Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

_

__init__() (dipy.align.Bunch 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.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.graph.Graph method)
(dipy.core.onetime.OneTimeProperty method)
(dipy.core.onetime.ResetMixin method)
(dipy.core.optimize.LooseVersion 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.xrange 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.DeterministicMaximumDirectionGetter method)
(dipy.direction.HemiSphere method)
(dipy.direction.InTemporaryDirectory method)
(dipy.direction.PeaksAndMetrics method)
(dipy.direction.PeaksAndMetricsDirectionGetter method)
(dipy.direction.ProbabilisticDirectionGetter method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.HemiSphere method)
(dipy.direction.peaks.InTemporaryDirectory method)
(dipy.direction.peaks.PeaksAndMetrics method)
(dipy.direction.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.direction.peaks.Sphere method)
(dipy.direction.peaks.repeat method)
(dipy.direction.peaks.xrange method)
(dipy.direction.probabilistic_direction_getter.DeterministicMaximumDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.DirectionGetter method)
(dipy.direction.probabilistic_direction_getter.PeakDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.PmfGen method)
(dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.SHCoeffPmfGen method)
(dipy.direction.probabilistic_direction_getter.SimplePmfGen method)
(dipy.direction.repeat method)
(dipy.direction.xrange method)
(dipy.external.fsl.Dpy method)
(dipy.external.fsl.FSLError method)
(dipy.external.fsl.InTemporaryDirectory method)
(dipy.external.fsl.Popen method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy 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.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.Sphere method)
(dipy.reconst.dti.TensorFit method)
(dipy.reconst.dti.TensorModel 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.interpolate.Interpolator method)
(dipy.reconst.interpolate.NearestNeighborInterpolator method)
(dipy.reconst.interpolate.OutsideImage method)
(dipy.reconst.interpolate.TriLinearInterpolator method)
(dipy.reconst.mapmri.MapmriFit method)
(dipy.reconst.mapmri.MapmriModel method)
(dipy.reconst.mapmri.ReconstFit method)
(dipy.reconst.mapmri.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.peaks.HemiSphere method)
(dipy.reconst.peaks.InTemporaryDirectory method)
(dipy.reconst.peaks.PeaksAndMetrics method)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.reconst.peaks.Sphere method)
(dipy.reconst.peaks.repeat method)
(dipy.reconst.peaks.xrange 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.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.Metric method)
(dipy.segment.clustering.QuickBundles method)
(dipy.segment.clustering.ResampleFeature 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.quickbundles.QuickBundles method)
(dipy.tracking.eudx.EuDX 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.ActTissueClassifier method)
(dipy.tracking.local.BinaryTissueClassifier method)
(dipy.tracking.local.DirectionGetter method)
(dipy.tracking.local.LocalTracking method)
(dipy.tracking.local.ThresholdTissueClassifier method)
(dipy.tracking.local.TissueClassifier method)
(dipy.tracking.local.localtracking.Bunch method)
(dipy.tracking.local.localtracking.LocalTracking method)
(dipy.tracking.markov.BoundaryStepper method)
(dipy.tracking.markov.CDT_NNO method)
(dipy.tracking.markov.ClosestDirectionTracker method)
(dipy.tracking.markov.DirectionFinder method)
(dipy.tracking.markov.FixedSizeStepper method)
(dipy.tracking.markov.MarkovIntegrator method)
(dipy.tracking.markov.NearestNeighborInterpolator method)
(dipy.tracking.markov.OutsideImage method)
(dipy.tracking.markov.ProbabilisticOdfWeightedTracker method)
(dipy.tracking.markov.xrange method)
(dipy.tracking.metrics.xrange method)
(dipy.workflows.base.IntrospectiveArgumentParser method)
(dipy.workflows.base.NumpyDocString method)
(dipy.workflows.docstring_parser.NumpyDocString method)
(dipy.workflows.docstring_parser.Reader method)

A

ABCMeta (class in dipy.segment.clustering)
abstractmethod() (in module dipy.segment.clustering)
ActTissueClassifier (class in dipy.tracking.local)
ad() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
adc() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
add_cluster() (dipy.segment.clustering.ClusterMap method)
add_description() (dipy.workflows.base.IntrospectiveArgumentParser method)
add_edge() (dipy.core.graph.Graph method)
add_epilogue() (dipy.workflows.base.IntrospectiveArgumentParser method)
add_node() (dipy.core.graph.Graph method)
add_noise() (in module dipy.sims.phantom)
(in module dipy.sims.voxel)
add_workflow() (dipy.workflows.base.IntrospectiveArgumentParser method)
Affine matrix
Affine transformation
affine_transform() (in module dipy.align.reslice)
(in module dipy.external.fsl)
AffineInversionError (class in dipy.align.imaffine)
AffineMap (class in dipy.align.imaffine)
AffineRegistration (class in dipy.align.imaffine)
ak() (dipy.reconst.dki.DiffusionKurtosisFit method)
akc() (dipy.reconst.dki.DiffusionKurtosisFit method)
align_centers_of_mass() (in module dipy.align.imaffine)
align_geometric_centers() (in module dipy.align.imaffine)
align_origins() (in module dipy.align.imaffine)
all_paths() (dipy.core.graph.Graph method)
all_tensor_evecs() (in module dipy.sims.voxel)
allocate() (dipy.align.imwarp.DiffeomorphicMap method)
ang_thr (dipy.direction.peaks.PeaksAndMetricsDirectionGetter attribute)
(dipy.direction.PeaksAndMetricsDirectionGetter attribute)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter attribute)
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() (in module dipy.tracking.streamline)
apply_warp() (in module dipy.external.fsl)
applymask() (in module dipy.segment.mask)
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)
array() (in module dipy.reconst.interpolate)
as_native_array() (in module dipy.data)
as_strided() (in module dipy.core.ndindex)
(in module dipy.reconst.multi_voxel)
assert_array_equal() (in module dipy.segment.benchmarks.bench_quickbundles)
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.dki)
(in module dipy.reconst.dti)
(in module dipy.reconst.sfm)
(in module dipy.reconst.shm)
auto_response() (in module dipy.reconst.csdeconv)
AveragePointwiseEuclideanMetric (class in dipy.segment.clustering)
(class in dipy.segment.metric)
axial_diffusivity() (in module dipy.reconst.dki)
(in module dipy.reconst.dti)
axial_kurtosis() (in module dipy.reconst.dki)
Axis angle
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)
basename() (in module dipy.workflows.segment)
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)
bet() (in module dipy.external.fsl)
bin_index() (dipy.align.imaffine.ParzenJointHistogram method)
bin_normalize_moving() (dipy.align.imaffine.ParzenJointHistogram method)
bin_normalize_static() (dipy.align.imaffine.ParzenJointHistogram method)
binary_dilation() (in module dipy.segment.mask)
BinaryTissueClassifier (class in dipy.tracking.local)
bootstrap_data_array() (in module dipy.reconst.shm)
bootstrap_data_voxel() (in module dipy.reconst.shm)
BoundaryStepper (class in dipy.tracking.markov)
bounding_box() (in module dipy.reconst.benchmarks.bench_bounding_box)
(in module dipy.segment.mask)
Bunch (class in dipy.align)
(class in dipy.align.imwarp)
(class in dipy.tracking.local.localtracking)
bundle_min_distance() (in module dipy.align.streamlinear)
bundle_min_distance_fast() (in module dipy.align.streamlinear)
bundle_sum_distance() (in module dipy.align.streamlinear)
BundleMinDistanceMatrixMetric (class in dipy.align.streamlinear)
BundleMinDistanceMetric (class in dipy.align.streamlinear)
bundles_distances_mdf() (in module dipy.segment.quickbundles)
BundleSumDistanceMatrixMetric (class in dipy.align.streamlinear)
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.gqi)
(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.gqi.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.gqi.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.gqi.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)
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.shm)
(in module dipy.reconst.shore)
cart_distance() (in module dipy.core.geometry)
CCMetric (class in dipy.align.metrics)
cdist() (in module dipy.tracking.streamline)
CDT_NNO (class in dipy.tracking.markov)
center_of_mass() (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 attribute)
(dipy.segment.quickbundles.QuickBundles attribute)
check_md5() (in module dipy.data.fetcher)
check_point() (dipy.tracking.local.ActTissueClassifier method)
(dipy.tracking.local.BinaryTissueClassifier method)
(dipy.tracking.local.ThresholdTissueClassifier method)
(dipy.tracking.local.TissueClassifier method)
children() (dipy.core.graph.Graph method)
choose_create_out_dir() (in module dipy.workflows.segment)
circumradius() (in module dipy.core.geometry)
clean_cc_mask() (in module dipy.segment.mask)
clear() (dipy.segment.clustering.ClusterMap method)
close() (dipy.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
ClosestDirectionTracker (class in dipy.tracking.markov)
Cluster (class in dipy.segment.clustering)
cluster() (dipy.segment.clustering.Clustering method)
(dipy.segment.clustering.QuickBundles method)
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 attribute)
clusters() (dipy.segment.quickbundles.QuickBundles method)
clusters_sizes() (dipy.segment.clustering.ClusterMap method)
(dipy.segment.quickbundles.QuickBundles method)
coeff_of_determination() (in module dipy.reconst.cross_validation)
color_fa() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
(in module dipy.reconst.dti)
(in module dipy.segment.mask)
communicate() (dipy.external.fsl.Popen method)
compare_orientation_sets() (in module dipy.core.sphere_stats)
component_re (dipy.core.optimize.LooseVersion attribute)
(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)
compute_demons_step() (dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SSDMetric method)
compute_forward() (dipy.align.metrics.CCMetric method)
(dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SSDMetric method)
(dipy.align.metrics.SimilarityMetric method)
compute_gauss_newton_step() (dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SSDMetric method)
compute_inversion_error() (dipy.align.imwarp.DiffeomorphicMap method)
compute_parzen_mi() (in module dipy.align.imaffine)
concatenate() (in module dipy.reconst.shm)
ConstrainedSDTModel (class in dipy.reconst.csdeconv)
ConstrainedSphericalDeconvModel (class in dipy.reconst.benchmarks.bench_csd)
(class in dipy.reconst.csdeconv)
convolve() (in module dipy.denoise.noise_estimate)
copyfileobj() (in module dipy.data.fetcher)
CosineMetric (class in dipy.segment.metric)
cpu_count() (in module dipy.align.reslice)
(in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.peaks)
create_displacements() (in module dipy.external.fsl)
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_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)
csdeconv() (in module dipy.reconst.csdeconv)

D

DataError (class in dipy.data)
dcm2nii() (in module dipy.external.fsl)
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.dti)
dedent_lines() (in module dipy.workflows.docstring_parser)
deepcopy() (in module dipy.tracking.streamline)
del_node() (dipy.core.graph.Graph method)
del_node_and_edges() (dipy.core.graph.Graph method)
design_matrix() (dipy.reconst.sfm.SparseFascicleModel method)
(in module dipy.reconst.dki)
(in module dipy.reconst.dti)
detect_corresponding_tracks() (in module dipy.tracking.learning)
detect_corresponding_tracks_plus() (in module dipy.tracking.learning)
determinant() (in module dipy.reconst.dti)
DeterministicMaximumDirectionGetter (class in dipy.direction)
(class in dipy.direction.probabilistic_direction_getter)
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)
DiffeomorphicRegistration (class in dipy.align.imwarp)
DiffusionKurtosisFit (class in dipy.reconst.dki)
DiffusionKurtosisModel (class in dipy.reconst.dki)
DiffusionSpectrumDeconvFit (class in dipy.reconst.dsi)
DiffusionSpectrumDeconvModel (class in dipy.reconst.dsi)
DiffusionSpectrumFit (class in dipy.reconst.dsi)
DiffusionSpectrumModel (class in dipy.reconst.dsi)
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.data (module)
dipy.data.fetcher (module)
dipy.denoise (module)
dipy.denoise.nlmeans (module)
dipy.denoise.noise_estimate (module)
dipy.direction (module)
dipy.direction.peaks (module)
dipy.direction.probabilistic_direction_getter (module)
dipy.external (module)
dipy.external.fsl (module)
dipy.io (module)
dipy.io.bvectxt (module)
dipy.io.dpy (module)
dipy.io.gradients (module)
dipy.io.pickles (module)
dipy.io.trackvis (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.dsi (module)
dipy.reconst.dti (module)
dipy.reconst.gqi (module)
dipy.reconst.interpolate (module)
dipy.reconst.mapmri (module)
dipy.reconst.multi_voxel (module)
dipy.reconst.odf (module)
dipy.reconst.peaks (module)
dipy.reconst.sfm (module)
dipy.reconst.shm (module)
dipy.reconst.shore (module)
dipy.segment (module)
dipy.segment.benchmarks (module)
dipy.segment.benchmarks.bench_quickbundles (module)
dipy.segment.clustering (module)
dipy.segment.mask (module)
dipy.segment.metric (module)
dipy.segment.quickbundles (module)
dipy.segment.threshold (module)
dipy.sims (module)
dipy.sims.phantom (module)
dipy.sims.voxel (module)
dipy.tracking (module)
dipy.tracking._utils (module)
dipy.tracking.benchmarks (module)
dipy.tracking.benchmarks.bench_streamline (module)
dipy.tracking.eudx (module)
dipy.tracking.learning (module)
dipy.tracking.life (module)
dipy.tracking.local (module)
dipy.tracking.local.localtracking (module)
dipy.tracking.markov (module)
dipy.tracking.metrics (module)
dipy.tracking.streamline (module)
dipy.workflows (module)
dipy.workflows.base (module)
dipy.workflows.docstring_parser (module)
dipy.workflows.reconst (module)
dipy.workflows.segment (module)
dipy.workflows.tracking (module)
DirectionFinder (class in dipy.tracking.markov)
DirectionGetter (class in dipy.direction.probabilistic_direction_getter)
(class in dipy.tracking.local)
directions (dipy.reconst.dki.TensorFit attribute)
(dipy.reconst.dti.TensorFit attribute)
dirname() (in module dipy.data)
disperse_charges() (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)
distance() (dipy.align.imaffine.MutualInformationMetric method)
(dipy.align.streamlinear.BundleMinDistanceMatrixMetric method)
(dipy.align.streamlinear.BundleMinDistanceMetric method)
(dipy.align.streamlinear.BundleSumDistanceMatrixMetric method)
(dipy.align.streamlinear.StreamlineDistanceMetric method)
distance_and_gradient() (dipy.align.imaffine.MutualInformationMetric method)
distance_matrix() (in module dipy.segment.metric)
distance_matrix_mdf() (in module dipy.align.streamlinear)
dki_design_matrix() (in module dipy.sims.voxel)
dki_prediction() (in module dipy.reconst.dki)
DKI_signal() (in module dipy.sims.voxel)
docstring_addendum (dipy.align.imaffine.AffineRegistration attribute)
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.segment.quickbundles)
(in module dipy.tracking.metrics)
downsampled_tracks() (dipy.segment.quickbundles.QuickBundles method)
Dpy (class in dipy.external.fsl)
(class in dipy.io)
(class in dipy.io.dpy)
dsi_deconv_voxels() (in module dipy.data)
dsi_voxels() (in module dipy.data)

E

eddy_correct() (in module dipy.external.fsl)
edges() (dipy.core.sphere.Sphere method)
(dipy.data.Sphere method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.Sphere method)
(dipy.reconst.dti.Sphere method)
(dipy.reconst.peaks.Sphere method)
eig_from_lo_tri() (in module dipy.reconst.dti)
eigenstats() (in module dipy.core.sphere_stats)
eigh() (in module dipy.reconst.dti)
EMMetric (class in dipy.align.metrics)
empty() (in module dipy.reconst.shm)
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_response() (in module dipy.reconst.csdeconv)
estimate_sigma() (in module dipy.denoise.noise_estimate)
Euclidean norm
EuclideanMetric (in module dipy.segment.metric)
EuDX (class in dipy.tracking.eudx)
eudx_both_directions() (in module dipy.tracking.eudx)
Euler angles
euler_characteristic_check() (in module dipy.core.sphere)
euler_matrix() (in module dipy.core.geometry)
evals (dipy.reconst.dki.TensorFit attribute)
(dipy.reconst.dti.TensorFit attribute)
evecs (dipy.reconst.dki.TensorFit attribute)
(dipy.reconst.dti.TensorFit attribute)
evolution (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
exemplars() (dipy.segment.quickbundles.QuickBundles method)
expand_fields() (dipy.align.imwarp.DiffeomorphicMap method)
ExponentialIsotropicFit (class in dipy.reconst.sfm)
ExponentialIsotropicModel (class in dipy.reconst.sfm)
extract() (dipy.segment.metric.Feature method)
eye() (in module dipy.reconst.shm)

F

fa() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
fa_trace_to_lambdas() (in module dipy.reconst.csdeconv)
faces() (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.HemiSphere method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.HemiSphere method)
(dipy.direction.peaks.Sphere method)
(dipy.reconst.dti.Sphere method)
(dipy.reconst.peaks.HemiSphere method)
(dipy.reconst.peaks.Sphere method)
faces_from_sphere_vertices() (in module dipy.core.sphere)
factorial() (in module dipy.reconst.mapmri)
(in module dipy.reconst.shore)
factorial2() (in module dipy.reconst.mapmri)
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_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_data() (in module dipy.data.fetcher)
fetch_isbi2013_2shell() (in module dipy.data)
(in module dipy.data.fetcher)
fetch_mni_template() (in module dipy.data)
(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.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_viz_icons() (in module dipy.data)
(in module dipy.data.fetcher)
FetcherError (class in dipy.data.fetcher)
fftn() (in module dipy.reconst.dsi)
fftshift() (in module dipy.reconst.dsi)
FiberFit (class in dipy.tracking.life)
FiberModel (class in dipy.tracking.life)
find_closest() (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.HemiSphere method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.HemiSphere method)
(dipy.direction.peaks.Sphere method)
(dipy.reconst.dti.Sphere method)
(dipy.reconst.peaks.HemiSphere method)
(dipy.reconst.peaks.Sphere method)
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.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.gqi.GeneralizedQSamplingModel method)
(dipy.reconst.gqi.OdfModel method)
(dipy.reconst.mapmri.MapmriModel method)
(dipy.reconst.mapmri.ReconstModel method)
(dipy.reconst.odf.OdfModel method)
(dipy.reconst.odf.ReconstModel 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)
fitted_signal() (dipy.reconst.shore.ShoreFit method)
FixedSizeStepper (class in dipy.tracking.markov)
flirt2aff() (in module dipy.external.fsl)
flirt2aff_files() (in module dipy.external.fsl)
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)
fopt (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
forward_sdeconv_mat() (in module dipy.reconst.csdeconv)
(in module dipy.reconst.shm)
forward_sdt_deconv_mat() (in module dipy.reconst.csdeconv)
fractional_anisotropy() (in module dipy.reconst.csdeconv)
(in module dipy.reconst.dti)
(in module dipy.segment.mask)
free_iteration() (dipy.align.metrics.CCMetric method)
(dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SSDMetric method)
(dipy.align.metrics.SimilarityMetric method)
frenet_serret() (in module dipy.tracking.metrics)
from_lower_triangular() (in module dipy.reconst.dki)
(in module dipy.reconst.dti)
from_pmf() (dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter class method)
(dipy.direction.ProbabilisticDirectionGetter class method)
from_shcoeff() (dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter class method)
(dipy.direction.ProbabilisticDirectionGetter class method)
from_sphere() (dipy.core.sphere.HemiSphere class method)
(dipy.core.subdivide_octahedron.HemiSphere class method)
(dipy.data.HemiSphere class method)
(dipy.direction.HemiSphere class method)
(dipy.direction.peaks.HemiSphere class method)
(dipy.reconst.peaks.HemiSphere class method)
FSLError (class in dipy.external.fsl)

G

ga() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
gen_dirac() (in module dipy.reconst.shm)
gen_PSF() (in module dipy.reconst.dsi)
GeneralizedQSamplingFit (class in dipy.reconst.gqi)
GeneralizedQSamplingModel (class in dipy.reconst.gqi)
generate_binary_structure() (in module dipy.segment.mask)
generate_combinations() (in module dipy.tracking.metrics)
genlaguerre() (in module dipy.reconst.shore)
geodesic_anisotropy() (in module dipy.reconst.dti)
get_3shell_gtab() (in module dipy.data)
get_affine() (dipy.align.imaffine.ScaleSpace method)
(dipy.align.imwarp.ScaleSpace method)
(dipy.align.scalespace.ScaleSpace method)
get_affine_inv() (dipy.align.imaffine.ScaleSpace method)
(dipy.align.imwarp.ScaleSpace method)
(dipy.align.scalespace.ScaleSpace method)
get_backward_field() (dipy.align.imwarp.DiffeomorphicMap method)
get_cmap() (in module dipy.data)
get_data() (in module dipy.data)
(in module dipy.segment.benchmarks.bench_quickbundles)
(in module dipy.sims.phantom)
(in module dipy.tracking.benchmarks.bench_streamline)
get_direction() (dipy.direction.DeterministicMaximumDirectionGetter method)
(dipy.direction.PeaksAndMetricsDirectionGetter method)
(dipy.direction.ProbabilisticDirectionGetter method)
(dipy.direction.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.DeterministicMaximumDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.DirectionGetter method)
(dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter method)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.tracking.local.DirectionGetter method)
get_direction_and_spacings() (in module dipy.align.imaffine)
(in module dipy.align.imwarp)
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)
get_expand_factors() (dipy.align.imaffine.ScaleSpace method)
(dipy.align.imwarp.ScaleSpace method)
(dipy.align.scalespace.ScaleSpace method)
get_flow_args() (dipy.workflows.base.IntrospectiveArgumentParser method)
get_forward_field() (dipy.align.imwarp.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_info() (in module dipy)
get_isbi2013_2shell_gtab() (in module dipy.data)
get_large_clusters() (dipy.segment.clustering.ClusterMap method)
get_map() (dipy.align.imwarp.DiffeomorphicRegistration method)
(dipy.align.imwarp.SymmetricDiffeomorphicRegistration method)
get_outputs() (dipy.workflows.base.IntrospectiveArgumentParser method)
get_pmf() (dipy.direction.probabilistic_direction_getter.SHCoeffPmfGen method)
(dipy.direction.probabilistic_direction_getter.SimplePmfGen method)
get_scaling() (dipy.align.imaffine.ScaleSpace method)
(dipy.align.imwarp.ScaleSpace method)
(dipy.align.scalespace.ScaleSpace 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)
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.benchmarks.bench_peaks)
(in module dipy.reconst.csdeconv)
(in module dipy.reconst.dti)
(in module dipy.tracking.eudx)
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)
(in module dipy.reconst.peaks)
Gimbal lock
glob() (in module dipy.workflows.segment)
grad_tensor() (in module dipy.tracking.life)
gradient() (dipy.align.imaffine.MutualInformationMetric method)
(in module dipy.align.metrics)
(in module dipy.tracking.life)
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)
gradient_table_from_bvals_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

half_to_full_qspace() (in module dipy.reconst.dsi)
hanning_filter() (in module dipy.reconst.dsi)
hat() (in module dipy.reconst.shm)
have_flirt() (in module dipy.external.fsl)
HemiSphere (class in dipy.core.sphere)
(class in dipy.core.subdivide_octahedron)
(class in dipy.data)
(class in dipy.direction)
(class in dipy.direction.peaks)
(class in dipy.reconst.peaks)
hermite() (in module dipy.reconst.mapmri)
histeq() (in module dipy.core.histeq)
Homogenous coordinates

I

Identity (class in dipy.segment.clustering)
IdentityFeature (class in dipy.segment.metric)
ifftshift() (in module dipy.reconst.dsi)
infer_shape() (dipy.segment.metric.Feature method)
info (dipy.core.gradients.GradientTable attribute)
(dipy.data.GradientTable attribute)
(dipy.reconst.benchmarks.bench_csd.GradientTable attribute)
initial_direction() (dipy.direction.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.direction.PeaksAndMetricsDirectionGetter method)
(dipy.direction.ProbabilisticDirectionGetter method)
(dipy.direction.probabilistic_direction_getter.DirectionGetter method)
(dipy.direction.probabilistic_direction_getter.ProbabilisticDirectionGetter method)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter method)
(dipy.tracking.local.DirectionGetter method)
initialize_iteration() (dipy.align.metrics.CCMetric method)
(dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SSDMetric method)
(dipy.align.metrics.SimilarityMetric method)
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.external.fsl)
(class in dipy.reconst.peaks)
interp_rbf() (in module dipy.core.sphere)
Interpolator (class in dipy.reconst.interpolate)
interpret_matrix() (dipy.align.imwarp.DiffeomorphicMap method)
intersect_sphere() (in module dipy.tracking.metrics)
IntrospectiveArgumentParser (class in dipy.workflows.base)
inv() (in module dipy.core.gradients)
inverse() (dipy.align.imwarp.DiffeomorphicMap method)
is_empty() (dipy.workflows.docstring_parser.Reader method)
is_order_invariant (dipy.segment.benchmarks.bench_quickbundles.Metric attribute)
(dipy.segment.clustering.Metric attribute)
(dipy.segment.metric.Feature attribute)
(dipy.segment.metric.Metric attribute)
(dipy.segment.metric.MinimumAverageDirectFlipMetric attribute)
isotropic() (in module dipy.reconst.dti)
IsotropicFit (class in dipy.reconst.sfm)
IsotropicModel (class in dipy.reconst.sfm)
IsotropicScaleSpace (class in dipy.align.imaffine)
(class in dipy.align.scalespace)
iter_fit_tensor() (in module dipy.reconst.dti)

J

join() (in module dipy.workflows.segment)

K

kfold_xval() (in module dipy.reconst.cross_validation)
kill() (dipy.external.fsl.Popen method)
kt (dipy.reconst.dki.DiffusionKurtosisFit attribute)
kurtosis_element() (in module dipy.sims.voxel)

L

l_shore() (in module dipy.reconst.shore)
label2cluster() (dipy.segment.quickbundles.QuickBundles method)
label2tracks() (dipy.segment.quickbundles.QuickBundles method)
label2tracksids() (dipy.segment.quickbundles.QuickBundles method)
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)
lcr_matrix() (in module dipy.reconst.shm)
LEcuyer() (in module dipy.core.rng)
length() (in module dipy.tracking.benchmarks.bench_streamline)
(in module dipy.tracking.metrics)
(in module dipy.tracking.streamline)
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)
(in module dipy.reconst.dti)
load() (in module dipy.data)
load_pickle() (in module dipy.io)
(in module dipy.io.pickles)
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.gqi)
(in module dipy.reconst.peaks)
local_skeleton_clustering() (in module dipy.segment.quickbundles)
local_tracker() (in module dipy.tracking.local.localtracking)
LocalTracking (class in dipy.tracking.local)
(class in dipy.tracking.local.localtracking)
longest_track_bundle() (in module dipy.tracking.metrics)
LooseVersion (class in dipy.core.optimize)
(class in dipy.reconst.shm)
lower_triangular() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
(in module dipy.reconst.dki)
(in module dipy.reconst.dti)
lpn() (in module dipy.reconst.csdeconv)
(in module dipy.reconst.shm)
LR_deconv() (in module dipy.reconst.dsi)

M

magn() (in module dipy.tracking.metrics)
map_coordinates() (in module dipy.reconst.dsi)
mapmri_coeff (dipy.reconst.mapmri.MapmriFit attribute)
mapmri_EAP() (in module dipy.reconst.mapmri)
mapmri_index_matrix() (in module dipy.reconst.mapmri)
mapmri_mu (dipy.reconst.mapmri.MapmriFit attribute)
mapmri_odf_matrix() (in module dipy.reconst.mapmri)
mapmri_phi_1d() (in module dipy.reconst.mapmri)
mapmri_phi_3d() (in module dipy.reconst.mapmri)
mapmri_phi_matrix() (in module dipy.reconst.mapmri)
mapmri_psi_1d() (in module dipy.reconst.mapmri)
mapmri_psi_3d() (in module dipy.reconst.mapmri)
mapmri_psi_matrix() (in module dipy.reconst.mapmri)
mapmri_R (dipy.reconst.mapmri.MapmriFit attribute)
MapmriFit (class in dipy.reconst.mapmri)
MapmriModel (class in dipy.reconst.mapmri)
markov_streamline() (in module dipy.tracking.markov)
MarkovIntegrator (class in dipy.tracking.markov)
matlab_life_results() (in module dipy.data)
max (dipy.reconst.shm.CsaOdfModel attribute)
mc() (in module dipy.external.fsl)
md() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.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() (in module dipy.reconst.dki)
(in module dipy.reconst.dti)
mean_kurtosis() (in module dipy.reconst.dki)
mean_orientation() (in module dipy.tracking.metrics)
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)
median_otsu_flow() (in module dipy.workflows.segment)
message (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
Metric (class in dipy.segment.benchmarks.bench_quickbundles)
(class in dipy.segment.clustering)
(class in dipy.segment.metric)
midpoint() (in module dipy.tracking.metrics)
midpoint2point() (in module dipy.tracking.metrics)
MidpointFeature (class in dipy.segment.metric)
min (dipy.reconst.shm.CsaOdfModel attribute)
min_seperation_angle (dipy.tracking.markov.DirectionFinder attribute)
minimize() (in module dipy.core.optimize)
MinimumAverageDirectFlipMetric (class in dipy.segment.metric)
minmax_normalize() (in module dipy.reconst.odf)
mirror() (dipy.core.sphere.HemiSphere method)
(dipy.core.subdivide_octahedron.HemiSphere method)
(dipy.data.HemiSphere method)
(dipy.direction.HemiSphere method)
(dipy.direction.peaks.HemiSphere method)
(dipy.reconst.peaks.HemiSphere method)
mk() (dipy.reconst.dki.DiffusionKurtosisFit method)
mode() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
(in module dipy.reconst.dti)
mrtrix_spherical_functions() (in module dipy.data)
msd() (dipy.reconst.shore.ShoreFit method)
msd_discrete() (dipy.reconst.dsi.DiffusionSpectrumFit 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_voxel_fit() (in module dipy.reconst.csdeconv)
(in module dipy.reconst.dsi)
(in module dipy.reconst.gqi)
(in module dipy.reconst.mapmri)
(in module dipy.reconst.multi_voxel)
(in module dipy.reconst.shore)
MultiTensor() (in module dipy.sims.voxel)
MultiVoxelFit (class in dipy.reconst.multi_voxel)
MutualInformationMetric (class in dipy.align.imaffine)

N

n_shore() (in module dipy.reconst.shore)
nanmean() (in module dipy.reconst.sfm)
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.multi_voxel)
(in module dipy.reconst.peaks)
nearest_pos_semi_def() (in module dipy.core.geometry)
NearestNeighborInterpolator (class in dipy.reconst.interpolate)
(class in dipy.tracking.markov)
next (dipy.core.sphere_stats.permutations attribute)
(dipy.direction.peaks.repeat attribute)
(dipy.direction.repeat attribute)
(dipy.reconst.peaks.repeat attribute)
nfev (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
nit (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
nlls_fit_tensor() (in module dipy.reconst.dti)
nlmeans() (in module dipy.denoise.nlmeans)
nlmeans_3d() (in module dipy.denoise.nlmeans)
NonNegativeLeastSquares (class in dipy.core.optimize)
norm() (in module dipy.reconst.dti)
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.gqi.GeneralizedQSamplingFit method)
(dipy.reconst.gqi.OdfFit method)
(dipy.reconst.mapmri.MapmriFit method)
(dipy.reconst.odf.OdfFit 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.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.gqi)
(class in dipy.reconst.odf)
(class in dipy.reconst.shm)
OdfModel (class in dipy.reconst.dsi)
(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)
Optimizer (class in dipy.align.imaffine)
(class in dipy.align.streamlinear)
(class in dipy.core.optimize)
optional_package() (in module dipy.core.profile)
(in module dipy.io.dpy)
(in module dipy.reconst.mapmri)
(in module dipy.reconst.sfm)
(in module dipy.reconst.shore)
orbital_phantom() (in module dipy.sims.phantom)
order_from_ncoef() (in module dipy.direction.probabilistic_direction_getter)
(in module dipy.reconst.shm)
orient_by_rois() (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)
OutsideImage (class in dipy.reconst.interpolate)
(class in dipy.tracking.markov)

P

parents() (dipy.core.graph.Graph method)
parse() (dipy.core.optimize.LooseVersion method)
(dipy.reconst.shm.LooseVersion method)
partitions() (dipy.segment.quickbundles.QuickBundles method)
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)
pdf() (dipy.reconst.dsi.DiffusionSpectrumDeconvFit method)
(dipy.reconst.dsi.DiffusionSpectrumFit 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)
(in module dipy.direction.probabilistic_direction_getter)
(in module dipy.reconst.peaks)
(in module dipy.tracking.markov)
peak_directions_nl() (in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.peaks)
PeakDirectionGetter (class in dipy.direction.probabilistic_direction_getter)
peaks_from_model() (in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.csdeconv)
(in module dipy.reconst.peaks)
PeaksAndMetrics (class in dipy.direction)
(class in dipy.direction.peaks)
(class in dipy.reconst.peaks)
PeaksAndMetricsDirectionGetter (class in dipy.direction)
(class in dipy.direction.peaks)
(class in dipy.reconst.peaks)
peek() (dipy.workflows.docstring_parser.Reader method)
permutations (class in dipy.core.sphere_stats)
perpendicular_directions() (in module dipy.core.geometry)
piesno() (in module dipy.denoise.noise_estimate)
pinv() (in module dipy.reconst.dti)
(in module dipy.reconst.shm)
pipe() (in module dipy.external.fsl)
pipe_cloexec() (dipy.external.fsl.Popen method)
pjoin() (in module dipy.data)
(in module dipy.data.fetcher)
(in module dipy.external.fsl)
planarity() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
(in module dipy.reconst.dti)
PmfGen (class in dipy.direction.probabilistic_direction_getter)
points_per_track() (dipy.segment.quickbundles.QuickBundles method)
polar() (in module dipy.core.gradients)
polar_zone_vertices() (in module dipy.reconst.gqi)
poll() (dipy.external.fsl.Popen method)
Pool() (in module dipy.align.reslice)
(in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.peaks)
Popen (class in dipy.external.fsl)
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.dti.TensorFit method)
(dipy.reconst.dti.TensorModel method)
(dipy.reconst.mapmri.MapmriFit method)
(dipy.reconst.multi_voxel.MultiVoxelFit 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)
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)
ProbabilisticDirectionGetter (class in dipy.direction)
(class in dipy.direction.probabilistic_direction_getter)
ProbabilisticOdfWeightedTracker (class in dipy.tracking.markov)
Profiler (class in dipy.core.profile)
project_hemisph_bvecs() (in module dipy.reconst.dsi)

Q

qa_thr (dipy.direction.peaks.PeaksAndMetricsDirectionGetter attribute)
(dipy.direction.PeaksAndMetricsDirectionGetter attribute)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter attribute)
QB_New (in module dipy.segment.benchmarks.bench_quickbundles)
QB_Old (in module dipy.segment.benchmarks.bench_quickbundles)
QballBaseModel (class in dipy.reconst.shm)
QballModel (class in dipy.reconst.shm)
quad() (in module dipy.reconst.csdeconv)
quadratic_form (dipy.reconst.dki.TensorFit attribute)
(dipy.reconst.dti.TensorFit attribute)
quantize_evecs() (in module dipy.reconst.dti)
Quaternion
quick_squash() (in module dipy.reconst.benchmarks.bench_squash)
QuickBundles (class in dipy.segment.clustering)
(class in dipy.segment.quickbundles)
qvals() (dipy.core.gradients.GradientTable method)
(dipy.data.GradientTable method)
(dipy.reconst.benchmarks.bench_csd.GradientTable method)

R

radial_diffusivity() (in module dipy.reconst.dki)
(in module dipy.reconst.dti)
radial_kurtosis() (in module dipy.reconst.dki)
randint() (in module dipy.reconst.shm)
randn() (in module dipy.reconst.benchmarks.bench_vec_val_sum)
random_uniform_on_sphere() (in module dipy.core.sphere_stats)
range (in module dipy.reconst.cross_validation)
(in module dipy.reconst.csdeconv)
(in module dipy.reconst.dki)
(in module dipy.reconst.dti)
(in module dipy.tracking.life)
rd() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.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)
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_isbi2013_2shell() (in module dipy.data)
(in module dipy.data.fetcher)
read_mni_template() (in module dipy.data)
(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_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.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
read_tracks() (dipy.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
read_tracksi() (dipy.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
read_viz_icons() (in module dipy.data)
(in module dipy.data.fetcher)
Reader (class in dipy.workflows.docstring_parser)
real_sph_harm() (in module dipy.reconst.csdeconv)
(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)
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)
ReconstModel (class in dipy.reconst.base)
(class in dipy.reconst.dki)
(class in dipy.reconst.dti)
(class in dipy.reconst.mapmri)
(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)
refdata (dipy.segment.clustering.ClusterMap attribute)
Reflection
register() (dipy.segment.clustering.ABCMeta method)
relative_peak_threshold (dipy.tracking.markov.DirectionFinder attribute)
relist_streamlines() (in module dipy.data)
(in module dipy.tracking.streamline)
remove_cluster() (dipy.segment.clustering.ClusterMap method)
(dipy.segment.quickbundles.QuickBundles method)
remove_clusters() (dipy.segment.quickbundles.QuickBundles method)
remove_similar_vertices() (in module dipy.core.sphere)
(in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.gqi)
(in module dipy.reconst.peaks)
remove_small_clusters() (dipy.segment.quickbundles.QuickBundles method)
remove_tracks() (dipy.segment.quickbundles.QuickBundles method)
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)
(class in dipy.reconst.peaks)
ResampleFeature (class in dipy.segment.clustering)
(class in dipy.segment.metric)
reset() (dipy.core.onetime.ResetMixin method)
(dipy.workflows.docstring_parser.Reader method)
reset_cache() (dipy.tracking.markov.CDT_NNO method)
ResetMixin (class in dipy.core.onetime)
reshape_peaks_for_visualization() (in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.peaks)
ResidualBootstrapWrapper (class in dipy.reconst.shm)
reslice() (in module dipy.align.reslice)
response_from_mask() (in module dipy.reconst.csdeconv)
restore_fit_tensor() (in module dipy.reconst.dti)
rk() (dipy.reconst.dki.DiffusionKurtosisFit method)
rodrigues_axis_rotation() (in module dipy.core.geometry)
Rotation matrix
Rotation vector
rtap() (dipy.reconst.mapmri.MapmriFit method)
rtop() (dipy.reconst.mapmri.MapmriFit 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)
run_flirt_imgs() (in module dipy.external.fsl)

S

sample_domain_regular() (in module dipy.align.imaffine)
sampling_matrix() (dipy.reconst.csdeconv.SphHarmModel method)
(dipy.reconst.shm.SphHarmModel method)
save_pickle() (in module dipy.io)
(in module dipy.io.pickles)
save_trk() (in module dipy.io.trackvis)
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)
(in module dipy.reconst.peaks)
seek_next_non_empty_line() (dipy.workflows.docstring_parser.Reader method)
segment_from_cfa() (in module dipy.segment.mask)
select_by_rois() (in module dipy.tracking.streamline)
select_random_set_of_streamlines() (in module dipy.tracking.streamline)
send_signal() (dipy.external.fsl.Popen method)
set_affine() (dipy.align.imaffine.AffineMap 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.tracking.benchmarks.bench_streamline)
(in module dipy.tracking.streamline)
set_number_of_points_python() (in module dipy.tracking.benchmarks.bench_streamline)
set_static_image() (dipy.align.metrics.SimilarityMetric method)
setattr_on_read() (in module dipy.core.onetime)
setup() (dipy.align.imaffine.MutualInformationMetric method)
(dipy.align.imaffine.ParzenJointHistogram method)
(dipy.align.streamlinear.BundleMinDistanceMatrixMetric method)
(dipy.align.streamlinear.BundleMinDistanceMetric method)
(dipy.align.streamlinear.StreamlineDistanceMetric method)
(dipy.tracking.life.FiberModel method)
setup_module() (in module dipy.io.dpy)
sf_to_sh() (in module dipy.reconst.shm)
sfm_design_matrix() (in module dipy.reconst.sfm)
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.peaks)
(in module dipy.reconst.shm)
shallow_copy() (dipy.align.imwarp.DiffeomorphicMap method)
shape (dipy.reconst.csdeconv.SphHarmFit attribute)
(dipy.reconst.dki.TensorFit attribute)
(dipy.reconst.dti.TensorFit attribute)
(dipy.reconst.multi_voxel.MultiVoxelFit attribute)
(dipy.reconst.shm.SphHarmFit attribute)
SHCoeffPmfGen (class in dipy.direction.probabilistic_direction_getter)
Shear matrix
shm_coeff (dipy.reconst.csdeconv.SphHarmFit attribute)
(dipy.reconst.shm.SphHarmFit attribute)
shore_coeff (dipy.reconst.shore.ShoreFit attribute)
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)
SimilarityMetric (class in dipy.align.metrics)
SimplePmfGen (class in dipy.direction.probabilistic_direction_getter)
single_tensor() (in module dipy.reconst.csdeconv)
(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)
SingleTensor() (in module dipy.sims.phantom)
(in module dipy.sims.voxel)
size() (dipy.segment.clustering.ClusterMap method)
SKLearnLinearSolver (class in dipy.core.optimize)
smooth_pinv() (in module dipy.reconst.shm)
sparse_nnls() (in module dipy.core.optimize)
SparseFascicleFit (class in dipy.reconst.sfm)
SparseFascicleModel (class in dipy.reconst.sfm)
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.shm)
Sphere (class in dipy.core.sphere)
(class in dipy.data)
(class in dipy.direction)
(class in dipy.direction.peaks)
(class in dipy.reconst.dti)
(class in dipy.reconst.peaks)
sphere (dipy.direction.probabilistic_direction_getter.PeakDirectionGetter attribute)
(dipy.tracking.markov.DirectionFinder attribute)
sphere2cart() (in module dipy.core.geometry)
(in module dipy.core.sphere)
(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)
(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)
splitext() (in module dipy.io.bvectxt)
(in module dipy.io.gradients)
(in module dipy.workflows.segment)
splprep() (in module dipy.tracking.metrics)
squared_radial_component() (in module dipy.reconst.gqi)
SSDMetric (class in dipy.align.metrics)
startpoint() (in module dipy.tracking.metrics)
sticks_and_ball() (in module dipy.sims.voxel)
SticksAndBall() (in module dipy.data)
(in module dipy.sims.voxel)
streamline_gradients() (in module dipy.tracking.life)
streamline_near_roi() (in module dipy.tracking.streamline)
streamline_signal() (dipy.tracking.life.LifeSignalMaker method)
(in module dipy.tracking.life)
streamline_tensors() (in module dipy.tracking.life)
StreamlineDistanceMetric (class in dipy.align.streamlinear)
StreamlineLinearRegistration (class in dipy.align.streamlinear)
StreamlineRegistrationMap (class in dipy.align.streamlinear)
subdivide() (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.HemiSphere method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.HemiSphere method)
(dipy.direction.peaks.Sphere method)
(dipy.reconst.dti.Sphere method)
(dipy.reconst.peaks.HemiSphere method)
(dipy.reconst.peaks.Sphere method)
SumPointwiseEuclideanMetric (class in dipy.segment.metric)
svd() (in module dipy.reconst.shm)
SymmetricDiffeomorphicRegistration (class in dipy.align.imwarp)

T

tensor_prediction() (in module dipy.reconst.dti)
TensorFit (class in dipy.reconst.dki)
(class in dipy.reconst.dti)
TensorModel (class in dipy.reconst.csdeconv)
(class in dipy.reconst.dti)
terminate() (dipy.external.fsl.Popen method)
test() (in module dipy)
(in module dipy.core)
(in module dipy.denoise)
(in module dipy.external)
(in module dipy.reconst)
(in module dipy.tracking)
threshold_propagator() (in module dipy.reconst.dsi)
ThresholdTissueClassifier (class in dipy.tracking.local)
TissueClassifier (class in dipy.tracking.local)
total_clusters (dipy.segment.quickbundles.QuickBundles attribute)
total_weight (dipy.direction.peaks.PeaksAndMetricsDirectionGetter attribute)
(dipy.direction.PeaksAndMetricsDirectionGetter attribute)
(dipy.reconst.peaks.PeaksAndMetricsDirectionGetter attribute)
trace() (dipy.reconst.dki.TensorFit method)
(dipy.reconst.dti.TensorFit method)
(in module dipy.reconst.dti)
transform() (dipy.align.imaffine.AffineMap method)
(dipy.align.imwarp.DiffeomorphicMap method)
(dipy.align.streamlinear.StreamlineRegistrationMap method)
transform_centers_of_mass() (in module dipy.align.imaffine)
transform_geometric_centers() (in module dipy.align.imaffine)
transform_inverse() (dipy.align.imaffine.AffineMap method)
(dipy.align.imwarp.DiffeomorphicMap method)
transform_origins() (in module dipy.align.imaffine)
transform_streamlines() (in module dipy.align.streamlinear)
(in module dipy.tracking.life)
(in module dipy.tracking.streamline)
trilinear_interp() (in module dipy.reconst.interpolate)
trilinear_interpolate4d() (in module dipy.direction.probabilistic_direction_getter)
TriLinearInterpolator (class in dipy.reconst.interpolate)
triple_odf_maxima() (in module dipy.reconst.gqi)
two_cingulum_bundles() (in module dipy.data)

U

unique() (in module dipy.reconst.shm)
unique_edges() (in module dipy.core.sphere)
(in module dipy.reconst.benchmarks.bench_peaks)
unique_rows() (in module dipy.tracking.life)
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)
update_argument() (dipy.workflows.base.IntrospectiveArgumentParser method)
update_gradient_dense() (dipy.align.imaffine.ParzenJointHistogram method)
update_gradient_sparse() (dipy.align.imaffine.ParzenJointHistogram method)
update_pdfs_dense() (dipy.align.imaffine.ParzenJointHistogram method)
update_pdfs_sparse() (dipy.align.imaffine.ParzenJointHistogram method)
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)
use_static_image_dynamics() (dipy.align.metrics.EMMetric method)
(dipy.align.metrics.SimilarityMetric method)

V

v_cycle_2d() (in module dipy.align.metrics)
v_cycle_3d() (in module dipy.align.metrics)
values_from_volume() (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.dti)
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.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
vertices() (dipy.core.sphere.Sphere method)
(dipy.data.Sphere method)
(dipy.direction.Sphere method)
(dipy.direction.peaks.Sphere method)
(dipy.reconst.dti.Sphere method)
(dipy.reconst.peaks.Sphere method)
virtuals() (dipy.segment.quickbundles.QuickBundles method)
voxel2streamline() (in module dipy.tracking.life)

W

wait() (dipy.external.fsl.Popen method)
warn() (in module dipy.align.imaffine)
(in module dipy.direction)
(in module dipy.direction.peaks)
(in module dipy.reconst.mapmri)
(in module dipy.reconst.peaks)
(in module dipy.reconst.shore)
(in module dipy.segment.mask)
(in module dipy.segment.quickbundles)
(in module dipy.tracking._utils)
(in module dipy.tracking.streamline)
(in module dipy.workflows.docstring_parser)
warp_displacements() (in module dipy.external.fsl)
warp_displacements_tracks() (in module dipy.external.fsl)
warp_endomorphism() (dipy.align.imwarp.DiffeomorphicMap method)
Wcons() (in module dipy.reconst.dki)
WichmannHill1982() (in module dipy.core.rng)
WichmannHill2006() (in module dipy.core.rng)
winding() (in module dipy.tracking.metrics)
with_einsum() (in module dipy.reconst.benchmarks.bench_vec_val_sum)
with_metaclass() (in module dipy.align.imwarp)
(in module dipy.align.metrics)
(in module dipy.align.streamlinear)
(in module dipy.core.optimize)
wls_fit_dki() (in module dipy.reconst.dki)
wls_fit_tensor() (in module dipy.reconst.dti)
write_bvals_bvecs() (in module dipy.external.fsl)
write_track() (dipy.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
write_tracks() (dipy.external.fsl.Dpy method)
(dipy.io.Dpy method)
(dipy.io.dpy.Dpy method)
Wrotate() (in module dipy.reconst.dki)
Wrotate_element() (in module dipy.reconst.dki)

X

x (dipy.core.sphere.Sphere attribute)
(dipy.data.Sphere attribute)
(dipy.direction.Sphere attribute)
(dipy.direction.peaks.Sphere attribute)
(dipy.reconst.dti.Sphere attribute)
(dipy.reconst.peaks.Sphere attribute)
xopt (dipy.align.imaffine.Optimizer attribute)
(dipy.align.streamlinear.Optimizer attribute)
(dipy.core.optimize.Optimizer attribute)
xrange (class in dipy.core.sphere)
(class in dipy.direction)
(class in dipy.direction.peaks)
(class in dipy.reconst.peaks)
(class in dipy.tracking.markov)
(class in dipy.tracking.metrics)

Y

y (dipy.core.sphere.Sphere attribute)
(dipy.data.Sphere attribute)
(dipy.direction.Sphere attribute)
(dipy.direction.peaks.Sphere attribute)
(dipy.reconst.dti.Sphere attribute)
(dipy.reconst.peaks.Sphere attribute)

Z

z (dipy.core.sphere.Sphere attribute)
(dipy.data.Sphere attribute)
(dipy.direction.Sphere attribute)
(dipy.direction.peaks.Sphere attribute)
(dipy.reconst.dti.Sphere attribute)
(dipy.reconst.peaks.Sphere attribute)