_hcp() (in module dipy.data) (in module dipy.data.fetcher) fetch_tissue_data() (in module dipy.data) (in module dipy.data.fetcher) fetch_viz_icons() (in module dipy.viz) FetcherError (class in dipy.data.fetcher) FetchFlow (class in dipy.workflows.io) fftn() (in module dipy.reconst.dsi) fftshift() (in module dipy.reconst.dsi) FiberFit (class in dipy.tracking.life) FiberModel (class in dipy.tracking.life) file_existence_check() (dipy.workflows.multi_io.IOIterator method) files_types (dipy.io.utils.Nifti1Image attribute) find_closest() (dipy.core.gradients.HemiSphere method) (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.core.subdivide_octahedron.HemiSphere method) (dipy.data.HemiSphere method) (dipy.data.Sphere method) (dipy.direction.Sphere method) (dipy.direction.peaks.Sphere method) (dipy.io.peaks.Sphere method) find_signal_means() (in module dipy.reconst.forecast) fit() (dipy.core.optimize.NonNegativeLeastSquares method) (dipy.core.optimize.SKLearnLinearSolver method) (dipy.reconst.base.ReconstModel method) (dipy.reconst.benchmarks.bench_csd.ConstrainedSphericalDeconvModel method) (dipy.reconst.csdeconv.ConstrainedSDTModel method) (dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel method) (dipy.reconst.csdeconv.TensorModel method) (dipy.reconst.dki.DiffusionKurtosisModel method) (dipy.reconst.dki.ReconstModel method) (dipy.reconst.dki_micro.DiffusionKurtosisModel method) (dipy.reconst.dki_micro.KurtosisMicrostructureModel method) (dipy.reconst.dsi.DiffusionSpectrumDeconvModel method) (dipy.reconst.dsi.DiffusionSpectrumModel method) (dipy.reconst.dsi.OdfModel method) (dipy.reconst.dti.ReconstModel method) (dipy.reconst.dti.TensorModel method) (dipy.reconst.forecast.ForecastModel method) (dipy.reconst.forecast.OdfModel method) (dipy.reconst.fwdti.FreeWaterTensorModel method) (dipy.reconst.fwdti.ReconstModel method) (dipy.reconst.gqi.GeneralizedQSamplingModel method) (dipy.reconst.gqi.OdfModel method) (dipy.reconst.ivim.IvimModelTRR method) (dipy.reconst.ivim.IvimModelVP method) (dipy.reconst.ivim.ReconstModel method) (dipy.reconst.mapmri.MapmriModel method) (dipy.reconst.mapmri.ReconstModel method) (dipy.reconst.mcsd.MultiShellDeconvModel method) (dipy.reconst.msdki.MeanDiffusionKurtosisModel method) (dipy.reconst.msdki.ReconstModel method) (dipy.reconst.odf.OdfModel method) (dipy.reconst.odf.ReconstModel method) (dipy.reconst.qtdmri.QtdmriModel method) (dipy.reconst.sfm.ExponentialIsotropicModel method) (dipy.reconst.sfm.IsotropicModel method) (dipy.reconst.sfm.ReconstModel method) (dipy.reconst.sfm.SparseFascicleModel method) (dipy.reconst.shm.OdfModel method) (dipy.reconst.shm.QballBaseModel method) (dipy.reconst.shore.ShoreModel method) (dipy.tracking.life.FiberModel method) (dipy.tracking.life.ReconstModel method) (dipy.workflows.reconst.ConstrainedSphericalDeconvModel method) (dipy.workflows.reconst.DiffusionKurtosisModel method) (dipy.workflows.reconst.TensorModel method) (dipy.workflows.stats.TensorModel method)

fitted_signal() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) floating (in module dipy.align) (in module dipy.align.imwarp) (in module dipy.align.metrics) (in module dipy.align.scalespace) floor() (in module dipy.core.rng) fmin_l_bfgs_b() (in module dipy.reconst.qtdmri) fopt() (dipy.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.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.csdeconv) (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.csdeconv) (in module dipy.reconst.dti) (in module dipy.segment.mask) (in module dipy.workflows.reconst) free_iteration() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) FreeWaterTensorFit (class in dipy.reconst.fwdti) FreeWaterTensorModel (class in dipy.reconst.fwdti) frenet_serret() (in module dipy.tracking.metrics) from_data() (dipy.direction.BootDirectionGetter method) from_iterable() (dipy.segment.bundles.chain method) from_lower_triangular() (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) from_pve() (dipy.tracking.local_tracking.AnatomicalStoppingCriterion method) from_sphere() (dipy.core.gradients.HemiSphere class method) (dipy.core.sphere.HemiSphere class method) (dipy.core.subdivide_octahedron.HemiSphere class method) (dipy.data.HemiSphere class method) fwdti_prediction() (in module dipy.reconst.fwdti)

G

ga() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) 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_binary_structure() (in module dipy.segment.mask) generate_bvecs() (in module dipy.core.gradients) generate_combinations() (in module dipy.tracking.metrics) generate_streamlines() (in module dipy.tracking.benchmarks.bench_streamline) genlaguerre() (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) (in module dipy.reconst.shore) genpca() (in module dipy.denoise.localpca) geodesic_anisotropy() (in module dipy.reconst.dti) (in module dipy.workflows.reconst) get_3shell_gtab() (in module dipy.data) get_affine() (dipy.align.imaffine.AffineMap method) (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) (dipy.workflows.align.AffineMap method) get_affine_inv() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_args_default() (in module dipy.workflows.base) (in module dipy.workflows.multi_io) get_backward_field() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) get_bundle_atlas_hcp842() (in module dipy.data) (in module dipy.data.fetcher) get_clusters() (dipy.segment.clustering.TreeClusterMap method) get_cmap() (in module dipy.data) get_direction_and_spacings() (in module dipy.align.imaffine) (in module dipy.align.imwarp) get_dki_model() (dipy.workflows.reconst.ReconstDkiFlow method) get_domain_shape() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_energy() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) get_exclude() (dipy.tracking.local_tracking.AnatomicalStoppingCriterion method) get_expand_factors() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace 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) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) get_fnames() (in module dipy.data) (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.sims.phantom) (in module dipy.tracking.benchmarks.bench_streamline) get_forward_field() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) get_gtab_taiwan_dsi() (in module dipy.data) get_image() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_include() (dipy.tracking.local_tracking.AnatomicalStoppingCriterion method) get_info() (in module dipy) get_io_iterator() (dipy.workflows.align.Workflow method) (dipy.workflows.combined_workflow.Workflow method) (dipy.workflows.denoise.Workflow method) (dipy.workflows.io.Workflow method) (dipy.workflows.mask.Workflow method) (dipy.workflows.reconst.Workflow method) (dipy.workflows.segment.Workflow method) (dipy.workflows.stats.Workflow method) (dipy.workflows.tracking.Workflow method) (dipy.workflows.viz.Workflow method) (dipy.workflows.workflow.Workflow method) get_isbi2013_2shell_gtab() (in module dipy.data) get_large_clusters() (dipy.segment.clustering.ClusterMap method) get_level() (in module dipy.workflows.flow_runner) get_map() (dipy.align.imwarp.DiffeomorphicRegistration method) (dipy.align.imwarp.SymmetricDiffeomorphicRegistration method) (dipy.workflows.align.SymmetricDiffeomorphicRegistration method) get_mode() (in module dipy.workflows.reconst) get_optionals() (dipy.workflows.combined_workflow.CombinedWorkflow method) get_reference_info() (in module dipy.io.stateful_tractogram) (in module dipy.io.utils) get_scaling() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_short_name() (dipy.workflows.align.ResliceFlow class method) (dipy.workflows.align.SlrWithQbxFlow class method) (dipy.workflows.align.Workflow class method) (dipy.workflows.combined_workflow.Workflow class method) (dipy.workflows.denoise.NLMeansFlow class method) (dipy.workflows.denoise.Workflow class method) (dipy.workflows.io.FetchFlow class method) (dipy.workflows.io.IoInfoFlow class method) (dipy.workflows.io.Workflow class method) (dipy.workflows.mask.MaskFlow class method) (dipy.workflows.mask.Workflow class method) (dipy.workflows.reconst.ReconstCSAFlow class method) (dipy.workflows.reconst.ReconstCSDFlow class method) (dipy.workflows.reconst.ReconstDkiFlow class method) (dipy.workflows.reconst.ReconstDtiFlow class method) (dipy.workflows.reconst.ReconstIvimFlow class method) (dipy.workflows.reconst.ReconstMAPMRIFlow class method) (dipy.workflows.reconst.Workflow class method) (dipy.workflows.segment.LabelsBundlesFlow class method) (dipy.workflows.segment.MedianOtsuFlow class method) (dipy.workflows.segment.RecoBundlesFlow class method) (dipy.workflows.segment.Workflow class method) (dipy.workflows.stats.BundleAnalysisPopulationFlow class method) (dipy.workflows.stats.LinearMixedModelsFlow class method) (dipy.workflows.stats.SNRinCCFlow class method) (dipy.workflows.stats.Workflow class method) (dipy.workflows.tracking.LocalFiberTrackingPAMFlow class method) (dipy.workflows.tracking.PFTrackingPAMFlow class method) (dipy.workflows.tracking.Workflow class method) (dipy.workflows.viz.HorizonFlow class method) (dipy.workflows.viz.Workflow class method) (dipy.workflows.workflow.Workflow class method)

get_sigmas() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_sim_voxels() (in module dipy.data) get_simplified_transform() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) get_skeleton() (in module dipy.data) get_small_clusters() (dipy.segment.clustering.ClusterMap method) get_spacing() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) get_sphere() (in module dipy.data) (in module dipy.reconst.csdeconv) (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) get_streamlines_copy() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) get_sub_runs() (dipy.workflows.align.Workflow method) (dipy.workflows.combined_workflow.CombinedWorkflow method) (dipy.workflows.combined_workflow.Workflow method) (dipy.workflows.denoise.Workflow method) (dipy.workflows.io.Workflow method) (dipy.workflows.mask.Workflow method) (dipy.workflows.reconst.Workflow method) (dipy.workflows.segment.Workflow method) (dipy.workflows.stats.Workflow method) (dipy.workflows.tracking.Workflow method) (dipy.workflows.viz.Workflow method) (dipy.workflows.workflow.Workflow method) get_target_tractogram_hcp() (in module dipy.data) (in module dipy.data.fetcher) get_tensor_model() (dipy.workflows.reconst.ReconstDtiFlow method) get_two_hcp842_bundles() (in module dipy.data.fetcher) getfullargspec() (in module dipy.workflows.io) getmembers() (in module dipy.workflows.io) gfa() (dipy.reconst.csdeconv.SphHarmFit method) (dipy.reconst.shm.SphHarmFit method) (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.gqi) (in module dipy.reconst.odf) gibbs_removal() (in module dipy.denoise.gibbs) Gimbal lock glob() (in module dipy.workflows.multi_io) GlobalHorizon (class in dipy.viz.gmem) grad_tensor() (in module dipy.tracking.life) gradient() (dipy.align.imaffine.MutualInformationMetric method) (dipy.workflows.align.MutualInformationMetric method) (in module dipy.align.metrics) (in module dipy.tracking.life) gradient_strength() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) gradient_table() (in module dipy.core.gradients) (in module dipy.data) (in module dipy.data.fetcher) (in module dipy.reconst.dti) (in module dipy.reconst.mapmri) (in module dipy.sims.phantom) (in module dipy.workflows.reconst) (in module dipy.workflows.stats) gradient_table_from_bvals_bvecs() (in module dipy.core.gradients) gradient_table_from_gradient_strength_bvecs() (in module dipy.core.gradients) (in module dipy.data.fetcher) (in module dipy.reconst.qtdmri) gradient_table_from_qvals_bvecs() (in module dipy.core.gradients) GradientTable (class in dipy.core.gradients) (class in dipy.data) (class in dipy.reconst.benchmarks.bench_csd) Graph (class in dipy.core.graph)

H

H() (in module dipy.reconst.qtdmri) half_to_full_qspace() (in module dipy.reconst.dsi) hanning_filter() (in module dipy.reconst.dsi) hat() (in module dipy.reconst.shm) header_class (dipy.io.utils.Nifti1Image attribute) HemiSphere (class in dipy.core.gradients) (class in dipy.core.sphere) (class in dipy.core.subdivide_octahedron) (class in dipy.data)

hermite() (in module dipy.reconst.mapmri) 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) Homogenous coordinates Horizon (class in dipy.viz.app) horizon() (in module dipy.viz.app) (in module dipy.workflows.viz) HorizonFlow (class in dipy.workflows.viz)

I

icm_ising (dipy.segment.tissue.IteratedConditionalModes attribute) Identity (class in dipy.segment.clustering) IdentityFeature (class in dipy.segment.metric) idwt3D() (in module dipy.core.wavelet) ifftshift() (in module dipy.reconst.dsi) ImageRegistrationFlow (class in dipy.workflows.align) indices (dipy.stats.analysis.cKDTree attribute) infer_shape() (dipy.segment.metric.Feature method) info() (dipy.core.gradients.GradientTable property) (dipy.data.GradientTable property) (dipy.reconst.benchmarks.bench_csd.GradientTable property) initial_direction() (dipy.direction.EuDXDirectionGetter method) (dipy.direction.peaks.EuDXDirectionGetter method) initialize_iteration() (dipy.align.metrics.CCMetric method) (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SSDMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.CCMetric method) (dipy.workflows.align.EMMetric method) (dipy.workflows.align.SSDMetric method) initialize_maximum_likelihood (dipy.segment.tissue.IteratedConditionalModes attribute) initialize_param_uniform (dipy.segment.tissue.ConstantObservationModel attribute) inside_sphere() (in module dipy.tracking.metrics) inside_sphere_points() (in module dipy.tracking.metrics) InTemporaryDirectory (class in dipy.direction) (class in dipy.direction.peaks) (class in dipy.io.gradients) interpolate_scalar_2d() (in module dipy.align.imaffine) interpolate_scalar_3d() (in module dipy.align.imaffine) (in module dipy.tracking.streamline) interpolate_vector_3d() (in module dipy.tracking.streamline) interpret_matrix() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) intersect_sphere() (in module dipy.tracking.metrics) IntrospectiveArgumentParser (class in dipy.workflows.base) (class in dipy.workflows.flow_runner) inv() (in module dipy.core.gradients) INVALIDPOINT (dipy.tracking.local_tracking.StreamlineStatus attribute) inverse() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method)

io_iterator() (in module dipy.workflows.multi_io) io_iterator_() (in module dipy.workflows.multi_io) (in module dipy.workflows.workflow) IoInfoFlow (class in dipy.workflows.io) IOIterator (class in dipy.workflows.multi_io) is_bbox_in_vox_valid() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) is_empty() (dipy.workflows.docstring_parser.Reader method) is_header_compatible() (in module dipy.io.streamline) (in module dipy.io.utils) is_hemispherical() (in module dipy.core.geometry) is_leaf() (dipy.segment.clustering.TreeCluster property) is_order_invariant (dipy.segment.benchmarks.bench_quickbundles.Metric attribute) (dipy.segment.clustering.Metric attribute) (dipy.segment.clustering.MinimumAverageDirectFlipMetric attribute) (dipy.segment.metric.Feature attribute) (dipy.segment.metric.Metric attribute) (dipy.segment.metric.MinimumAverageDirectFlipMetric attribute) isfunction() (in module dipy.workflows.io) 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.imaffine) (class in dipy.align.scalespace) itemgetter (class in dipy.io.stateful_tractogram) iter_fit_tensor() (in module dipy.reconst.dti) iter_preorder() (dipy.segment.clustering.TreeClusterMap method) IteratedConditionalModes (class in dipy.segment.tissue) 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) IvimModel() (in module dipy.reconst.ivim) (in module dipy.workflows.reconst) IvimModelTRR (class in dipy.reconst.ivim) IvimModelVP (class in dipy.reconst.ivim)

K

kfold_xval() (in module dipy.reconst.cross_validation) kmax() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) kt() (dipy.reconst.dki.DiffusionKurtosisFit property) (dipy.reconst.dki_micro.DiffusionKurtosisFit property)

kurtosis_element() (in module dipy.sims.voxel) kurtosis_maximum() (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) KurtosisMicrostructuralFit (class in dipy.reconst.dki_micro) KurtosisMicrostructureModel (class in dipy.reconst.dki_micro)

L

l1_crossvalidation() (in module dipy.reconst.qtdmri) l_shore() (in module dipy.reconst.shore) LabelsBundlesFlow (class in dipy.workflows.segment) lambert_equal_area_projection_cart() (in module dipy.core.geometry) lambert_equal_area_projection_polar() (in module dipy.core.geometry) lazy_index() (in module dipy.reconst.csdeconv) (in module dipy.reconst.shm) lb_forecast() (in module dipy.reconst.forecast) lcr_matrix() (in module dipy.reconst.shm) leafsize (dipy.stats.analysis.cKDTree attribute) least_squares() (in module dipy.reconst.ivim) leastsq() (in module dipy.reconst.forecast) LEcuyer() (in module dipy.core.rng) length() (in module dipy.align.streamlinear) (in module dipy.segment.bundles) (in module dipy.tracking.benchmarks.bench_streamline) (in module dipy.tracking.metrics) (in module dipy.tracking.streamline) (in module dipy.tracking.utils) (in module dipy.viz.app) length_python() (in module dipy.tracking.benchmarks.bench_streamline) LifeSignalMaker (class in dipy.tracking.life) Linear transformation linearity() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dti) LinearMixedModelsFlow (class in dipy.workflows.stats) literal_eval() (in module dipy.workflows.reconst) load() (dipy.viz.app.EventCounter class method) (in module dipy.data) load_dpy() (in module dipy.io.streamline) load_fib() (in module dipy.io.streamline) load_module() (dipy.workflows.io.FetchFlow method) load_nifti() (in module dipy.io.image) (in module dipy.stats.analysis) (in module dipy.workflows.align) (in module dipy.workflows.denoise) (in module dipy.workflows.io) (in module dipy.workflows.mask) (in module dipy.workflows.reconst) (in module dipy.workflows.segment) (in module dipy.workflows.stats) (in module dipy.workflows.tracking) (in module dipy.workflows.viz)

load_peaks() (in module dipy.io.peaks) (in module dipy.stats.analysis) (in module dipy.workflows.tracking) (in module dipy.workflows.viz) load_pickle() (in module dipy.io) (in module dipy.io.pickles) load_polydata() (in module dipy.io.vtk) load_tck() (in module dipy.io.streamline) load_tractogram() (in module dipy.io.streamline) (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.stats.analysis) (in module dipy.tracking.benchmarks.bench_streamline) load_trk() (in module dipy.io.streamline) load_vtk() (in module dipy.io.streamline) load_vtk_streamlines() (in module dipy.io.streamline) (in module dipy.io.vtk) loads_compat() (in module dipy.data) local_maxima() (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.benchmarks.bench_peaks) (in module dipy.reconst.dki) (in module dipy.reconst.gqi) local_tracker() (in module dipy.tracking.local_tracking) LocalFiberTrackingPAMFlow (class in dipy.workflows.tracking) localpca() (in module dipy.denoise.localpca) LocalTracking (class in dipy.tracking.local_tracking) (class in dipy.workflows.tracking) longest_track_bundle() (in module dipy.tracking.metrics) LooseVersion (class in dipy.reconst.shm) lower_triangular() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) (in module dipy.workflows.reconst) lower_triangular_to_cholesky() (in module dipy.reconst.fwdti) lpn() (in module dipy.reconst.csdeconv) (in module dipy.reconst.shm) LR_deconv() (in module dipy.reconst.dsi)

M

m (dipy.stats.analysis.cKDTree attribute) magn() (in module dipy.tracking.metrics) mahalanobis() (in module dipy.stats.analysis) make5d() (in module dipy.io.utils) manage_output_overwrite() (dipy.workflows.align.Workflow method) (dipy.workflows.combined_workflow.Workflow method) (dipy.workflows.denoise.Workflow method) (dipy.workflows.io.Workflow method) (dipy.workflows.mask.Workflow method) (dipy.workflows.reconst.Workflow method) (dipy.workflows.segment.Workflow method) (dipy.workflows.stats.Workflow method) (dipy.workflows.tracking.Workflow method) (dipy.workflows.viz.Workflow method) (dipy.workflows.workflow.Workflow method) map_coordinates() (in module dipy.reconst.dsi) (in module dipy.stats.analysis) 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) MaskFlow (class in dipy.workflows.mask) matlab_life_results() (in module dipy.data) max (dipy.reconst.shm.CsaOdfModel attribute) (dipy.workflows.reconst.CsaOdfModel attribute) maxes (dipy.stats.analysis.cKDTree attribute) md() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) md5() (in module dipy.data.fetcher) mdf() (in module dipy.segment.metric) MDFpy (class in dipy.segment.benchmarks.bench_quickbundles) mean_curvature() (in module dipy.tracking.metrics) mean_diffusivity() (dipy.reconst.forecast.ForecastFit method) (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.workflows.reconst) mean_kurtosis() (in module dipy.reconst.dki) 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) measure() (in module dipy.reconst.benchmarks.bench_bounding_box) (in module dipy.reconst.benchmarks.bench_peaks) (in module dipy.reconst.benchmarks.bench_squash) (in module dipy.reconst.benchmarks.bench_vec_val_sum) (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.tracking.benchmarks.bench_streamline)

median_filter() (in module dipy.segment.mask) median_otsu() (in module dipy.segment.mask) (in module dipy.workflows.segment) (in module dipy.workflows.stats) MedianOtsuFlow (class in dipy.workflows.segment) message() (dipy.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.Optimizer property) Metric (class in dipy.segment.benchmarks.bench_quickbundles) (class in dipy.segment.clustering) (class in dipy.segment.metric) mfactorial() (in module dipy.reconst.mapmri) midpoint() (in module dipy.tracking.metrics) midpoint2point() (in module dipy.tracking.metrics) MidpointFeature (class in dipy.segment.metric) min (dipy.reconst.shm.CsaOdfModel attribute) (dipy.workflows.reconst.CsaOdfModel attribute) minimize() (in module dipy.core.optimize) minimum_at() (in module dipy.tracking.utils) MinimumAverageDirectFlipMetric (class in dipy.segment.clustering) (class in dipy.segment.metric) minmax_normalize() (in module dipy.reconst.odf) mins (dipy.stats.analysis.cKDTree attribute) mirror() (dipy.core.gradients.HemiSphere method) (dipy.core.sphere.HemiSphere method) (dipy.core.subdivide_octahedron.HemiSphere method) (dipy.data.HemiSphere method) mk() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) mode() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dti) monitor() (dipy.viz.app.EventCounter method) mppca() (in module dipy.denoise.localpca) 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) mult_aff() (in module dipy.align.imwarp) multi_median() (in module dipy.segment.mask) 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.csdeconv) (in module dipy.reconst.dsi) (in module dipy.reconst.forecast) (in module dipy.reconst.fwdti) (in module dipy.reconst.gqi) (in module dipy.reconst.ivim) (in module dipy.reconst.mapmri) (in module dipy.reconst.mcsd) (in module dipy.reconst.multi_voxel) (in module dipy.reconst.qtdmri) (in module dipy.reconst.shore) 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) (class in dipy.workflows.align)

N

n (dipy.stats.analysis.cKDTree attribute) n_shore() (in module dipy.reconst.shore) nanmean() (in module dipy.reconst.sfm) nbytes() (in module dipy.segment.bundles) (in module dipy.segment.clustering) (in module dipy.tracking.streamline) ndbincount() (in module dipy.tracking.utils) ndindex() (in module dipy.core.ndindex) (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.benchmarks.bench_squash) (in module dipy.reconst.csdeconv) (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.fwdti) (in module dipy.reconst.msdki) (in module dipy.reconst.multi_voxel) near_roi() (in module dipy.tracking.utils) nearest_pos_semi_def() (in module dipy.core.geometry) negloglikelihood (dipy.segment.tissue.ConstantObservationModel attribute) nfev() (dipy.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.Optimizer property) ng() (dipy.reconst.mapmri.MapmriFit method) ng_parallel() (dipy.reconst.mapmri.MapmriFit method) ng_perpendicular() (dipy.reconst.mapmri.MapmriFit method)

nifti1_symmat() (in module dipy.io.utils) (in module dipy.workflows.reconst) Nifti1Image (class in dipy.io.utils) nit() (dipy.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.Optimizer property) nlls_cost() (dipy.reconst.ivim.IvimModelVP method) nlls_fit_tensor() (in module dipy.reconst.dti) nlmeans() (in module dipy.denoise.nlmeans) (in module dipy.workflows.denoise) nlmeans_3d() (in module dipy.denoise.nlmeans) nlmeans_block() (in module dipy.denoise.non_local_means) 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) NonNegativeLeastSquares (class in dipy.core.optimize) norm() (in module dipy.reconst.dti) norm_of_laplacian_signal() (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) normalize_data() (in module dipy.reconst.shm) normalize_qa() (in module dipy.reconst.gqi) normalized_vector() (in module dipy.core.geometry) npa() (in module dipy.reconst.gqi) num_grad() (in module dipy.reconst.benchmarks.bench_csd) NumpyDocString (class in dipy.workflows.base) (class in dipy.workflows.docstring_parser)

O

odf() (dipy.reconst.csdeconv.SphHarmFit method) (dipy.reconst.dki.TensorFit method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.dsi.OdfFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.forecast.ForecastFit method) (dipy.reconst.forecast.OdfFit method) (dipy.reconst.fwdti.TensorFit method) (dipy.reconst.gqi.GeneralizedQSamplingFit method) (dipy.reconst.gqi.OdfFit method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.odf.OdfFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.shm.OdfFit 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.dsi) (class in dipy.reconst.forecast) (class in dipy.reconst.gqi) (class in dipy.reconst.odf) (class in dipy.reconst.shm) OdfModel (class in dipy.reconst.dsi) (class in dipy.reconst.forecast) (class in dipy.reconst.gqi) (class in dipy.reconst.odf) (class in dipy.reconst.shm) old_squash() (in module dipy.reconst.benchmarks.bench_squash) ols_fit_dki() (in module dipy.reconst.dki) ols_fit_tensor() (in module dipy.reconst.dti) on_sphere() (dipy.reconst.csdeconv.AxSymShResponse 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) (dipy.segment.bundles.StreamlineLinearRegistration method) (dipy.workflows.align.AffineRegistration method) (dipy.workflows.align.SymmetricDiffeomorphicRegistration method)

Optimizer (class in dipy.align.imaffine) (class in dipy.align.streamlinear) (class in dipy.core.optimize) (class in dipy.reconst.mapmri) optional_package() (in module dipy.core.profile) (in module dipy.io.vtk) (in module dipy.reconst.forecast) (in module dipy.reconst.ivim) (in module dipy.reconst.mapmri) (in module dipy.reconst.mcsd) (in module dipy.reconst.qtdmri) (in module dipy.reconst.sfm) (in module dipy.reconst.shore) (in module dipy.stats.analysis) (in module dipy.viz) (in module dipy.viz.app) (in module dipy.viz.panel) (in module dipy.viz.projections) (in module dipy.viz.regtools) (in module dipy.workflows.stats) optional_parameters() (dipy.workflows.base.IntrospectiveArgumentParser property) (dipy.workflows.flow_runner.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.stats.analysis) (in module dipy.tracking.streamline) orientation_from_string() (in module dipy.io) (in module dipy.io.bvectxt) orientation_to_string() (in module dipy.io) (in module dipy.io.bvectxt) ornt_mapping() (in module dipy.io) (in module dipy.io.bvectxt) otsu() (in module dipy.segment.mask) (in module dipy.segment.threshold) output_parameters() (dipy.workflows.base.IntrospectiveArgumentParser property) (dipy.workflows.flow_runner.IntrospectiveArgumentParser property) OUTSIDEIMAGE (dipy.tracking.local_tracking.StreamlineStatus attribute) overlay_images() (in module dipy.viz.regtools) overlay_slices() (in module dipy.viz.regtools)

P

parents() (dipy.core.graph.Graph method) parse() (dipy.reconst.shm.LooseVersion 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) (class in dipy.workflows.tracking) ParzenJointHistogram (class in dipy.align.imaffine) patch_maximum() (in module dipy.reconst.gqi) patch_sum() (in module dipy.reconst.gqi) patch_vertices() (in module dipy.reconst.gqi) path_length() (in module dipy.tracking.utils) pdf() (dipy.reconst.dsi.DiffusionSpectrumDeconvFit method) (dipy.reconst.dsi.DiffusionSpectrumFit method) (dipy.reconst.mapmri.MapmriFit method) (dipy.reconst.qtdmri.QtdmriFit method) (dipy.reconst.shore.ShoreFit method) pdf_grid() (dipy.reconst.shore.ShoreFit method) pdf_interp_coords() (in module dipy.reconst.dsi) pdf_odf() (in module dipy.reconst.dsi) peak_directions() (in module dipy.direction) (in module dipy.direction.peaks) peak_directions_nl() (in module dipy.direction) (in module dipy.direction.peaks) peak_values() (in module dipy.stats.analysis) peaks_from_model() (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.csdeconv) (in module dipy.workflows.reconst) peaks_to_niftis() (in module dipy.io.peaks) (in module dipy.workflows.reconst) PeaksAndMetrics (class in dipy.direction) (class in dipy.direction.peaks) (class in dipy.io.peaks) peek() (dipy.workflows.docstring_parser.Reader method) PerArrayDict (class in dipy.io.stateful_tractogram) PerArraySequenceDict (class in dipy.io.stateful_tractogram) perform_transformation() (dipy.workflows.align.ImageRegistrationFlow method) perfusion_fraction() (dipy.reconst.ivim.IvimFit property) permutationinverse() (in module dipy.core.wavelet) permutations (class in dipy.core.sphere_stats) perpendicular_directions() (in module dipy.core.geometry) pft_tracker() (in module dipy.tracking.local_tracking) PFTrackingPAMFlow (class in dipy.workflows.tracking) phi() (dipy.reconst.ivim.IvimModelVP method) piesno() (in module dipy.denoise.noise_estimate) pinv() (in module dipy.reconst.dti) (in module dipy.reconst.shm) pjoin() (in module dipy.data) (in module dipy.data.fetcher) (in module dipy.workflows.viz) planarity() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dti) plot_2d_diffeomorphic_map() (in module dipy.viz.regtools) plot_slices() (in module dipy.viz.regtools)

polar() (in module dipy.core.gradients) polar_zone_vertices() (in module dipy.reconst.gqi) Pool() (in module dipy.align.reslice) (in module dipy.direction) (in module dipy.direction.peaks) positional_parameters() (dipy.workflows.base.IntrospectiveArgumentParser property) (dipy.workflows.flow_runner.IntrospectiveArgumentParser property) predict() (dipy.core.optimize.SKLearnLinearSolver method) (dipy.reconst.benchmarks.bench_csd.ConstrainedSphericalDeconvModel method) (dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel method) (dipy.reconst.csdeconv.SphHarmFit method) (dipy.reconst.csdeconv.TensorModel method) (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki.DiffusionKurtosisModel method) (dipy.reconst.dki.TensorFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.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.fwdti.TensorFit 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.sfm.ExponentialIsotropicFit method) (dipy.reconst.sfm.IsotropicFit method) (dipy.reconst.sfm.SparseFascicleFit method) (dipy.reconst.shm.SphHarmFit method) (dipy.tracking.life.FiberFit method) (dipy.workflows.reconst.ConstrainedSphericalDeconvModel method) (dipy.workflows.reconst.DiffusionKurtosisModel method) (dipy.workflows.reconst.TensorModel method) (dipy.workflows.stats.TensorModel method) principal_components() (in module dipy.tracking.metrics) print_level() (dipy.align.imaffine.ScaleSpace method) (dipy.align.imwarp.ScaleSpace method) (dipy.align.scalespace.ScaleSpace method) print_stats() (dipy.core.profile.Profiler method) print_summary() (dipy.align.imaffine.Optimizer method) (dipy.align.streamlinear.Optimizer method) (dipy.core.optimize.Optimizer method) (dipy.reconst.mapmri.Optimizer method) prob_image (dipy.segment.tissue.ConstantObservationModel attribute) prob_neighborhood (dipy.segment.tissue.IteratedConditionalModes attribute) ProbabilisticDirectionGetter (class in dipy.direction) (class in dipy.workflows.tracking) product (class in dipy.io.stateful_tractogram) 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) PYERROR (dipy.tracking.local_tracking.StreamlineStatus attribute)

Q

qa_thr (dipy.direction.EuDXDirectionGetter attribute) (dipy.direction.peaks.EuDXDirectionGetter attribute) QB_New (in module dipy.segment.benchmarks.bench_quickbundles) QballBaseModel (class in dipy.reconst.shm) QballModel (class in dipy.reconst.shm) qbx_and_merge() (in module dipy.align.streamlinear) (in module dipy.segment.bundles) (in module dipy.segment.clustering) (in module dipy.viz.app) 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) quad() (in module dipy.reconst.csdeconv) quadratic_form() (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) quantize_evecs() (in module dipy.reconst.dti) Quaternion query() (dipy.stats.analysis.cKDTree method) query_ball_point() (dipy.stats.analysis.cKDTree method) query_ball_tree() (dipy.stats.analysis.cKDTree method) query_pairs() (dipy.stats.analysis.cKDTree method) quick_squash() (in module dipy.reconst.benchmarks.bench_squash) QuickBundles (class in dipy.segment.clustering) (class in dipy.stats.analysis) QuickBundlesX (class in dipy.segment.clustering) qvals() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.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.dki_micro) (in module dipy.reconst.dti) (in module dipy.workflows.reconst) radial_kurtosis() (in module dipy.reconst.dki) randint() (in module dipy.reconst.shm) randn() (in module dipy.reconst.benchmarks.bench_vec_val_sum) 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) (dipy.io.streamline.Space attribute) (dipy.viz.app.Space attribute) (dipy.workflows.tracking.Space attribute) ravel_multi_index() (in module dipy.tracking.utils) rd() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) read() (dipy.workflows.docstring_parser.Reader method) read_bundles_2_subjects() (in module dipy.data) (in module dipy.data.fetcher) read_bvals_bvecs() (in module dipy.data.fetcher) (in module dipy.io) (in module dipy.io.gradients) (in module dipy.workflows.reconst) (in module dipy.workflows.stats) read_bvec_file() (in module dipy.io) (in module dipy.io.bvectxt) read_cenir_multib() (in module dipy.data) (in module dipy.data.fetcher) read_cfin_dwi() (in module dipy.data) (in module dipy.data.fetcher) read_cfin_t1() (in module dipy.data) (in module dipy.data.fetcher) read_isbi2013_2shell() (in module dipy.data) (in module dipy.data.fetcher) read_ivim() (in module dipy.data) (in module dipy.data.fetcher) read_mni_template() (in module dipy.data) (in module dipy.data.fetcher) read_qtdMRI_test_retest_2subjects() (in module dipy.data.fetcher) read_scil_b0() (in module dipy.data) (in module dipy.data.fetcher) read_sherbrooke_3shell() (in module dipy.data) (in module dipy.data.fetcher) read_siemens_scil_b0() (in module dipy.data.fetcher) read_stanford_hardi() (in module dipy.data) (in module dipy.data.fetcher) read_stanford_labels() (in module dipy.data) (in module dipy.data.fetcher) (in module dipy.reconst.benchmarks.bench_csd) read_stanford_pve_maps() (in module dipy.data) (in module dipy.data.fetcher) read_stanford_t1() (in module dipy.data) (in module dipy.data.fetcher) read_syn_data() (in module dipy.data) (in module dipy.data.fetcher) read_taiwan_ntu_dsi() (in module dipy.data) (in module dipy.data.fetcher) read_tissue_data() (in module dipy.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 method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) read_tracks() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) read_tracksi() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) read_viz_icons() (in module dipy.viz) Reader (class in dipy.workflows.docstring_parser) real_sph_harm() (in module dipy.reconst.csdeconv) (in module dipy.reconst.forecast) (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) (in module dipy.reconst.shm) (in module dipy.reconst.shore) real_sym_sh_basis() (in module dipy.reconst.csdeconv) (in module dipy.reconst.shm) real_sym_sh_mrtrix() (in module dipy.reconst.shm) RecoBundles (class in dipy.segment.bundles) (class in dipy.workflows.segment) RecoBundlesFlow (class in dipy.workflows.segment) recognize() (dipy.segment.bundles.RecoBundles method) (dipy.workflows.segment.RecoBundles method) ReconstCSAFlow (class in dipy.workflows.reconst) ReconstCSDFlow (class in dipy.workflows.reconst) ReconstDkiFlow (class in dipy.workflows.reconst) ReconstDtiFlow (class in dipy.workflows.reconst) ReconstFit (class in dipy.reconst.base) (class in dipy.reconst.mapmri) (class in dipy.reconst.multi_voxel) (class in dipy.reconst.odf) (class in dipy.reconst.sfm) (class in dipy.tracking.life) ReconstIvimFlow (class in dipy.workflows.reconst) ReconstMAPMRIFlow (class in dipy.workflows.reconst) ReconstModel (class in dipy.reconst.base) (class in dipy.reconst.dki) (class in dipy.reconst.dti) (class in dipy.reconst.fwdti) (class in dipy.reconst.ivim) (class in dipy.reconst.mapmri) (class in dipy.reconst.msdki) (class in dipy.reconst.odf) (class in dipy.reconst.sfm) (class in dipy.tracking.life)

recursive_response() (in module dipy.reconst.csdeconv) reduce() (in module dipy.reconst.benchmarks.bench_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) refine() (dipy.segment.bundles.RecoBundles method) (dipy.workflows.segment.RecoBundles method) Reflection register() (dipy.segment.clustering.ABCMeta method) relist_streamlines() (in module dipy.data) (in module dipy.tracking.streamline) remove_actors() (dipy.viz.app.Horizon method) 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) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) remove_similar_vertices() (in module dipy.core.sphere) (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.gqi) reorient_bvecs() (in module dipy.core.gradients) reorient_on_axis() (in module dipy.io) (in module dipy.io.bvectxt) reorient_vectors() (in module dipy.io) (in module dipy.io.bvectxt) repeat (class in dipy.direction) (class in dipy.direction.peaks) ResampleFeature (class in dipy.segment.clustering) (class in dipy.segment.metric) 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) (in module dipy.direction.peaks) (in module dipy.io.peaks) ResidualBootstrapWrapper (class in dipy.reconst.shm) reslice() (in module dipy.align.reslice) (in module dipy.workflows.align) ResliceFlow (class in dipy.workflows.align) response_from_mask() (in module dipy.reconst.csdeconv) restore_fit_tensor() (in module dipy.reconst.dti) restricted_evals() (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) rho_matrix() (in module dipy.reconst.forecast) rigid() (dipy.workflows.align.ImageRegistrationFlow method) RigidTransform3D (class in dipy.workflows.align) rk() (dipy.reconst.dki.DiffusionKurtosisFit method) (dipy.reconst.dki_micro.DiffusionKurtosisFit method) rodrigues_axis_rotation() (in module dipy.core.geometry) Rotation matrix Rotation vector round_bvals() (in module dipy.core.gradients) (in module dipy.reconst.msdki) 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) run() (dipy.workflows.align.ApplyTransformFlow method) (dipy.workflows.align.ImageRegistrationFlow method) (dipy.workflows.align.ResliceFlow method) (dipy.workflows.align.SlrWithQbxFlow method) (dipy.workflows.align.SynRegistrationFlow method) (dipy.workflows.align.Workflow method) (dipy.workflows.combined_workflow.Workflow method) (dipy.workflows.denoise.NLMeansFlow method) (dipy.workflows.denoise.Workflow method) (dipy.workflows.io.FetchFlow method) (dipy.workflows.io.IoInfoFlow method) (dipy.workflows.io.Workflow method) (dipy.workflows.mask.MaskFlow method) (dipy.workflows.mask.Workflow method) (dipy.workflows.reconst.ReconstCSAFlow method) (dipy.workflows.reconst.ReconstCSDFlow method) (dipy.workflows.reconst.ReconstDkiFlow method) (dipy.workflows.reconst.ReconstDtiFlow method) (dipy.workflows.reconst.ReconstIvimFlow method) (dipy.workflows.reconst.ReconstMAPMRIFlow method) (dipy.workflows.reconst.Workflow method) (dipy.workflows.segment.LabelsBundlesFlow method) (dipy.workflows.segment.MedianOtsuFlow method) (dipy.workflows.segment.RecoBundlesFlow method) (dipy.workflows.segment.Workflow method) (dipy.workflows.stats.BundleAnalysisPopulationFlow method) (dipy.workflows.stats.LinearMixedModelsFlow method) (dipy.workflows.stats.SNRinCCFlow method) (dipy.workflows.stats.Workflow method) (dipy.workflows.tracking.LocalFiberTrackingPAMFlow method) (dipy.workflows.tracking.PFTrackingPAMFlow method) (dipy.workflows.tracking.Workflow method) (dipy.workflows.viz.HorizonFlow method) (dipy.workflows.viz.Workflow method) (dipy.workflows.workflow.Workflow method) run_flow() (in module dipy.workflows.flow_runner) run_sub_flow() (dipy.workflows.combined_workflow.CombinedWorkflow method)

S

S0_hat() (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) (dipy.reconst.msdki.MeanDiffusionKurtosisFit property) S0_predicted() (dipy.reconst.ivim.IvimFit property) sample_domain_regular() (in module dipy.align.imaffine) sampling_matrix() (dipy.reconst.csdeconv.SphHarmModel method) (dipy.reconst.shm.SphHarmModel method) save() (dipy.viz.app.EventCounter method) save_dpy() (in module dipy.io.streamline) save_fib() (in module dipy.io.streamline) save_nifti() (in module dipy.io.image) (in module dipy.io.peaks) (in module dipy.workflows.align) (in module dipy.workflows.denoise) (in module dipy.workflows.mask) (in module dipy.workflows.reconst) (in module dipy.workflows.segment) (in module dipy.workflows.stats) save_peaks() (in module dipy.io.peaks) (in module dipy.workflows.reconst) save_pickle() (in module dipy.io) (in module dipy.io.pickles) save_polydata() (in module dipy.io.vtk) save_qa_metric() (in module dipy.io.image) (in module dipy.workflows.align) save_tck() (in module dipy.io.streamline) save_tractogram() (in module dipy.io.streamline) (in module dipy.viz.app) (in module dipy.workflows.tracking) save_trk() (in module dipy.io.streamline) save_vtk() (in module dipy.io.streamline) save_vtk_streamlines() (in module dipy.io.streamline) (in module dipy.io.vtk) ScaleSpace (class in dipy.align.imaffine) (class in dipy.align.imwarp) (class in dipy.align.scalespace) search_descending() (in module dipy.direction) (in module dipy.direction.peaks) seeds_from_mask() (in module dipy.tracking.utils) seek_next_non_empty_line() (dipy.workflows.docstring_parser.Reader method) seg_stats (dipy.segment.tissue.ConstantObservationModel attribute) segment_from_cfa() (in module dipy.segment.mask) (in module dipy.workflows.stats) select_by_rois() (in module dipy.tracking.streamline) select_random_set_of_streamlines() (in module dipy.align.streamlinear) (in module dipy.segment.bundles) (in module dipy.tracking.streamline) set_affine() (dipy.align.imaffine.AffineMap method) (dipy.workflows.align.AffineMap method) set_inputs() (dipy.workflows.multi_io.IOIterator method) set_level_iters() (dipy.align.imwarp.DiffeomorphicRegistration method) set_levels_above() (dipy.align.metrics.SimilarityMetric method) set_levels_below() (dipy.align.metrics.SimilarityMetric method) set_moving_image() (dipy.align.metrics.SimilarityMetric method) set_number_of_points() (in module dipy.align.streamlinear) (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.segment.bundles) (in module dipy.segment.clustering) (in module dipy.stats.analysis) (in module dipy.tracking.benchmarks.bench_streamline) (in module dipy.tracking.streamline) set_number_of_points_python() (in module dipy.tracking.benchmarks.bench_streamline) set_out_dir() (dipy.workflows.multi_io.IOIterator method) set_out_fnames() (dipy.workflows.multi_io.IOIterator method) set_output_keys() (dipy.workflows.multi_io.IOIterator method) set_static_image() (dipy.align.metrics.SimilarityMetric method) set_sub_flows_optionals() (dipy.workflows.combined_workflow.CombinedWorkflow method) setup (dipy.align.imaffine.ParzenJointHistogram attribute) setup() (dipy.align.imaffine.MutualInformationMetric method) (dipy.align.streamlinear.BundleMinDistanceMatrixMetric method) (dipy.align.streamlinear.BundleMinDistanceMetric method) (dipy.align.streamlinear.StreamlineDistanceMetric method) (dipy.segment.bundles.BundleMinDistanceMetric method) (dipy.tracking.life.FiberModel method) (dipy.workflows.align.MutualInformationMetric method) (in module dipy.tracking.benchmarks.bench_streamline) setup_module() (in module dipy.io.vtk) (in module dipy.viz.app) (in module dipy.viz.panel) (in module dipy.viz.projections) (in module dipy.viz.regtools) setup_test() (in module dipy) sf_to_sh() (in module dipy.reconst.shm) sfactorial() (in module dipy.reconst.mapmri) 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.csdeconv) (in module dipy.reconst.shm) sh_to_sf() (in module dipy.reconst.shm) sh_to_sf_matrix() (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.shm) shallow_copy() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) shape() (dipy.reconst.csdeconv.SphHarmFit property) (dipy.reconst.dki.TensorFit property) (dipy.reconst.dti.TensorFit property) (dipy.reconst.fwdti.TensorFit property) (dipy.reconst.ivim.IvimFit property) (dipy.reconst.multi_voxel.MultiVoxelFit property) (dipy.reconst.shm.SphHarmFit property) Shear matrix shifted_origin() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) shm_coeff() (dipy.reconst.csdeconv.SphHarmFit property) (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) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method) SimilarityMetric (class in dipy.align.metrics)

simple_plot() (in module dipy.viz.regtools) (in module dipy.workflows.stats) single_tensor() (in module dipy.reconst.csdeconv) (in module dipy.sims.phantom) (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) size (dipy.stats.analysis.cKDTree attribute) size() (dipy.segment.clustering.ClusterMap method) SKLearnLinearSolver (class in dipy.core.optimize) slash_to_under() (in module dipy.workflows.multi_io) slicer_panel() (in module dipy.viz.app) (in module dipy.viz.panel) slr_with_qbx() (in module dipy.align.streamlinear) (in module dipy.workflows.align) SlrWithQbxFlow (class in dipy.workflows.align) smooth_pinv() (in module dipy.reconst.shm) SNRinCCFlow (class in dipy.workflows.stats) solve_qp() (in module dipy.reconst.mcsd) Space (class in dipy.io.stateful_tractogram) (class in dipy.io.streamline) (class in dipy.viz.app) (class in dipy.workflows.tracking) space() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) space_attribute() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) sparse_distance_matrix() (dipy.stats.analysis.cKDTree method) 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.csdeconv) (in module dipy.reconst.mapmri) (in module dipy.reconst.shm) sph_project() (in module dipy.viz.projections) Sphere (class in dipy.core.sphere) (class in dipy.data) (class in dipy.direction) (class in dipy.direction.peaks) (class in dipy.io.peaks) sphere2cart() (in module dipy.core.geometry) (in module dipy.core.sphere) (in module dipy.reconst.dki) (in module dipy.sims.voxel) sphere_distance() (in module dipy.core.geometry) spherical_harmonics() (in module dipy.reconst.shm) sphericity() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dti) SphHarmFit (class in dipy.reconst.csdeconv) (class in dipy.reconst.shm) SphHarmModel (class in dipy.reconst.csdeconv) (class in dipy.reconst.shm) splev() (in module dipy.tracking.metrics) spline() (in module dipy.tracking.metrics) split_dki_param() (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.workflows.reconst) splitext() (in module dipy.io.bvectxt) (in module dipy.io.gradients) splprep() (in module dipy.tracking.metrics) squared_radial_component() (in module dipy.reconst.gqi) SSDMetric (class in dipy.align.metrics) (class in dipy.workflows.align) startpoint() (in module dipy.tracking.metrics) StatefulTractogram (class in dipy.io.stateful_tractogram) (class in dipy.io.streamline) (class in dipy.viz.app) (class in dipy.workflows.tracking) sticks_and_ball() (in module dipy.data) (in module dipy.sims.voxel) stoc_search_cost() (dipy.reconst.ivim.IvimModelVP method) streamline_gradients() (in module dipy.tracking.life) streamline_near_roi() (in module dipy.tracking.utils) streamline_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) (class in dipy.segment.bundles) StreamlineRegistrationMap (class in dipy.align.streamlinear) Streamlines (in module dipy.align.streamlinear) (in module dipy.io.dpy) (in module dipy.io.stateful_tractogram) (in module dipy.segment.benchmarks.bench_quickbundles) (in module dipy.segment.bundles) (in module dipy.stats.analysis) (in module dipy.tracking) (in module dipy.tracking.benchmarks.bench_streamline) (in module dipy.tracking.streamline) (in module dipy.viz.app) streamlines() (dipy.io.stateful_tractogram.StatefulTractogram property) (dipy.io.stateful_tractogram.Tractogram property) (dipy.io.streamline.StatefulTractogram property) (dipy.io.streamline.Tractogram property) (dipy.viz.app.StatefulTractogram property) (dipy.workflows.tracking.StatefulTractogram property) StreamlineStatus (class in dipy.tracking.local_tracking) subdivide() (dipy.core.gradients.HemiSphere method) (dipy.core.sphere.HemiSphere method) (dipy.core.sphere.Sphere method) (dipy.core.subdivide_octahedron.HemiSphere method) (dipy.data.HemiSphere method) (dipy.data.Sphere method) (dipy.direction.Sphere method) (dipy.direction.peaks.Sphere method) (dipy.io.peaks.Sphere method) subsegment() (in module dipy.tracking.utils) SumPointwiseEuclideanMetric (class in dipy.segment.metric) svd() (in module dipy.reconst.shm) SymmetricDiffeomorphicRegistration (class in dipy.align.imwarp) (class in dipy.workflows.align) SynRegistrationFlow (class in dipy.workflows.align)

T

target() (in module dipy.tracking.utils) target_line_based() (in module dipy.tracking.utils) tau() (dipy.core.gradients.GradientTable method) (dipy.data.GradientTable method) (dipy.reconst.benchmarks.bench_csd.GradientTable method) temporal_basis() (in module dipy.reconst.qtdmri) tensor_prediction() (in module dipy.reconst.dti) TensorFit (class in dipy.reconst.dki) (class in dipy.reconst.dti) (class in dipy.reconst.fwdti) TensorModel (class in dipy.reconst.csdeconv) (class in dipy.reconst.dti) (class in dipy.workflows.reconst) (class in dipy.workflows.stats) test() (in module dipy) (in module dipy.core) (in module dipy.denoise) (in module dipy.reconst) (in module dipy.tracking) threshold_propagator() (in module dipy.reconst.dsi) ThresholdStoppingCriterion (class in dipy.workflows.tracking) time() (in module dipy.align.streamlinear) (in module dipy.segment.bundles) (in module dipy.segment.clustering) (in module dipy.workflows.segment) TissueClassifierHMRF (class in dipy.segment.tissue) to_center() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) to_corner() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) to_rasmm() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) to_vox() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method) to_voxmm() (dipy.io.stateful_tractogram.StatefulTractogram method) (dipy.io.streamline.StatefulTractogram method) (dipy.viz.app.StatefulTractogram method) (dipy.workflows.tracking.StatefulTractogram method)

to_world() (dipy.io.stateful_tractogram.Tractogram method) (dipy.io.streamline.Tractogram method) tortuosity() (dipy.reconst.dki_micro.KurtosisMicrostructuralFit property) (in module dipy.reconst.dki_micro) total_weight (dipy.direction.EuDXDirectionGetter attribute) (dipy.direction.peaks.EuDXDirectionGetter attribute) trace() (dipy.reconst.dki.TensorFit method) (dipy.reconst.dti.TensorFit method) (dipy.reconst.fwdti.TensorFit method) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) TRACKPOINT (dipy.tracking.local_tracking.StreamlineStatus attribute) Tractogram (class in dipy.io.stateful_tractogram) (class in dipy.io.streamline) transform() (dipy.align.imaffine.AffineMap method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.align.streamlinear.StreamlineRegistrationMap method) (dipy.workflows.align.AffineMap method) (dipy.workflows.align.DiffeomorphicMap method) transform_centers_of_mass() (in module dipy.align.imaffine) (in module dipy.workflows.align) transform_geometric_centers() (in module dipy.align.imaffine) transform_inverse() (dipy.align.imaffine.AffineMap method) (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.AffineMap method) (dipy.workflows.align.DiffeomorphicMap method) transform_origins() (in module dipy.align.imaffine) transform_streamlines() (in module dipy.align.streamlinear) (in module dipy.io.vtk) (in module dipy.stats.analysis) (in module dipy.tracking.life) (in module dipy.tracking.streamline) (in module dipy.workflows.align) transform_tracking_output() (in module dipy.tracking.utils) translate() (dipy.workflows.align.ImageRegistrationFlow method) TranslationTransform3D (class in dipy.workflows.align) traverse_postorder() (dipy.segment.clustering.TreeClusterMap method) tree (dipy.stats.analysis.cKDTree attribute) TreeCluster (class in dipy.segment.clustering) TreeClusterMap (class in dipy.segment.clustering) triple_odf_maxima() (in module dipy.reconst.gqi) two_cingulum_bundles() (in module dipy.data)

U

unique() (in module dipy.reconst.shm) unique_bvals() (in module dipy.core.gradients) (in module dipy.reconst.msdki) unique_edges() (in module dipy.core.sphere) (in module dipy.reconst.benchmarks.bench_peaks) unique_rows() (in module dipy.tracking.life) (in module dipy.tracking.utils) unique_sets() (in module dipy.core.sphere) Unit vector unlist_streamlines() (in module dipy.align.streamlinear) (in module dipy.tracking.streamline) 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.workflows.align.SymmetricDiffeomorphicRegistration method) update_argument() (dipy.workflows.base.IntrospectiveArgumentParser method) (dipy.workflows.flow_runner.IntrospectiveArgumentParser method)

update_gradient_dense (dipy.align.imaffine.ParzenJointHistogram attribute) update_gradient_sparse (dipy.align.imaffine.ParzenJointHistogram attribute) update_header() (dipy.io.utils.Nifti1Image method) update_param (dipy.segment.tissue.ConstantObservationModel attribute) update_param_new (dipy.segment.tissue.ConstantObservationModel attribute) update_pdfs_dense (dipy.align.imaffine.ParzenJointHistogram attribute) update_pdfs_sparse (dipy.align.imaffine.ParzenJointHistogram attribute) update_progressbar() (in module dipy.data.fetcher) 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) urlopen() (in module dipy.data.fetcher) use_moving_image_dynamics() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.EMMetric method) use_static_image_dynamics() (dipy.align.metrics.EMMetric method) (dipy.align.metrics.SimilarityMetric method) (dipy.workflows.align.EMMetric method)

V

v_cycle_2d() (in module dipy.align.metrics) v_cycle_3d() (in module dipy.align.metrics) valid_exts (dipy.io.utils.Nifti1Image attribute) values_from_volume() (in module dipy.stats.analysis) (in module dipy.tracking.streamline) vec2vec_rotmat() (in module dipy.core.geometry) (in module dipy.reconst.csdeconv) (in module dipy.sims.phantom) (in module dipy.sims.voxel) vec_val_vect() (in module dipy.reconst.benchmarks.bench_vec_val_sum) (in module dipy.reconst.dki) (in module dipy.reconst.dki_micro) (in module dipy.reconst.dti) (in module dipy.reconst.fwdti) vector_cosine() (in module dipy.core.geometry) vector_norm() (in module dipy.core.geometry) (in module dipy.core.gradients) (in module dipy.core.sphere) (in module dipy.reconst.dti) VectorOfEndpointsFeature (class in dipy.segment.metric)

version() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) vertices() (dipy.core.sphere.Sphere method) (dipy.data.Sphere method) (dipy.direction.Sphere method) (dipy.direction.peaks.Sphere method) (dipy.io.peaks.Sphere method) visualise_gradient_table_G_Delta_rainbow() (in module dipy.reconst.qtdmri) volume_fractions() (dipy.reconst.mcsd.MSDeconvFit property) VOX (dipy.io.stateful_tractogram.Space attribute) (dipy.io.streamline.Space attribute) (dipy.viz.app.Space attribute) (dipy.workflows.tracking.Space attribute) voxel2streamline() (in module dipy.tracking.life) VOXMM (dipy.io.stateful_tractogram.Space attribute) (dipy.io.streamline.Space attribute) (dipy.viz.app.Space attribute) (dipy.workflows.tracking.Space attribute)

W

warn() (in module dipy.align.imaffine) (in module dipy.core.gradients) (in module dipy.direction) (in module dipy.direction.peaks) (in module dipy.reconst.forecast) (in module dipy.reconst.mapmri) (in module dipy.reconst.qtdmri) (in module dipy.reconst.shore) (in module dipy.segment.mask) (in module dipy.tracking._utils) (in module dipy.tracking.streamline) (in module dipy.tracking.utils) (in module dipy.workflows.docstring_parser) (in module dipy.workflows.reconst) warp_endomorphism() (dipy.align.imwarp.DiffeomorphicMap method) (dipy.workflows.align.DiffeomorphicMap method) Wcons() (in module dipy.reconst.dki) whole_brain_slr() (in module dipy.align.streamlinear) WichmannHill1982() (in module dipy.core.rng) WichmannHill2006() (in module dipy.core.rng) winding() (in module dipy.tracking.metrics) with_einsum() (in module dipy.reconst.benchmarks.bench_vec_val_sum) wls_fit_dki() (in module dipy.reconst.dki) 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.align) (class in dipy.workflows.combined_workflow) (class in dipy.workflows.denoise) (class in dipy.workflows.io) (class in dipy.workflows.mask) (class in dipy.workflows.reconst) (class in dipy.workflows.segment) (class in dipy.workflows.stats) (class in dipy.workflows.tracking) (class in dipy.workflows.viz) (class in dipy.workflows.workflow) wraps() (in module dipy.tracking.utils) write_track() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) write_tracks() (dipy.io.Dpy method) (dipy.io.dpy.Dpy method) (dipy.io.streamline.Dpy method) (dipy.workflows.viz.Dpy method) Wrotate() (in module dipy.reconst.dki) Wrotate_element() (in module dipy.reconst.dki)

X

x() (dipy.core.sphere.Sphere property) (dipy.data.Sphere property) (dipy.direction.Sphere property) (dipy.direction.peaks.Sphere property) (dipy.io.peaks.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.align.imaffine.Optimizer property) (dipy.align.streamlinear.Optimizer property) (dipy.core.optimize.Optimizer property) (dipy.reconst.mapmri.Optimizer property)

Y

y() (dipy.core.sphere.Sphere property) (dipy.data.Sphere property) (dipy.direction.Sphere property) (dipy.direction.peaks.Sphere property) (dipy.io.peaks.Sphere property)

Z

z() (dipy.core.sphere.Sphere property) (dipy.data.Sphere property) (dipy.direction.Sphere property) (dipy.direction.peaks.Sphere property) (dipy.io.peaks.Sphere property)