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

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_

__init__() (nipy.algorithms.fwhm.ReselImage method) (nipy.algorithms.fwhm.Resels method) (nipy.algorithms.interpolation.ImageInterpolator method) (nipy.algorithms.kernel_smooth.LinearFilter method) (nipy.algorithms.statistics.classification.Classifier method) (nipy.algorithms.statistics.nlsmodel.NLSModel method) (nipy.algorithms.statistics.regression.AREstimator method) (nipy.algorithms.statistics.regression.ArrayOutput method) (nipy.algorithms.statistics.regression.RegressionOutput method) (nipy.algorithms.statistics.regression.RegressionOutputList method) (nipy.algorithms.statistics.regression.TOutput method) (nipy.algorithms.statistics.rft.ChiBarSquared method) (nipy.algorithms.statistics.rft.ChiSquared method) (nipy.algorithms.statistics.rft.ECcone method) (nipy.algorithms.statistics.rft.ECquasi method) (nipy.algorithms.statistics.rft.FStat method) (nipy.algorithms.statistics.rft.Hotelling method) (nipy.algorithms.statistics.rft.IntrinsicVolumes method) (nipy.algorithms.statistics.rft.MultilinearForm method) (nipy.algorithms.statistics.rft.OneSidedF method) (nipy.algorithms.statistics.rft.Roy method) (nipy.algorithms.statistics.rft.TStat method) (nipy.algorithms.statistics.rft.fnsum method) (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.image.SliceMaker method) (nipy.core.image.image_list.ImageList method) (nipy.core.image.roi.ContinuousROI method) (nipy.core.image.roi.CoordinateMapROI method) (nipy.core.image.roi.DiscreteROI method) (nipy.core.image.roi.ROI method) (nipy.core.image.roi.ROISequence method) (nipy.core.image.roi.ROIall method) (nipy.core.image.xyz_image.XYZImage method) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.array_coords.ArrayCoordMap method) (nipy.core.reference.array_coords.Grid method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) (nipy.core.reference.coordinate_system.CoordinateSystem method) (nipy.interfaces.spm.SpmInfo method) (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.batteryrunners.BatteryRunner method) (nipy.io.imageformats.batteryrunners.Report method) (nipy.io.imageformats.binaryheaders.BinaryHeader method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.filename_parser.TypesFilenamesError method) (nipy.io.imageformats.filetuples.FileTuples method) (nipy.io.imageformats.filetuples.FileTuplesError method) (nipy.io.imageformats.headers.Header method) (nipy.io.imageformats.minc.MincError method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.minc.netcdf_fileobj method) (nipy.io.imageformats.nifti1.Nifti1Extension method) (nipy.io.imageformats.nifti1.Nifti1Extensions method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.orientations.OrientationError method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) (nipy.io.imageformats.volumeutils.HeaderDataError method) (nipy.io.imageformats.volumeutils.HeaderTypeError method) (nipy.io.imageformats.volumeutils.Recoder method) (nipy.modalities.fmri.fmri.FmriImageList method) (nipy.modalities.fmri.fmristat.delay.Contrast method) (nipy.modalities.fmri.fmristat.model.AR1 method) (nipy.modalities.fmri.fmristat.model.ModelOutputImage method) (nipy.modalities.fmri.fmristat.model.OLS method) (nipy.modalities.fmri.fmristat.utils.WholeBrainNormalize method) (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.Factor method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Formula method) (nipy.modalities.fmri.formula.RandomEffects method) (nipy.modalities.fmri.formula.Term method) (nipy.modalities.fmri.spm.model.SecondStage method) (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.clustering.ggmixture.Gamma method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.clustering.gmm.grid_descriptor method) (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.datasets.transforms.affine_transform.AffineTransform method) (nipy.neurospin.datasets.transforms.transform.CompositionError method) (nipy.neurospin.datasets.transforms.transform.Transform method) (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) (nipy.neurospin.eda.dimension_reduction.MDS method) (nipy.neurospin.eda.dimension_reduction.NLDR method) (nipy.neurospin.eda.dimension_reduction.PCA method) (nipy.neurospin.eda.dimension_reduction.eps_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_LE method) (nipy.neurospin.eda.dimension_reduction.knn_LPP method) (nipy.neurospin.glm.glm.contrast method) (nipy.neurospin.glm.glm.glm method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.group.displacement_field.displacement_field method) (nipy.neurospin.group.displacement_field.gaussian_random_field method) (nipy.neurospin.group.permutation_test.permutation_test_onesample method) (nipy.neurospin.group.permutation_test.permutation_test_onesample_graph method) (nipy.neurospin.group.permutation_test.permutation_test_twosample method) (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) (nipy.neurospin.image.image.Image method) (nipy.neurospin.image.image.MaskedImage method) (nipy.neurospin.registration.affine.Affine method) (nipy.neurospin.registration.affine.Rigid method) (nipy.neurospin.registration.affine.Similarity method) (nipy.neurospin.registration.grid_transform.GridTransform method) (nipy.neurospin.registration.grid_transform.SplineTransform method) (nipy.neurospin.registration.iconic_registration.IconicRegistration method) (nipy.neurospin.registration.registration.FmriRealign4d method) (nipy.neurospin.registration.spacetime_registration.Image4d method) (nipy.neurospin.registration.spacetime_registration.Realign4d method) (nipy.neurospin.segmentation.vem.VemTissueClassification method) (nipy.neurospin.spatial_models.parcellation.Parcellation method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.ROI method) (nipy.neurospin.statistical_mapping.LinearModel method) (nipy.neurospin.utils.design_matrix.BlockParadigm method) (nipy.neurospin.utils.design_matrix.DesignMatrix method) (nipy.neurospin.utils.design_matrix.EventRelatedParadigm method) (nipy.neurospin.utils.design_matrix.Paradigm method) (nipy.neurospin.utils.emp_null.ENN method), [1] (nipy.neurospin.utils.emp_null.FDR method) (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) (nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer method) (nipy.utils.data.Bomber method) (nipy.utils.data.DataError method) (nipy.utils.data.Datasource method) (nipy.utils.data.VersionedDatasource method) (nipy.utils.onetime.OneTimeProperty method) (nipy.utils.tmpdirs.InTemporaryDirectory method) (nipy.utils.tmpdirs.TemporaryDirectory method)

A

adapt_header() (in module nipy.io.imageformats.header_ufuncs) add_codes() (nipy.io.imageformats.volumeutils.Recoder method) add_subjects() (nipy.neurospin.spatial_models.parcellation.Parcellation method) add_type() (nipy.io.imageformats.filetuples.FileTuples method) adjacency() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Affine (class in nipy.neurospin.registration.affine) affine (nipy.core.image.affine_image.AffineImage attribute) (nipy.core.image.xyz_image.XYZImage attribute) (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) (nipy.neurospin.registration.grid_transform.GridTransform attribute) (nipy.neurospin.registration.grid_transform.SplineTransform attribute) affine() (nipy.core.image.image.Image static method) affine_img_src() (in module nipy.neurospin.viz_tools.maps_3d) affine_transform_from_array() (in module nipy.io.nifti_ref) AffineImage (class in nipy.core.image.affine_image) AffineTransform (class in nipy.core.reference.coordinate_map) (class in nipy.neurospin.datasets.transforms.affine_transform) AFNI all_distances() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) all_fdr() (nipy.neurospin.utils.emp_null.FDR method) all_fdr_from_pvals() (nipy.neurospin.utils.emp_null.FDR method) allopen() (in module nipy.io.imageformats.volumeutils) AnalyzeHeader (class in nipy.io.imageformats.analyze) AnalyzeImage (class in nipy.io.imageformats.analyze) angle_axis2euler() (in module nipy.io.imageformats.eulerangles) angle_axis2mat() (in module nipy.io.imageformats.quaternions) angle_axis2quat() (in module nipy.io.imageformats.quaternions) annotate() (nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer method) anti_symmeterize() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) append (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) append_balls() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) append_discrete_ROI() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) append_io_dim() (in module nipy.core.reference.coordinate_map) append_roi() (nipy.neurospin.spatial_models.roi.MultiROI method) apply_affine() (in module nipy.neurospin.datasets.transforms.affine_utils) (in module nipy.neurospin.image.image) apply_affine_to_tuple() (in module nipy.neurospin.image.image) apply_orientation() (in module nipy.io.imageformats.orientations) apply_perm() (in module nipy.neurospin.clustering.bgmm) AR1 (class in nipy.modalities.fmri.fmristat.model) ARcomponents() (in module nipy.modalities.fmri.spm.correlation) ARcovariance() (in module nipy.modalities.fmri.spm.correlation) AREstimator (class in nipy.algorithms.statistics.regression) args (nipy.io.imageformats.filename_parser.TypesFilenamesError attribute) (nipy.io.imageformats.filetuples.FileTuplesError attribute) (nipy.io.imageformats.minc.MincError attribute) (nipy.io.imageformats.orientations.OrientationError attribute) (nipy.io.imageformats.volumeutils.HeaderDataError attribute) (nipy.io.imageformats.volumeutils.HeaderTypeError attribute) (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) (nipy.neurospin.datasets.transforms.transform.CompositionError attribute) (nipy.utils.data.DataError attribute) array_from_file() (in module nipy.io.imageformats.volumeutils) array_to_file() (in module nipy.io.imageformats.volumeutils) ArrayCoordMap (class in nipy.core.reference.array_coords) ArrayOutput (class in nipy.algorithms.statistics.regression) as_ball() (nipy.neurospin.spatial_models.roi.ROI method)

as_base_exp() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_basic() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_byteswapped() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) as_closest_canonical() (in module nipy.io.imageformats.funcs) as_coeff_exponent() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_coeff_factors() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_coeff_terms() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_coefficient() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_dummy() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_image() (in module nipy.io.files) as_independent() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_leading_term() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_multiple_balls() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) as_numer_denom() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_poly() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_powers_dict() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_real_imag() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) as_unittest() (in module nipy.io.imageformats.testing.lightunit) (in module nipy.testing.lightunit) as_volume_img() (in module nipy.neurospin.datasets.converters) (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) asarray() (nipy.io.imageformats.compat.NiftiImage method) asDict() (nipy.io.imageformats.compat.NiftiImage method) asNifti1Image() (in module nipy.neurospin.image.image) assumptions0 (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) atoms() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) autocrop_img() (in module nipy.neurospin.viz_tools.maps_3d) average_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) average_link_distance() (in module nipy.neurospin.clustering.hierarchical_clustering) average_link_distance_segment() (in module nipy.neurospin.clustering.hierarchical_clustering) average_link_euclidian() (in module nipy.neurospin.clustering.hierarchical_clustering) average_link_graph() (in module nipy.neurospin.clustering.hierarchical_clustering) average_link_graph_segment() (in module nipy.neurospin.clustering.hierarchical_clustering) average_log_like() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) axes() (nipy.core.image.affine_image.AffineImage static method) (nipy.core.image.image.Image static method) (nipy.core.image.xyz_image.XYZImage static method)

B

background (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) ball_search() (in module nipy.algorithms.statistics.rft) BatteryRunner (class in nipy.io.imageformats.batteryrunners) bayes_factor() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) best_fitting_GMM() (in module nipy.neurospin.clustering.gmm) Beta (class in nipy.modalities.fmri.formula) BGMM (class in nipy.neurospin.clustering.bgmm) bic() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) binaryblock (nipy.io.imageformats.analyze.AnalyzeHeader attribute) (nipy.io.imageformats.nifti1.Nifti1Header attribute) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader attribute) BinaryHeader (class in nipy.io.imageformats.binaryheaders) binomial() (in module nipy.algorithms.statistics.rft) BipartiteGraph (class in nipy.neurospin.graph.graph)

BlockParadigm (class in nipy.neurospin.utils.design_matrix) blocks() (in module nipy.modalities.fmri.utils) BOLD Bomber (class in nipy.utils.data) bonferroni() (in module nipy.neurospin.statistical_mapping) bootstrap_group() (in module nipy.neurospin.utils.reproducibility_measures) bounding_box() (in module nipy.core.reference.slices) boxplot_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) BPmatch() (in module nipy.neurospin.graph.BPmatch) BPmatch_slow() (in module nipy.neurospin.graph.BPmatch) BPmatch_slow_asym() (in module nipy.neurospin.graph.BPmatch) BPmatch_slow_asym_dev() (in module nipy.neurospin.graph.BPmatch) BrainVisa bsa_dpmm() (in module nipy.neurospin.spatial_models.bayesian_structural_analysis) bsa_dpmm2() (in module nipy.neurospin.spatial_models.bayesian_structural_analysis) BSD build_dmtx() (in module nipy.neurospin.utils.design_matrix) build_LR() (in module nipy.neurospin.spatial_models.structural_bfls)

C

calculate_scale() (in module nipy.io.imageformats.volumeutils) calibrate() (nipy.neurospin.group.permutation_test.permutation_test method) (nipy.neurospin.group.permutation_test.permutation_test_onesample method) (nipy.neurospin.group.permutation_test.permutation_test_onesample_graph method) (nipy.neurospin.group.permutation_test.permutation_test_twosample method) can_cast() (in module nipy.io.imageformats.volumeutils) cartesian_smoothing() (in module nipy.neurospin.utils.smoothing) cc() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) CCA() (in module nipy.neurospin.eda.dimension_reduction) centers() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) change_exponent() (nipy.algorithms.statistics.rft.ECquasi method) check() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.Gamma method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.parcellation.Parcellation method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) check_compatible_height() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) check_consistency() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) check_data() (nipy.neurospin.eda.dimension_reduction.eps_Isomap method) (nipy.neurospin.eda.dimension_reduction.MDS method) (nipy.neurospin.eda.dimension_reduction.NLDR method) (nipy.neurospin.eda.dimension_reduction.PCA method) (nipy.neurospin.eda.dimension_reduction.knn_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_LE method) (nipy.neurospin.eda.dimension_reduction.knn_LPP method) check_deps() (in module nipy.utils.perlpie) check_feature_matrices() (nipy.neurospin.graph.graph.BipartiteGraph method) check_features() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) check_fix() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.batteryrunners.BatteryRunner method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) check_header() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.DiscreteROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) check_isometry() (in module nipy.neurospin.eda.dimension_reduction) check_only() (nipy.io.imageformats.batteryrunners.BatteryRunner method) check_pv() (nipy.neurospin.utils.emp_null.FDR method) check_x() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) ChiBarSquared (class in nipy.algorithms.statistics.rft) ChiSquared (class in nipy.algorithms.statistics.rft) clamp() (in module nipy.neurospin.registration.iconic_registration) Classifier (class in nipy.algorithms.statistics.classification) clean() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) cleanup() (nipy.utils.tmpdirs.InTemporaryDirectory method) (nipy.utils.tmpdirs.TemporaryDirectory method) cliques() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) close() (nipy.io.imageformats.minc.netcdf_fileobj method) closing() (nipy.neurospin.graph.field.Field method) cluster_reproducibility() (in module nipy.neurospin.utils.reproducibility_measures) cluster_stats() (in module nipy.neurospin.statistical_mapping) cluster_threshold() (in module nipy.neurospin.utils.reproducibility_measures) coeff() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) coefs (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute) combinations() (in module nipy.algorithms.statistics.utils) compare() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) compare_pretty() (nipy.modalities.fmri.formula.Beta static method) (nipy.modalities.fmri.formula.FactorTerm static method) (nipy.modalities.fmri.formula.Term static method) compatible() (nipy.algorithms.statistics.rft.ECquasi method) complete() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) complete_roi_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

complex() (in module nipy.algorithms.statistics.utils) component_likelihood() (nipy.neurospin.clustering.ggmixture.GGGM method) compose() (in module nipy.core.reference.coordinate_map) composed_with() (nipy.neurospin.datasets.transforms.affine_transform.AffineTransform method) (nipy.neurospin.datasets.transforms.transform.Transform method) composed_with_transform() (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) CompositionError (class in nipy.neurospin.datasets.transforms.transform) Compute_Amers() (in module nipy.neurospin.spatial_models.structural_bfls) compute_children() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) compute_cluster_stats() (in module nipy.neurospin.group.permutation_test) compute_conditional_posterior_mean() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_discrete_position() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) compute_inner_blocks() (nipy.neurospin.group.displacement_field.displacement_field method) compute_log_conditional_displacements_posterior() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_conditional_posterior() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_posterior() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_prior() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_region_likelihood() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_region_likelihood_slow() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_log_voxel_likelihood() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_marginal_likelihood() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) compute_mask() (in module nipy.neurospin.utils.mask) compute_mask_files() (in module nipy.neurospin.utils.mask) compute_mask_sessions() (in module nipy.neurospin.utils.mask) compute_region_stat() (in module nipy.neurospin.group.permutation_test) concat_images() (in module nipy.io.imageformats.funcs) concatenate_graphs() (in module nipy.neurospin.graph.graph) conditional_posterior_proba() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) conjugate() (in module nipy.io.imageformats.quaternions) (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) conjunction() (in module nipy.neurospin.utils.reproducibility_measures) constrained_voronoi() (nipy.neurospin.graph.field.Field method) ContinuousROI (class in nipy.core.image.roi) Contrast (class in nipy.modalities.fmri.fmristat.delay) contrast (class in nipy.neurospin.glm.glm) contrast() (nipy.neurospin.glm.glm.glm method) (nipy.neurospin.statistical_mapping.LinearModel method) contrast_from_cols_or_rows() (in module nipy.modalities.fmri.formula) converse_edge() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) convolve_functions() (in module nipy.modalities.fmri.utils) convolve_regressors() (in module nipy.neurospin.utils.design_matrix) coord_bsa() (in module nipy.neurospin.utils.reproducibility_measures) coord_dtype (nipy.core.reference.coordinate_system.CoordinateSystem attribute) coord_transform() (in module nipy.neurospin.viz_tools.coord_tools) CoordinateMap (class in nipy.core.reference.coordinate_map) CoordinateMapROI (class in nipy.core.image.roi) CoordinateSystem (class in nipy.core.reference.coordinate_system) copy() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.parcellation.Parcellation method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) correct_motion() (nipy.neurospin.registration.registration.FmriRealign4d method) (nipy.neurospin.registration.spacetime_registration.Realign4d method) could_extract_minus_sign() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) count (nipy.core.image.roi.ROISequence attribute) count() (nipy.io.imageformats.nifti1.Nifti1Extensions method) count_ops() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) cov() (nipy.modalities.fmri.formula.RandomEffects method) create_dimension() (nipy.io.imageformats.minc.netcdf_fileobj method) create_variable() (nipy.io.imageformats.minc.netcdf_fileobj method) cross_eps() (nipy.neurospin.graph.graph.BipartiteGraph method) cross_eps_robust() (nipy.neurospin.graph.graph.BipartiteGraph method) cross_knn() (nipy.neurospin.graph.graph.BipartiteGraph method) cube_with_strides_center() (in module nipy.algorithms.statistics.utils) custom_watershed() (nipy.neurospin.graph.field.Field method) cut_redundancies() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

D

data (nipy.io.imageformats.compat.NiftiImage attribute) (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) data_generator() (in module nipy.core.image.generators) DataError (class in nipy.utils.data) Datasource (class in nipy.utils.data) decompose2d() (in module nipy.algorithms.statistics.utils) decompose3d() (in module nipy.algorithms.statistics.utils) define() (in module nipy.modalities.fmri.formula) define_graph_attributes() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) degrees() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) demo_ortho_slicer() (in module nipy.neurospin.viz_tools.ortho_slicer) demo_plot_map() (in module nipy.neurospin.viz_tools.activation_maps) demo_plot_map_3d() (in module nipy.neurospin.viz_tools.maps_3d) demo_ward_msb() (in module nipy.neurospin.clustering.bootstrap_hc) denom_poly() (nipy.algorithms.statistics.rft.ECquasi method) density() (nipy.algorithms.statistics.rft.ChiBarSquared method) (nipy.algorithms.statistics.rft.ChiSquared method) (nipy.algorithms.statistics.rft.ECcone method) (nipy.algorithms.statistics.rft.FStat method) (nipy.algorithms.statistics.rft.Hotelling method) (nipy.algorithms.statistics.rft.MultilinearForm method) (nipy.algorithms.statistics.rft.OneSidedF method) (nipy.algorithms.statistics.rft.Roy method) (nipy.algorithms.statistics.rft.TStat method) depth_from_leaves() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) deriv() (nipy.algorithms.statistics.rft.ECquasi method) design() (nipy.modalities.fmri.formula.Factor method) (nipy.modalities.fmri.formula.Formula method) (nipy.modalities.fmri.formula.RandomEffects method) design_expr (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute)

DesignMatrix (class in nipy.neurospin.utils.design_matrix) diagnose_binaryblock() (nipy.io.imageformats.analyze.AnalyzeHeader class method) (nipy.io.imageformats.nifti1.Nifti1Header class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader class method) diff() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) diffusion() (nipy.neurospin.graph.field.Field method) dijkstra() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) dilation() (nipy.neurospin.graph.field.Field method) dim_cmap() (in module nipy.neurospin.viz_tools.cm) dirichlet_eval() (in module nipy.neurospin.clustering.bgmm) discrete_to_roi_features() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) DiscreteROI (class in nipy.core.image.roi) displacement_field (class in nipy.neurospin.group.displacement_field) dkl_dirichlet() (in module nipy.neurospin.clustering.bgmm) dkl_gaussian() (in module nipy.neurospin.clustering.bgmm) dkl_wishart() (in module nipy.neurospin.clustering.bgmm) dmtx_light() (in module nipy.neurospin.utils.design_matrix) doit() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) draw_cross() (nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer method) draw_samples() (in module nipy.neurospin.utils.reproducibility_measures) drop_io_dim() (in module nipy.core.reference.coordinate_map) DTI dtype (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute) (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) dummy_index (nipy.modalities.fmri.formula.Beta attribute) dump() (nipy.neurospin.statistical_mapping.LinearModel method) DWI

E

ECcone (class in nipy.algorithms.statistics.rft) ECquasi (class in nipy.algorithms.statistics.rft) EEGlab EMalgo() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) EMalgo_from_histo() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) empty_parcels() (nipy.neurospin.spatial_models.parcellation.Parcellation method) endianness (nipy.io.imageformats.analyze.AnalyzeHeader attribute) (nipy.io.imageformats.nifti1.Nifti1Header attribute) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader attribute) ENN (class in nipy.neurospin.utils.emp_null), [1] eps() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) eps_Isomap (class in nipy.neurospin.eda.dimension_reduction) equivalent() (in module nipy.core.reference.coordinate_map) erosion() (nipy.neurospin.graph.field.Field method) errno (nipy.utils.data.DataError attribute) Estep() (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) estimate() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.clustering.ggmixture.Gamma method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.utils.design_matrix.DesignMatrix method) estimate_displacements_SA() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) estimate_mean() (in module nipy.algorithms.statistics.onesample) estimate_parameters() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) estimate_parameters_from_histo() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) estimate_pooled_covariance() (in module nipy.modalities.fmri.spm.model) estimate_varatio() (in module nipy.algorithms.statistics.onesample)

estimateAR() (in module nipy.modalities.fmri.fmristat.model) Euclidian_distance() (in module nipy.neurospin.eda.dimension_reduction) Euclidian_mds() (in module nipy.neurospin.eda.dimension_reduction) euler2angle_axis() (in module nipy.io.imageformats.eulerangles) euler2mat() (in module nipy.io.imageformats.eulerangles) euler2quat() (in module nipy.io.imageformats.eulerangles) eval() (nipy.neurospin.registration.iconic_registration.IconicRegistration method) evalf() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) evaluate() (nipy.algorithms.interpolation.ImageInterpolator method) (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) event_design() (in module nipy.modalities.fmri.design) EventRelatedParadigm (class in nipy.neurospin.utils.design_matrix) events() (in module nipy.modalities.fmri.utils) evidence() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) execute() (nipy.modalities.fmri.fmristat.model.AR1 method) (nipy.modalities.fmri.fmristat.model.OLS method) (nipy.modalities.fmri.spm.model.SecondStage method) expand() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) explore() (nipy.neurospin.registration.iconic_registration.IconicRegistration method) extend (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) extent (nipy.io.imageformats.compat.NiftiImage attribute) extract_additively() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) extract_clusters_from_diam() (in module nipy.neurospin.group.permutation_test) extract_clusters_from_graph() (in module nipy.neurospin.group.permutation_test) extract_clusters_from_thresh() (in module nipy.neurospin.group.permutation_test) extract_multiplicatively() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) eye() (in module nipy.io.imageformats.quaternions)

F

f_generator() (in module nipy.core.image.generators) Factor (class in nipy.modalities.fmri.formula) FactorTerm (class in nipy.modalities.fmri.formula) fancy_plot() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) fancy_plot_() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) fdiff() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) FDR (class in nipy.neurospin.utils.emp_null) fdr() (nipy.neurospin.utils.emp_null.ENN method), [1] fdrcurve() (nipy.neurospin.utils.emp_null.ENN method), [1] feature() (nipy.core.image.roi.CoordinateMapROI method) (nipy.core.image.roi.DiscreteROI method) (nipy.core.image.roi.ROIall method) feature_argmax() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) feature_map() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) ffx() (in module nipy.neurospin.utils.ffx) ffx_from_stat() (in module nipy.neurospin.utils.ffx) Field (class in nipy.neurospin.graph.field) filename (nipy.utils.data.DataError attribute) filespec_to_files() (nipy.io.imageformats.analyze.AnalyzeImage static method) (nipy.io.imageformats.compat.NiftiImage static method) (nipy.io.imageformats.minc.MincImage static method) (nipy.io.imageformats.nifti1.Nifti1Image static method) (nipy.io.imageformats.spatialimages.SpatialImage static method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage static method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage static method) FileTuples (class in nipy.io.imageformats.filetuples) FileTuplesError (class in nipy.io.imageformats.filetuples) fillpositive() (in module nipy.io.imageformats.quaternions) find_cut_coords() (in module nipy.neurospin.viz_tools.coord_tools) find_data_dir() (in module nipy.utils.data) find_mni_template() (in module nipy.neurospin.viz_tools.anat_cache) finite_range() (in module nipy.io.imageformats.volumeutils) fit() (nipy.algorithms.statistics.classification.Classifier method) (nipy.algorithms.statistics.nlsmodel.NLSModel method) (nipy.neurospin.glm.glm.glm method) flip() (in module nipy.core.image.xyz_image) flip_axis() (in module nipy.io.imageformats.orientations) floyd() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) fltcols() (in module nipy.interfaces.spm) flush() (nipy.io.imageformats.minc.netcdf_fileobj method) Fmask() (in module nipy.modalities.fmri.spm.model) fmin_steepest() (in module nipy.neurospin.utils.optimize) FMRI fmri_generator() (in module nipy.modalities.fmri.fmri) FmriImageList (class in nipy.modalities.fmri.fmri) FmriRealign4d (class in nipy.neurospin.registration.registration) fname_presuffix() (in module nipy.interfaces.spm) fnames_presuffix() (in module nipy.interfaces.spm) fnsum (class in nipy.algorithms.statistics.rft) for_file_pair() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) Forest (class in nipy.neurospin.graph.forest) Formula (class in nipy.modalities.fmri.formula) formula (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) four_to_three() (in module nipy.io.imageformats.funcs) fourier_basis() (in module nipy.modalities.fmri.design) (in module nipy.modalities.fmri.utils) free_energy() (nipy.neurospin.segmentation.vem.VemTissueClassification method) from_3d_grid() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) from_adjacency() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

from_binary_image() (nipy.neurospin.spatial_models.roi.DiscreteROI method) from_filename() (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage class method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) from_fileobj() (nipy.io.imageformats.analyze.AnalyzeHeader class method) (nipy.io.imageformats.minc.MincHeader class method) (nipy.io.imageformats.nifti1.Nifti1Extensions class method) (nipy.io.imageformats.nifti1.Nifti1Header class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader class method) from_files() (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage class method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) from_filespec() (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage class method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) from_image() (nipy.core.image.image_list.ImageList class method) (nipy.core.image.xyz_image.XYZImage static method) (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage class method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) (nipy.modalities.fmri.fmri.FmriImageList class method) from_labelled_image() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.DiscreteROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) from_mapping() (nipy.io.imageformats.analyze.AnalyzeHeader class method) (nipy.io.imageformats.nifti1.Nifti1Header class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader class method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader class method) from_matrix_vector() (in module nipy.core.transforms.affines) (in module nipy.neurospin.datasets.transforms.affine_utils) from_params() (nipy.core.image.xyz_image.XYZTransform static method) (nipy.core.reference.coordinate_map.AffineTransform static method) from_position() (nipy.neurospin.spatial_models.roi.DiscreteROI method) from_position_and_image() (nipy.neurospin.spatial_models.roi.DiscreteROI method) from_shape() (nipy.core.reference.array_coords.ArrayCoordMap static method) from_start_step() (nipy.core.image.xyz_image.XYZTransform static method) (nipy.core.reference.coordinate_map.AffineTransform static method) from_time() (nipy.neurospin.registration.spacetime_registration.Image4d method) fromarray() (in module nipy.core.image.image) fromcol() (nipy.modalities.fmri.formula.Factor static method) fromrec() (nipy.modalities.fmri.formula.Factor static method) (nipy.modalities.fmri.formula.Formula static method) (nipy.modalities.fmri.formula.RandomEffects static method) FSL FStat (class in nipy.algorithms.statistics.rft) fttest() (in module nipy.neurospin.utils.reproducibility_measures) full_rank() (in module nipy.neurospin.utils.design_matrix) fullrank() (in module nipy.modalities.fmri.formula) func (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) fusion() (in module nipy.neurospin.clustering.hierarchical_clustering) fwhm2resel() (nipy.algorithms.fwhm.ReselImage method) (nipy.algorithms.fwhm.Resels method) fwhm2sigma() (in module nipy.algorithms.kernel_smooth)

G

Gamma (class in nipy.neurospin.clustering.ggmixture) Gamma_Gaussian_fit() (in module nipy.neurospin.utils.emp_null) gamma_params() (in module nipy.modalities.fmri.hrf) gauss_dist() (in module nipy.neurospin.segmentation.vem) gaussian_random_field (class in nipy.neurospin.group.displacement_field) generate_coordinates() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) generate_normals() (in module nipy.neurospin.clustering.bgmm) generate_output() (in module nipy.modalities.fmri.fmristat.model) generate_perm() (in module nipy.neurospin.clustering.bgmm) generate_Wishart() (in module nipy.neurospin.clustering.bgmm) geodesic_kmeans() (nipy.neurospin.graph.field.Field method) get_3d_peaks() (in module nipy.neurospin.statistical_mapping) get_affine() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) get_axis_renames() (nipy.io.imageformats.nifti1.Nifti1Header method) get_base_affine() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_best_affine() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_bounds() (in module nipy.neurospin.datasets.transforms.affine_utils) get_children() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_cluster_position_from_thresholded_map() (in module nipy.neurospin.utils.reproducibility_measures) get_code() (nipy.io.imageformats.nifti1.Nifti1Extension method) get_codes() (nipy.io.imageformats.nifti1.Nifti1Extensions method) get_content() (nipy.io.imageformats.nifti1.Nifti1Extension method) get_data() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.xyz_image.XYZImage method) (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) get_data_dtype() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_data_offset() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_data_path() (in module nipy.utils.data) get_data_shape() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_datatype() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_descendents() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_dim_info() (nipy.io.imageformats.nifti1.Nifti1Header method) get_E() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_edges() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) (nipy.neurospin.spatial_models.roi.DiscreteROI method) get_field() (nipy.neurospin.graph.field.Field method) get_file_of_type() (nipy.io.imageformats.filetuples.FileTuples method) get_filename() (nipy.utils.data.Datasource method) (nipy.utils.data.VersionedDatasource method) get_filenames() (nipy.io.imageformats.filetuples.FileTuples method) get_header() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) get_height() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) get_home_dir() (in module nipy.utils.environment) get_intent() (nipy.io.imageformats.nifti1.Nifti1Header method) get_intent_code() (nipy.io.imageformats.nifti1.Nifti1Header method) get_inverse() (nipy.neurospin.datasets.transforms.affine_transform.AffineTransform method) (nipy.neurospin.datasets.transforms.transform.Transform method) get_k() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_local_maxima() (nipy.neurospin.graph.field.Field method)

get_mask_bounds() (in module nipy.neurospin.viz_tools.coord_tools) get_nipy_system_dir() (in module nipy.utils.environment) get_nipy_user_dir() (in module nipy.utils.environment) get_origin_affine() (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) get_parents() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_peak_position_from_thresholded_map() (in module nipy.neurospin.utils.reproducibility_measures) get_qform() (nipy.io.imageformats.nifti1.Nifti1Header method) get_qform_code() (nipy.io.imageformats.nifti1.Nifti1Header method) get_qform_quaternion() (nipy.io.imageformats.nifti1.Nifti1Header method) get_roi_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_scaled_data() (nipy.io.imageformats.minc.MincHeader method) get_sform() (nipy.io.imageformats.nifti1.Nifti1Header method) get_sform_code() (nipy.io.imageformats.nifti1.Nifti1Header method) get_shape() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) get_size() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_sizeondisk() (nipy.io.imageformats.nifti1.Nifti1Extension method) (nipy.io.imageformats.nifti1.Nifti1Extensions method) get_slice_code() (nipy.io.imageformats.nifti1.Nifti1Header method) get_slice_duration() (nipy.io.imageformats.nifti1.Nifti1Header method) get_slice_times() (nipy.io.imageformats.nifti1.Nifti1Header method) get_slope_inter() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) get_term() (nipy.modalities.fmri.formula.Factor method) get_transform() (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) get_unscaled_data() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) get_unscaled_img() (in module nipy.neurospin.utils.mask) get_V() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_vertices() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_weights() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) get_world_coords() (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) get_zooms() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) getDataArray() (nipy.io.imageformats.compat.NiftiImage method) getExtent() (nipy.io.imageformats.compat.NiftiImage method) getFilename() (nipy.io.imageformats.compat.NiftiImage method) getinfo() (nipy.neurospin.clustering.gmm.grid_descriptor method) getInverseQForm() (nipy.io.imageformats.compat.NiftiImage method) getInverseSForm() (nipy.io.imageformats.compat.NiftiImage method) getO() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) getomega() (nipy.algorithms.statistics.nlsmodel.NLSModel method) getparams() (in module nipy.modalities.fmri.formula) getPixDims() (nipy.io.imageformats.compat.NiftiImage method) getQForm() (nipy.io.imageformats.compat.NiftiImage method) getQFormCode() (nipy.io.imageformats.compat.NiftiImage method) getQOffset() (nipy.io.imageformats.compat.NiftiImage method) getQOrientation() (nipy.io.imageformats.compat.NiftiImage method) getQuaternion() (nipy.io.imageformats.compat.NiftiImage method) getRepetitionTime() (nipy.io.imageformats.compat.NiftiImage method) getScaledData() (nipy.io.imageformats.compat.NiftiImage method) getSForm() (nipy.io.imageformats.compat.NiftiImage method) getSFormCode() (nipy.io.imageformats.compat.NiftiImage method) getSOrientation() (nipy.io.imageformats.compat.NiftiImage method) getterms() (in module nipy.modalities.fmri.formula) getTestCaseNames() (in module nipy.io.imageformats.testing.nosepatch) (in module nipy.testing.nosepatch) getTimepoints() (nipy.io.imageformats.compat.NiftiImage method) getTimeUnit() (nipy.io.imageformats.compat.NiftiImage method) getVolumeExtent() (nipy.io.imageformats.compat.NiftiImage method) getVoxDims() (nipy.io.imageformats.compat.NiftiImage method) getXYZUnit() (nipy.io.imageformats.compat.NiftiImage method) getZ() (nipy.algorithms.statistics.nlsmodel.NLSModel method) GGGM (class in nipy.neurospin.clustering.ggmixture) GGM (class in nipy.neurospin.clustering.ggmixture) glm (class in nipy.neurospin.glm.glm) GMM (class in nipy.neurospin.clustering.gmm) GPL Graph (class in nipy.neurospin.graph.graph) Grid (class in nipy.core.reference.array_coords) grid_coords() (in module nipy.neurospin.registration.spacetime_registration) grid_descriptor (class in nipy.neurospin.clustering.gmm) GridTransform (class in nipy.neurospin.registration.grid_transform) guess_priors() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) guess_regularizing() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method)

H

has() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) has_all_symbols() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) has_any_symbols() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) has_piecewise (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) hdr_getterfunc() (in module nipy.io.imageformats.volumeutils) Header (class in nipy.io.imageformats.headers) header (nipy.core.image.affine_image.AffineImage attribute) (nipy.core.image.image.Image attribute) (nipy.core.image.xyz_image.XYZImage attribute) (nipy.io.imageformats.compat.NiftiImage attribute)

HeaderDataError (class in nipy.io.imageformats.volumeutils) HeaderTypeError (class in nipy.io.imageformats.volumeutils) height_threshold() (nipy.neurospin.group.permutation_test.permutation_test method) (nipy.neurospin.group.permutation_test.permutation_test_onesample method) (nipy.neurospin.group.permutation_test.permutation_test_onesample_graph method) (nipy.neurospin.group.permutation_test.permutation_test_twosample method) histo_repro() (in module nipy.neurospin.utils.reproducibility_measures) homogeneity() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Hotelling (class in nipy.algorithms.statistics.rft) hparcel() (in module nipy.neurospin.spatial_models.hierarchical_parcellation) HPD() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

I

ICA IconicRegistration (class in nipy.neurospin.registration.iconic_registration) identity() (nipy.core.image.xyz_image.XYZTransform static method) (nipy.core.reference.coordinate_map.AffineTransform static method) if_datasource() (in module nipy.testing.decorators) if_example_data() (in module nipy.testing.decorators) if_templates() (in module nipy.testing.decorators) igamma_params() (in module nipy.modalities.fmri.hrf) IJK() (nipy.neurospin.registration.grid_transform.GridTransform method) (nipy.neurospin.registration.grid_transform.SplineTransform method) Image (class in nipy.core.image.image) (class in nipy.neurospin.image.image) Image4d (class in nipy.neurospin.registration.spacetime_registration) ImageInterpolator (class in nipy.algorithms.interpolation) ImageList (class in nipy.core.image.image_list) index (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) index() (nipy.core.reference.coordinate_system.CoordinateSystem method) infer_latent_dim() (in module nipy.neurospin.eda.dimension_reduction) infer_LR() (in module nipy.neurospin.spatial_models.bayesian_structural_analysis) init() (nipy.neurospin.clustering.ggmixture.GGGM method) init_displacement_blocks() (nipy.neurospin.group.displacement_field.displacement_field method) init_fdr() (nipy.neurospin.clustering.ggmixture.GGGM method) init_hidden_variables() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) init_motion_detection() (nipy.neurospin.registration.spacetime_registration.Realign4d method) initialize() (nipy.algorithms.statistics.classification.Classifier method) (nipy.algorithms.statistics.nlsmodel.NLSModel method) (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) initialize_and_estimate() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) insert (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) instance_to_filename() (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage class method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) integ() (nipy.algorithms.statistics.rft.ChiBarSquared method) (nipy.algorithms.statistics.rft.ChiSquared method) (nipy.algorithms.statistics.rft.ECcone method) (nipy.algorithms.statistics.rft.ECquasi method) (nipy.algorithms.statistics.rft.FStat method) (nipy.algorithms.statistics.rft.Hotelling method) (nipy.algorithms.statistics.rft.MultilinearForm method) (nipy.algorithms.statistics.rft.OneSidedF method) (nipy.algorithms.statistics.rft.Roy method) (nipy.algorithms.statistics.rft.TStat method) integrate() (nipy.algorithms.fwhm.ReselImage method) (nipy.algorithms.fwhm.Resels method) (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) InTemporaryDirectory (class in nipy.utils.tmpdirs) interp (nipy.neurospin.registration.iconic_registration.IconicRegistration attribute) interp_slice_order() (in module nipy.neurospin.registration.spacetime_registration) intersect_masks() (in module nipy.neurospin.utils.mask) IntrinsicVolumes (class in nipy.algorithms.statistics.rft) inv() (nipy.neurospin.registration.affine.Affine method) (nipy.neurospin.registration.affine.Rigid method) (nipy.neurospin.registration.affine.Similarity method) inv_affine (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) inverse() (in module nipy.io.imageformats.quaternions) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) inverse_affine() (in module nipy.neurospin.image.image) inverse_mapping() (nipy.neurospin.datasets.transforms.affine_transform.AffineTransform method) invertR() (in module nipy.modalities.fmri.fmristat.invert) io_orientation() (in module nipy.io.imageformats.orientations) is_bounded (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_commutative (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_complex (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_composite (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_connected() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

is_even (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_factor() (in module nipy.modalities.fmri.formula) is_factor_term() (in module nipy.modalities.fmri.formula) is_finite (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_formula() (in module nipy.modalities.fmri.formula) is_hypergeometric() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) is_image() (in module nipy.core.image.image) is_imaginary (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_infinitesimal (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_integer (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_irrational (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_negative (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_noninteger (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_nonnegative (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_nonpositive (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_nonzero (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_number (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_odd (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_polynomial() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) is_positive (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_prime (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_rational (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_rational_function() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) is_real (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_term() (in module nipy.modalities.fmri.formula) is_unbounded (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) is_zero (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) isfield() (nipy.neurospin.spatial_models.parcellation.Parcellation method) isleaf() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) isolated() (in module nipy.neurospin.utils.random_threshold) isomap() (in module nipy.neurospin.eda.dimension_reduction) isroot() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) isunit() (in module nipy.io.imageformats.quaternions) items() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) iter_basic_args() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method)

J

join_complexes() (in module nipy.algorithms.statistics.utils)

K

kappa() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) keys() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) (nipy.io.imageformats.volumeutils.Recoder method) kmeans() (in module nipy.neurospin.clustering.clustering) knn() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) knn_Isomap (class in nipy.neurospin.eda.dimension_reduction) knn_LE (class in nipy.neurospin.eda.dimension_reduction)

knn_LPP (class in nipy.neurospin.eda.dimension_reduction) knownfailure() (in module nipy.testing.decorators) Kruskal() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Kruskal_dev() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

L

laplace_dist() (in module nipy.neurospin.segmentation.vem) largest_cc() (in module nipy.neurospin.utils.mask) LE() (in module nipy.neurospin.eda.dimension_reduction) LE_dev() (in module nipy.neurospin.eda.dimension_reduction) leadterm() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) learn() (nipy.algorithms.statistics.classification.Classifier method) (nipy.neurospin.utils.emp_null.ENN method), [1] leaves_of_a_subtree() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) left_incidence() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) LGPL like_from_data() (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) likelihood() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) limit() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) linear_interp() (in module nipy.modalities.fmri.utils) linear_model_fit() (in module nipy.neurospin.statistical_mapping) LinearFilter (class in nipy.algorithms.kernel_smooth)

LinearModel (class in nipy.neurospin.statistical_mapping) list_files() (nipy.utils.data.Datasource method) (nipy.utils.data.VersionedDatasource method) list_of_neighbors() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) list_of_subtrees() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) load() (in module nipy.io.files) (in module nipy.io.imageformats.loadsave) (in module nipy.neurospin.glm.glm) (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) load_protocol_from_csv_file() (in module nipy.neurospin.utils.design_matrix) local_maxima() (nipy.neurospin.graph.field.Field method) local_sym_normalize() (in module nipy.neurospin.eda.dimension_reduction) log_gammainv_pdf() (in module nipy.neurospin.group.spatial_relaxation_onesample) log_gaussian_pdf() (in module nipy.neurospin.group.spatial_relaxation_onesample) log_raise() (nipy.io.imageformats.batteryrunners.Report method) LPP() (in module nipy.neurospin.eda.dimension_reduction) lseries() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method)

M

m2screenshot() (in module nipy.neurospin.viz_tools.maps_3d) main() (in module nipy.testing.nitest) (in module nipy.utils.perlpie) main_cc() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) main_effect (nipy.modalities.fmri.formula.Factor attribute) make_bsa_image() (in module nipy.neurospin.spatial_models.bsa_io) make_crmap() (in module nipy.neurospin.spatial_models.bayesian_structural_analysis) make_datasource() (in module nipy.utils.data) make_dt_codes() (in module nipy.io.imageformats.volumeutils) make_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) make_feature_from_info() (nipy.neurospin.spatial_models.parcellation.Parcellation method) make_forest() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) make_graph() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) make_grid() (nipy.neurospin.clustering.gmm.grid_descriptor method) make_image() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.DiscreteROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) make_job() (in module nipy.interfaces.spm) make_label_dec() (in module nipy.testing.decorators) make_recarray() (in module nipy.modalities.fmri.formula) map_label() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) map_reproducibility() (in module nipy.neurospin.utils.reproducibility_measures) mapping() (nipy.neurospin.datasets.transforms.affine_transform.AffineTransform method) mask (nipy.neurospin.image.image.MaskedImage attribute) mask() (nipy.core.image.roi.CoordinateMapROI method) (nipy.core.image.roi.ROIall method) mask_intersection() (in module nipy.neurospin.statistical_mapping) MaskedImage (class in nipy.neurospin.image.image) mat2euler() (in module nipy.io.imageformats.eulerangles) mat2quat() (in module nipy.io.imageformats.quaternions) match() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) match_trivial() (in module nipy.neurospin.graph.BPmatch) matches() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) Matlab matrix_generator() (in module nipy.core.image.generators) max_dist() (in module nipy.neurospin.group.permutation_test) maximum_link_distance() (in module nipy.neurospin.clustering.hierarchical_clustering) maximum_link_distance_segment() (in module nipy.neurospin.clustering.hierarchical_clustering)

maximum_link_euclidian() (in module nipy.neurospin.clustering.hierarchical_clustering) MDS (class in nipy.neurospin.eda.dimension_reduction) mds() (in module nipy.neurospin.eda.dimension_reduction) mds_embedding() (in module nipy.neurospin.eda.dimension_reduction) mds_parameters() (in module nipy.neurospin.eda.dimension_reduction) mean (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute) merge() (in module nipy.neurospin.spatial_models.structural_bfls) merge_ascending() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) merge_descending() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) merge_simple_branches() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) message (nipy.io.imageformats.batteryrunners.Report attribute) (nipy.io.imageformats.filename_parser.TypesFilenamesError attribute) (nipy.io.imageformats.filetuples.FileTuplesError attribute) (nipy.io.imageformats.minc.MincError attribute) (nipy.io.imageformats.orientations.OrientationError attribute) (nipy.io.imageformats.volumeutils.HeaderDataError attribute) (nipy.io.imageformats.volumeutils.HeaderTypeError attribute) (nipy.neurospin.datasets.transforms.transform.CompositionError attribute) (nipy.utils.data.DataError attribute) mfx_ttest() (in module nipy.neurospin.utils.reproducibility_measures) MincError (class in nipy.io.imageformats.minc) MincHeader (class in nipy.io.imageformats.minc) MincImage (class in nipy.io.imageformats.minc) mixture_likelihood() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) mlab_tempfile() (in module nipy.interfaces.matlab) model_generator() (in module nipy.modalities.fmri.fmristat.model) ModelOutputImage (class in nipy.modalities.fmri.fmristat.model) msid() (nipy.neurospin.registration.spacetime_registration.Realign4d method) mst() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Mstep() (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) mu_ball() (in module nipy.algorithms.statistics.rft) mu_sphere() (in module nipy.algorithms.statistics.rft) mult() (in module nipy.io.imageformats.quaternions) MultilinearForm (class in nipy.algorithms.statistics.rft) multinomial() (in module nipy.neurospin.clustering.bgmm) MultiROI (class in nipy.neurospin.spatial_models.roi) multivariate_stat (class in nipy.neurospin.group.spatial_relaxation_onesample)

N

n() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) name (nipy.modalities.fmri.formula.Beta attribute) (nipy.modalities.fmri.formula.FactorTerm attribute) (nipy.modalities.fmri.formula.Term attribute) natural_spline() (in module nipy.modalities.fmri.design) (in module nipy.modalities.fmri.formula) ndim() (nipy.core.image.affine_image.AffineImage static method) (nipy.core.image.image.Image static method) (nipy.core.image.xyz_image.XYZImage static method) nearly_equivalent() (in module nipy.io.imageformats.quaternions) needs_review() (in module nipy.testing.decorators) netcdf_fileobj (class in nipy.io.imageformats.minc) new() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) next() (nipy.algorithms.statistics.nlsmodel.NLSModel method) (nipy.core.image.image_list.ImageList method) (nipy.core.image.roi.CoordinateMapROI method) (nipy.core.image.roi.DiscreteROI method) (nipy.core.image.roi.ROIall method) (nipy.modalities.fmri.fmri.FmriImageList method) ni_affine_pixdim_from_affine() (in module nipy.io.nifti_ref) Nifti1Extension (class in nipy.io.imageformats.nifti1) Nifti1Extensions (class in nipy.io.imageformats.nifti1) Nifti1Header (class in nipy.io.imageformats.nifti1) Nifti1Image (class in nipy.io.imageformats.nifti1) NiftiImage (class in nipy.io.imageformats.compat) nipy.algorithms.diagnostics.screens (module) nipy.algorithms.diagnostics.timediff (module) nipy.algorithms.diagnostics.tsdiffplot (module) nipy.algorithms.fwhm (module) nipy.algorithms.interpolation (module) nipy.algorithms.kernel_smooth (module) nipy.algorithms.resample (module) nipy.algorithms.statistics.classification (module) nipy.algorithms.statistics.nlsmodel (module) nipy.algorithms.statistics.onesample (module) nipy.algorithms.statistics.regression (module) nipy.algorithms.statistics.rft (module) nipy.algorithms.statistics.utils (module) nipy.core.image.affine_image (module) nipy.core.image.generators (module) nipy.core.image.image (module) nipy.core.image.image_list (module) nipy.core.image.roi (module) nipy.core.image.xyz_image (module) nipy.core.reference.array_coords (module) nipy.core.reference.coordinate_map (module) nipy.core.reference.coordinate_system (module) nipy.core.reference.slices (module) nipy.core.transforms.affines (module) nipy.interfaces.matlab (module) nipy.interfaces.spm (module) nipy.io.files (module) nipy.io.imageformats.analyze (module) nipy.io.imageformats.batteryrunners (module) nipy.io.imageformats.binaryheaders (module) nipy.io.imageformats.compat (module) nipy.io.imageformats.eulerangles (module) nipy.io.imageformats.filename_parser (module) nipy.io.imageformats.filetuples (module) nipy.io.imageformats.funcs (module) nipy.io.imageformats.header_ufuncs (module) nipy.io.imageformats.headers (module) nipy.io.imageformats.loadsave (module) nipy.io.imageformats.minc (module) nipy.io.imageformats.nifti1 (module) nipy.io.imageformats.orientations (module) nipy.io.imageformats.quaternions (module) nipy.io.imageformats.spatialimages (module) nipy.io.imageformats.spm2analyze (module) nipy.io.imageformats.spm99analyze (module) nipy.io.imageformats.testing.lightunit (module) nipy.io.imageformats.testing.nosepatch (module) nipy.io.imageformats.volumeutils (module) nipy.io.nifti_ref (module) nipy.modalities.fmri.design (module) nipy.modalities.fmri.fmri (module) nipy.modalities.fmri.fmristat.delay (module) nipy.modalities.fmri.fmristat.hrf (module) nipy.modalities.fmri.fmristat.invert (module) nipy.modalities.fmri.fmristat.model (module) nipy.modalities.fmri.fmristat.utils (module) nipy.modalities.fmri.formula (module) nipy.modalities.fmri.hrf (module) nipy.modalities.fmri.pca (module) nipy.modalities.fmri.spm.correlation (module) nipy.modalities.fmri.spm.model (module)

nipy.modalities.fmri.spm.reml (module) nipy.modalities.fmri.spm.trace (module) nipy.modalities.fmri.utils (module) nipy.neurospin.clustering.bgmm (module) nipy.neurospin.clustering.bootstrap_hc (module) nipy.neurospin.clustering.clustering (module) nipy.neurospin.clustering.ggmixture (module) nipy.neurospin.clustering.gmm (module) nipy.neurospin.clustering.hierarchical_clustering (module) nipy.neurospin.datasets.converters (module) nipy.neurospin.datasets.transforms.affine_transform (module) nipy.neurospin.datasets.transforms.affine_utils (module) nipy.neurospin.datasets.transforms.transform (module) nipy.neurospin.datasets.volumes.volume_data (module) nipy.neurospin.datasets.volumes.volume_field (module) nipy.neurospin.datasets.volumes.volume_grid (module) nipy.neurospin.datasets.volumes.volume_img (module) nipy.neurospin.eda.dimension_reduction (module) nipy.neurospin.glm.glm (module) nipy.neurospin.graph.BPmatch (module) nipy.neurospin.graph.field (module) nipy.neurospin.graph.forest (module) nipy.neurospin.graph.graph (module) nipy.neurospin.group.displacement_field (module) nipy.neurospin.group.permutation_test (module) nipy.neurospin.group.spatial_relaxation_onesample (module) nipy.neurospin.image.image (module) nipy.neurospin.registration.affine (module) nipy.neurospin.registration.grid_transform (module) nipy.neurospin.registration.iconic_registration (module) nipy.neurospin.registration.registration (module) nipy.neurospin.registration.spacetime_registration (module) nipy.neurospin.segmentation.vem (module) nipy.neurospin.spatial_models.bayesian_structural_analysis (module) nipy.neurospin.spatial_models.bsa_io (module) nipy.neurospin.spatial_models.hierarchical_parcellation (module) nipy.neurospin.spatial_models.hroi (module) nipy.neurospin.spatial_models.parcel_io (module) nipy.neurospin.spatial_models.parcellation (module) nipy.neurospin.spatial_models.roi (module) nipy.neurospin.spatial_models.structural_bfls (module) nipy.neurospin.statistical_mapping (module) nipy.neurospin.utils.design_matrix (module) nipy.neurospin.utils.emp_null (module) nipy.neurospin.utils.ffx (module) nipy.neurospin.utils.mask (module) nipy.neurospin.utils.optimize (module) nipy.neurospin.utils.random_threshold (module) nipy.neurospin.utils.reproducibility_measures (module) nipy.neurospin.utils.simul_multisubject_fmri_dataset (module) nipy.neurospin.utils.smoothing (module) nipy.neurospin.utils.two_binomial_mixture (module) nipy.neurospin.utils.zscore (module) nipy.neurospin.viz_tools.activation_maps (module) nipy.neurospin.viz_tools.anat_cache (module) nipy.neurospin.viz_tools.cm (module) nipy.neurospin.viz_tools.coord_tools (module) nipy.neurospin.viz_tools.maps_3d (module) nipy.neurospin.viz_tools.ortho_slicer (module) nipy.testing.decorators (module) nipy.testing.lightunit (module) nipy.testing.nitest (module) nipy.testing.nosepatch (module) nipy.utils.data (module) nipy.utils.environment (module) nipy.utils.onetime (module) nipy.utils.perlpie (module) nipy.utils.tmpdirs (module) NLDR (class in nipy.neurospin.eda.dimension_reduction) NLSModel (class in nipy.algorithms.statistics.nlsmodel) norm() (in module nipy.io.imageformats.quaternions) normal() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) normal_eval() (in module nipy.neurospin.clustering.bgmm) normalize() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) NROI_from_field() (in module nipy.neurospin.spatial_models.hroi) NROI_from_watershed() (in module nipy.neurospin.spatial_models.hroi) nseries() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) null_distribution() (in module nipy.neurospin.utils.random_threshold)

O

OLS (class in nipy.modalities.fmri.fmristat.model) ols() (in module nipy.neurospin.glm.glm) one_subj_parcellation() (in module nipy.neurospin.spatial_models.parcel_io) onesample_stat() (in module nipy.neurospin.group.permutation_test) onesample_test() (in module nipy.neurospin.statistical_mapping) OneSidedF (class in nipy.algorithms.statistics.rft) OneTimeProperty (class in nipy.utils.onetime) opening() (nipy.neurospin.graph.field.Field method) optim_hparcel() (in module nipy.neurospin.spatial_models.hierarchical_parcellation) optimize() (nipy.neurospin.registration.iconic_registration.IconicRegistration method) orientation_affine() (in module nipy.io.imageformats.orientations) OrientationError (class in nipy.io.imageformats.orientations)

orth() (in module nipy.modalities.fmri.spm.reml) Orthonormalize() (in module nipy.neurospin.eda.dimension_reduction) OrthoSlicer (class in nipy.neurospin.viz_tools.ortho_slicer) output_AR1() (in module nipy.algorithms.statistics.regression) (in module nipy.modalities.fmri.fmristat.model) output_F() (in module nipy.algorithms.statistics.regression) (in module nipy.modalities.fmri.fmristat.model) output_resid() (in module nipy.algorithms.statistics.regression) (in module nipy.modalities.fmri.fmristat.model) output_T() (in module nipy.algorithms.statistics.regression) (in module nipy.modalities.fmri.fmristat.model)

P

Paradigm (class in nipy.neurospin.utils.design_matrix) param (nipy.neurospin.registration.affine.Affine attribute) (nipy.neurospin.registration.affine.Rigid attribute) (nipy.neurospin.registration.affine.Similarity attribute) (nipy.neurospin.registration.grid_transform.GridTransform attribute) (nipy.neurospin.registration.grid_transform.SplineTransform attribute) parameters() (nipy.neurospin.clustering.ggmixture.Gamma method) (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) params (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute) parcel_input() (in module nipy.neurospin.spatial_models.parcel_io) Parcellation (class in nipy.neurospin.spatial_models.parcellation) Parcellation_based_analysis() (in module nipy.neurospin.spatial_models.parcel_io) Parcellation_output() (in module nipy.neurospin.spatial_models.parcel_io) parcellation_output_with_paths() (in module nipy.neurospin.spatial_models.parcel_io) parcels() (in module nipy.core.image.generators) partial_floyd_graph() (in module nipy.neurospin.eda.dimension_reduction) partition() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) PCA (class in nipy.neurospin.eda.dimension_reduction) pca() (in module nipy.modalities.fmri.pca) pca_image() (in module nipy.modalities.fmri.pca) peak_reproducibility() (in module nipy.neurospin.utils.reproducibility_measures) peak_XYZ() (in module nipy.neurospin.group.permutation_test) perl_dash_pie() (in module nipy.utils.perlpie) perm_prfx() (in module nipy.neurospin.spatial_models.hierarchical_parcellation) permutation_test (class in nipy.neurospin.group.permutation_test) permutation_test_onesample (class in nipy.neurospin.group.permutation_test) permutation_test_onesample_graph (class in nipy.neurospin.group.permutation_test) permutation_test_twosample (class in nipy.neurospin.group.permutation_test) PET pixdim (nipy.io.imageformats.compat.NiftiImage attribute) plot() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.utils.emp_null.ENN method), [1] plot2() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) plot2D() (in module nipy.neurospin.clustering.gmm) plot_anat_3d() (in module nipy.neurospin.viz_tools.maps_3d) plot_discrete_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) plot_feature() (nipy.neurospin.spatial_models.roi.DiscreteROI method) plot_height() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) plot_map() (in module nipy.neurospin.viz_tools.activation_maps) (nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer method) plot_map_3d() (in module nipy.neurospin.viz_tools.maps_3d) plot_roi_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultiROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) plot_tsdiffs() (in module nipy.algorithms.diagnostics.tsdiffplot) plot_tsdiffs_image() (in module nipy.algorithms.diagnostics.tsdiffplot) plugin() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method)

pool() (nipy.core.image.roi.CoordinateMapROI method) (nipy.core.image.roi.DiscreteROI method) (nipy.core.image.roi.ROIall method) pop (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) pop() (in module nipy.neurospin.clustering.bgmm) (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) population() (nipy.neurospin.spatial_models.parcellation.Parcellation method) posterior() (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) precond (nipy.neurospin.registration.affine.Affine attribute) (nipy.neurospin.registration.affine.Rigid attribute) (nipy.neurospin.registration.affine.Similarity attribute) preconditioner() (in module nipy.neurospin.registration.affine) predict() (nipy.algorithms.statistics.classification.Classifier method) (nipy.algorithms.statistics.nlsmodel.NLSModel method) prepare_arrays() (in module nipy.neurospin.statistical_mapping) pretty_mapping() (in module nipy.io.imageformats.volumeutils) prevalence_map() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) PRFX() (nipy.neurospin.spatial_models.parcellation.Parcellation method) print_extended_help() (in module nipy.utils.perlpie) print_field() (nipy.neurospin.graph.field.Field method) probability_under_prior() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) product() (in module nipy.core.reference.coordinate_map) (in module nipy.core.reference.coordinate_system) propagate_upward() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) propagate_upward_and() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) pth_from_pvals() (nipy.neurospin.utils.emp_null.FDR method) pvalue() (nipy.algorithms.statistics.rft.ChiBarSquared method) (nipy.algorithms.statistics.rft.ChiSquared method) (nipy.algorithms.statistics.rft.ECcone method) (nipy.algorithms.statistics.rft.FStat method) (nipy.algorithms.statistics.rft.Hotelling method) (nipy.algorithms.statistics.rft.MultilinearForm method) (nipy.algorithms.statistics.rft.OneSidedF method) (nipy.algorithms.statistics.rft.Roy method) (nipy.algorithms.statistics.rft.TStat method) (nipy.neurospin.glm.glm.contrast method) (nipy.neurospin.group.permutation_test.permutation_test method) (nipy.neurospin.group.permutation_test.permutation_test_onesample method) (nipy.neurospin.group.permutation_test.permutation_test_onesample_graph method) (nipy.neurospin.group.permutation_test.permutation_test_twosample method)

Q

Q() (in module nipy.algorithms.statistics.rft) quasi() (nipy.algorithms.statistics.rft.ChiBarSquared method) (nipy.algorithms.statistics.rft.ChiSquared method) (nipy.algorithms.statistics.rft.ECcone method) (nipy.algorithms.statistics.rft.FStat method) (nipy.algorithms.statistics.rft.Hotelling method) (nipy.algorithms.statistics.rft.MultilinearForm method) (nipy.algorithms.statistics.rft.OneSidedF method) (nipy.algorithms.statistics.rft.Roy method) (nipy.algorithms.statistics.rft.TStat method)

quat2angle_axis() (in module nipy.io.imageformats.quaternions) quat2euler() (in module nipy.io.imageformats.eulerangles) quat2mat() (in module nipy.io.imageformats.quaternions)

R

RandomEffects (class in nipy.modalities.fmri.formula) randthresh() (in module nipy.neurospin.utils.random_threshold) randthresh_connex() (in module nipy.neurospin.utils.random_threshold) randthresh_fixwind_gaussnull() (in module nipy.neurospin.utils.random_threshold) randthresh_fixwind_gaussnull_connex() (in module nipy.neurospin.utils.random_threshold) randthresh_fixwind_knownull() (in module nipy.neurospin.utils.random_threshold) randthresh_fixwind_knownull_connex() (in module nipy.neurospin.utils.random_threshold) randthresh_main() (in module nipy.neurospin.utils.random_threshold) randthresh_varwind_gaussnull() (in module nipy.neurospin.utils.random_threshold) randthresh_varwind_gaussnull_connex() (in module nipy.neurospin.utils.random_threshold) randthresh_varwind_knownull() (in module nipy.neurospin.utils.random_threshold) randthresh_varwind_knownull_connex() (in module nipy.neurospin.utils.random_threshold) rank() (in module nipy.modalities.fmri.formula) RD_cliques() (in module nipy.neurospin.spatial_models.structural_bfls) read() (nipy.io.imageformats.minc.netcdf_fileobj method) read_data() (in module nipy.io.imageformats.header_ufuncs) read_from_csv() (nipy.neurospin.utils.design_matrix.DesignMatrix method) read_unscaled_data() (in module nipy.io.imageformats.header_ufuncs) Realign4d (class in nipy.neurospin.registration.spacetime_registration) realign4d() (in module nipy.neurospin.registration.spacetime_registration) Recoder (class in nipy.io.imageformats.volumeutils) reduce_to_leaves() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) reference (nipy.core.image.xyz_image.XYZImage attribute) reference() (nipy.core.image.affine_image.AffineImage static method) (nipy.core.image.image.Image static method) register() (in module nipy.neurospin.registration.registration) RegressionOutput (class in nipy.algorithms.statistics.regression) RegressionOutputList (class in nipy.algorithms.statistics.regression) reml() (in module nipy.modalities.fmri.spm.reml) remove (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) remove_edges() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) remove_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) remove_roi_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) remove_trivial_edges() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) removeO() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) renamed_axes() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.xyz_image.XYZImage method) renamed_domain() (in module nipy.core.reference.coordinate_map) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) renamed_range() (in module nipy.core.reference.coordinate_map) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) renamed_reference() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.xyz_image.XYZImage method) reorder() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) reorder_from_leaves_to_roots() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method)

reordered_axes() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.xyz_image.XYZImage method) reordered_domain() (in module nipy.core.reference.coordinate_map) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) reordered_range() (in module nipy.core.reference.coordinate_map) (nipy.core.image.xyz_image.XYZTransform method) (nipy.core.reference.coordinate_map.AffineTransform method) (nipy.core.reference.coordinate_map.CoordinateMap method) reordered_reference() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.image.Image method) (nipy.core.image.xyz_image.XYZImage method) replace_inside() (in module nipy.neurospin.viz_tools.cm) Report (class in nipy.io.imageformats.batteryrunners) representative_feature() (nipy.neurospin.spatial_models.roi.DiscreteROI method) resample() (in module nipy.algorithms.resample) (in module nipy.neurospin.image.image) (nipy.neurospin.registration.registration.FmriRealign4d method) (nipy.neurospin.registration.spacetime_registration.Realign4d method) resample4d() (in module nipy.neurospin.registration.spacetime_registration) resample_all_inmask() (nipy.neurospin.registration.spacetime_registration.Realign4d method) resample_img2img() (in module nipy.algorithms.resample) resample_inmask() (nipy.neurospin.registration.spacetime_registration.Realign4d method) resampled_to_affine() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.xyz_image.XYZImage method) resampled_to_img() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.xyz_image.XYZImage method) (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) resel2fwhm() (nipy.algorithms.fwhm.ReselImage method) (nipy.algorithms.fwhm.Resels method) ReselImage (class in nipy.algorithms.fwhm) Resels (class in nipy.algorithms.fwhm) reset() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) results_generator() (in module nipy.modalities.fmri.fmristat.model) reverse (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) rewrite() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) right_incidence() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Rigid (class in nipy.neurospin.registration.affine) ROC() (nipy.neurospin.clustering.ggmixture.GGGM method) ROI (class in nipy.core.image.roi) (class in nipy.neurospin.spatial_models.roi) roi_confidence() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) roi_ellipse_fn() (in module nipy.core.image.roi) roi_from_array_sampling_coordmap() (in module nipy.core.image.roi) roi_prevalence() (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) roi_sphere_fn() (in module nipy.core.image.roi) ROIall (class in nipy.core.image.roi) ROISequence (class in nipy.core.image.roi) rollaxis() (in module nipy.core.image.image) rooted_subtree() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) rotate_vector() (in module nipy.io.imageformats.quaternions) rotation_mat2vec() (in module nipy.neurospin.registration.affine) Roy (class in nipy.algorithms.statistics.rft) rtime (nipy.io.imageformats.compat.NiftiImage attribute) run_jobdef() (in module nipy.interfaces.spm) run_matlab() (in module nipy.interfaces.matlab) run_matlab_script() (in module nipy.interfaces.matlab)

S

SAEM() (nipy.neurospin.clustering.ggmixture.GGGM method) safe_dtype() (in module nipy.core.reference.coordinate_system) safe_variance() (nipy.neurospin.registration.spacetime_registration.Realign4d method) sample() (in module nipy.neurospin.image.image) (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.group.displacement_field.displacement_field method) (nipy.neurospin.group.displacement_field.gaussian_random_field method) sample_all_blocks() (nipy.neurospin.group.displacement_field.displacement_field method) sample_and_average() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) sample_indicator() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) sample_log_conditional_posterior() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) save() (in module nipy.io.files) (in module nipy.io.imageformats.loadsave) (in module nipy.neurospin.datasets.converters) (nipy.io.imageformats.analyze.AnalyzeImage class method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage class method) (nipy.io.imageformats.nifti1.Nifti1Image class method) (nipy.io.imageformats.spatialimages.SpatialImage class method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage class method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage class method) (nipy.modalities.fmri.fmristat.model.ModelOutputImage method) (nipy.neurospin.glm.glm.glm method) scale_min_max() (in module nipy.io.imageformats.volumeutils) scale_space() (in module nipy.algorithms.statistics.rft) scans_for_fname() (in module nipy.interfaces.spm) scans_for_fnames() (in module nipy.interfaces.spm) screen() (in module nipy.algorithms.diagnostics.screens) SecondStage (class in nipy.modalities.fmri.spm.model) segment_graph_rd() (in module nipy.neurospin.spatial_models.structural_bfls) series() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) series_from_mask() (in module nipy.neurospin.utils.mask) set() (nipy.neurospin.image.image.Image method) (nipy.neurospin.image.image.MaskedImage method) set_data_dtype() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) set_data_shape() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) set_dim_info() (nipy.io.imageformats.nifti1.Nifti1Header method) set_dim_info_from_names() (nipy.io.imageformats.nifti1.Nifti1Header method) set_discrete_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_discrete_feature_from_image() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_discrete_feature_from_index() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_drift() (in module nipy.neurospin.utils.design_matrix) set_edges() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_euclidian() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_feature() (nipy.neurospin.spatial_models.parcellation.Parcellation method) (nipy.neurospin.spatial_models.roi.DiscreteROI method) set_feature_from_image() (nipy.neurospin.spatial_models.roi.DiscreteROI method) set_feature_from_masked_data() (nipy.neurospin.spatial_models.roi.DiscreteROI method) set_field() (nipy.neurospin.graph.field.Field method) set_file_of_type() (nipy.io.imageformats.filetuples.FileTuples method) set_filenames() (nipy.io.imageformats.filetuples.FileTuples method) set_gaussian() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_group_labels() (nipy.neurospin.spatial_models.parcellation.Parcellation method) set_height() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) set_info() (nipy.neurospin.spatial_models.parcellation.Parcellation method) set_intent() (nipy.io.imageformats.nifti1.Nifti1Header method) set_labels() (nipy.neurospin.spatial_models.parcellation.Parcellation method) set_origin_from_affine() (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) set_priors() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) set_qform() (nipy.io.imageformats.nifti1.Nifti1Header method) set_roi_feature() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_roi_feature_from_image() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_sform() (nipy.io.imageformats.nifti1.Nifti1Header method) set_slice_duration() (nipy.io.imageformats.nifti1.Nifti1Header method) set_slice_times() (nipy.io.imageformats.nifti1.Nifti1Header method) set_slope_inter() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) set_source_fov() (nipy.neurospin.registration.iconic_registration.IconicRegistration method) set_subjects() (nipy.neurospin.spatial_models.parcellation.Parcellation method) set_train_data() (nipy.neurospin.eda.dimension_reduction.eps_Isomap method) (nipy.neurospin.eda.dimension_reduction.MDS method) (nipy.neurospin.eda.dimension_reduction.NLDR method) (nipy.neurospin.eda.dimension_reduction.PCA method) (nipy.neurospin.eda.dimension_reduction.knn_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_LE method) (nipy.neurospin.eda.dimension_reduction.knn_LPP method) set_weights() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_xyz() (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.roi.MultipleROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) set_zooms() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method)

setattr_on_read() (in module nipy.utils.onetime) setDataArray() (nipy.io.imageformats.compat.NiftiImage method) setDescription() (nipy.io.imageformats.compat.NiftiImage method) setFilename() (nipy.io.imageformats.compat.NiftiImage method) setIntercept() (nipy.io.imageformats.compat.NiftiImage method) setPixDims() (nipy.io.imageformats.compat.NiftiImage method) setQFac() (nipy.io.imageformats.compat.NiftiImage method) setQForm() (nipy.io.imageformats.compat.NiftiImage method) setQFormCode() (nipy.io.imageformats.compat.NiftiImage method) setQOffset() (nipy.io.imageformats.compat.NiftiImage method) setQuaternion() (nipy.io.imageformats.compat.NiftiImage method) setRepetitionTime() (nipy.io.imageformats.compat.NiftiImage method) setSForm() (nipy.io.imageformats.compat.NiftiImage method) setSFormCode() (nipy.io.imageformats.compat.NiftiImage method) setSlope() (nipy.io.imageformats.compat.NiftiImage method) setTimeUnit() (nipy.io.imageformats.compat.NiftiImage method) setVoxDims() (nipy.io.imageformats.compat.NiftiImage method) setXFormCode() (nipy.io.imageformats.compat.NiftiImage method) setXYZUnit() (nipy.io.imageformats.compat.NiftiImage method) shape (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) (nipy.neurospin.registration.grid_transform.GridTransform attribute) (nipy.neurospin.registration.grid_transform.SplineTransform attribute) shape() (nipy.core.image.affine_image.AffineImage static method) (nipy.core.image.image.Image static method) (nipy.core.image.xyz_image.XYZImage static method) shape_generator() (in module nipy.core.image.generators) shifted_domain_origin() (in module nipy.core.reference.coordinate_map) shifted_range_origin() (in module nipy.core.reference.coordinate_map) show() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.ggmixture.GGGM method) (nipy.neurospin.clustering.ggmixture.GGM method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.Graph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) (nipy.neurospin.utils.design_matrix.DesignMatrix method) (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) show_components() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) sigma2fwhm() (in module nipy.algorithms.kernel_smooth) Similarity (class in nipy.neurospin.registration.affine) similarity (nipy.neurospin.registration.iconic_registration.IconicRegistration attribute) simulated_pvalue() (in module nipy.neurospin.statistical_mapping) singles() (in module nipy.neurospin.graph.BPmatch) size (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) skeleton() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) slice_generator() (in module nipy.core.image.generators) slice_parcels() (in module nipy.core.image.generators) SliceMaker (class in nipy.core.image.image) smooth() (nipy.algorithms.kernel_smooth.LinearFilter method) solve4linearsymbol() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Term method) sort (nipy.core.image.roi.ROISequence attribute) (nipy.io.imageformats.nifti1.Nifti1Extensions attribute) sorted_values() (in module nipy.neurospin.group.permutation_test) spatial_coordmap (nipy.core.image.affine_image.AffineImage attribute) SpatialImage (class in nipy.io.imageformats.spatialimages) spectral_decomposition() (in module nipy.modalities.fmri.fmristat.hrf) spherical_search() (in module nipy.algorithms.statistics.rft) SplineTransform (class in nipy.neurospin.registration.grid_transform) split() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) split_group() (in module nipy.neurospin.utils.reproducibility_measures) splitext_addext() (in module nipy.io.imageformats.filename_parser) SPM SPM approach SPM software Spm2AnalyzeHeader (class in nipy.io.imageformats.spm2analyze) Spm2AnalyzeImage (class in nipy.io.imageformats.spm2analyze) Spm99AnalyzeHeader (class in nipy.io.imageformats.spm99analyze) Spm99AnalyzeImage (class in nipy.io.imageformats.spm99analyze) spm_path() (nipy.interfaces.spm.SpmInfo static method) SpmAnalyzeHeader (class in nipy.io.imageformats.spm99analyze) SpmInfo (class in nipy.interfaces.spm) square_gaussian_filter() (in module nipy.neurospin.group.displacement_field) square_gaussian_filter1d() (in module nipy.neurospin.group.displacement_field) squeeze_image() (in module nipy.io.imageformats.funcs) SSE() (nipy.algorithms.statistics.nlsmodel.NLSModel method) stack2designs() (in module nipy.modalities.fmri.design) stack_contrasts() (in module nipy.modalities.fmri.design) stack_designs() (in module nipy.modalities.fmri.design) stat() (nipy.neurospin.glm.glm.contrast method) statistics_from_position() (in module nipy.neurospin.utils.reproducibility_measures) step_function() (in module nipy.modalities.fmri.utils) stratify() (nipy.modalities.fmri.formula.Factor method) strerror (nipy.utils.data.DataError attribute) structarr (nipy.io.imageformats.analyze.AnalyzeHeader attribute) (nipy.io.imageformats.nifti1.Nifti1Header attribute) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader attribute) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader attribute) subfield() (nipy.neurospin.graph.field.Field method) subforest() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) subgraph() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) subgraph_left() (nipy.neurospin.graph.graph.BipartiteGraph method) subgraph_right() (nipy.neurospin.graph.graph.BipartiteGraph method) subgrid_affine() (in module nipy.neurospin.image.image) subs() (nipy.modalities.fmri.formula.Beta method) (nipy.modalities.fmri.formula.Factor method) (nipy.modalities.fmri.formula.FactorTerm method) (nipy.modalities.fmri.formula.Formula method) (nipy.modalities.fmri.formula.RandomEffects method) (nipy.modalities.fmri.formula.Term method) subsample() (in module nipy.core.image.image) (in module nipy.neurospin.registration.iconic_registration) summary() (nipy.neurospin.glm.glm.contrast method) surrogate_3d_dataset() (in module nipy.neurospin.utils.simul_multisubject_fmri_dataset) surrogate_4d_dataset() (in module nipy.neurospin.utils.simul_multisubject_fmri_dataset) swiss_roll() (in module nipy.neurospin.eda.dimension_reduction) symmeterize() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) sync() (nipy.io.imageformats.minc.netcdf_fileobj method) synchronized_order() (in module nipy.core.image.image)

T

taylor_approx() (in module nipy.modalities.fmri.fmristat.hrf) TemporaryDirectory (class in nipy.utils.tmpdirs) tempTest() (in module nipy.neurospin.clustering.clustering) Term (class in nipy.modalities.fmri.formula) terms (nipy.modalities.fmri.formula.Factor attribute) (nipy.modalities.fmri.formula.Formula attribute) (nipy.modalities.fmri.formula.RandomEffects attribute) test() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.eda.dimension_reduction.MDS method) (nipy.neurospin.eda.dimension_reduction.NLDR method) (nipy.neurospin.eda.dimension_reduction.PCA method) (nipy.neurospin.eda.dimension_reduction.eps_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_LE method) (nipy.neurospin.eda.dimension_reduction.knn_LPP method) test_EC2() (in module nipy.algorithms.statistics.utils) test_EC3() (in module nipy.algorithms.statistics.utils) test_stat() (in module nipy.neurospin.utils.random_threshold) three_classes_GMM_fit() (in module nipy.neurospin.utils.emp_null) threshold() (nipy.neurospin.utils.emp_null.ENN method), [1] (nipy.neurospin.utils.emp_null.FDR method) threshold_bifurcations() (nipy.neurospin.graph.field.Field method) threshold_connect_components() (in module nipy.neurospin.utils.mask) threshold_from_student() (nipy.neurospin.utils.emp_null.FDR method) time_slice_diffs() (in module nipy.algorithms.diagnostics.timediff) title() (nipy.neurospin.viz_tools.ortho_slicer.OrthoSlicer method) to_filename() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) to_files() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method) to_filespec() (nipy.io.imageformats.analyze.AnalyzeImage method) (nipy.io.imageformats.compat.NiftiImage method) (nipy.io.imageformats.minc.MincImage method) (nipy.io.imageformats.nifti1.Nifti1Image method) (nipy.io.imageformats.spatialimages.SpatialImage method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeImage method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeImage method)

to_image() (nipy.core.image.xyz_image.XYZImage method) to_matrix_vector() (in module nipy.core.transforms.affines) (in module nipy.neurospin.datasets.transforms.affine_utils) to_multiple_roi() (nipy.neurospin.spatial_models.roi.MultiROI method) to_neighb() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) tocoordmap() (nipy.core.image.roi.ContinuousROI method) todiscrete() (nipy.core.image.roi.ContinuousROI method) TOutput (class in nipy.algorithms.statistics.regression) train() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) (nipy.neurospin.eda.dimension_reduction.MDS method) (nipy.neurospin.eda.dimension_reduction.NLDR method) (nipy.neurospin.eda.dimension_reduction.PCA method) (nipy.neurospin.eda.dimension_reduction.eps_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_Isomap method) (nipy.neurospin.eda.dimension_reduction.knn_LE method) (nipy.neurospin.eda.dimension_reduction.knn_LPP method) Transform (class in nipy.neurospin.datasets.transforms.transform) transform() (in module nipy.neurospin.registration.registration) (nipy.neurospin.image.image.Image method) (nipy.neurospin.image.image.MaskedImage method) transposed_values (nipy.core.reference.array_coords.ArrayCoordMap attribute) tree_depth() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) trRV() (in module nipy.modalities.fmri.spm.trace) TStat (class in nipy.algorithms.statistics.rft) ttest() (in module nipy.neurospin.utils.reproducibility_measures) TwoBinomialMixture (class in nipy.neurospin.utils.two_binomial_mixture) twosample_stat() (in module nipy.neurospin.group.permutation_test) twosample_test() (in module nipy.neurospin.statistical_mapping) types_filenames() (in module nipy.io.imageformats.filename_parser) TypesFilenamesError (class in nipy.io.imageformats.filename_parser)

U

uncorrected_threshold() (nipy.neurospin.utils.emp_null.ENN method), [1] unload() (nipy.io.imageformats.compat.NiftiImage method) UnsupportedDataType (class in nipy.io.imageformats.volumeutils) unweighted_likelihood() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) update() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) (nipy.neurospin.clustering.gmm.GMM method) update_block() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_block_SA() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_displacements() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_displacements_SA() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_effects() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_labels() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_lambda_fh() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method)

update_mean_effect() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_means() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) update_parameters_fh() (nipy.neurospin.utils.two_binomial_mixture.TwoBinomialMixture method) update_parameters_mcmc() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_parameters_saem() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_precisions() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) update_summary_statistics() (nipy.neurospin.group.spatial_relaxation_onesample.multivariate_stat method) update_weights() (nipy.neurospin.clustering.bgmm.BGMM method) (nipy.neurospin.clustering.bgmm.VBGMM method) updateCalMinMax() (nipy.io.imageformats.compat.NiftiImage method) updateFromDict() (nipy.io.imageformats.compat.NiftiImage method) updateHeader() (nipy.io.imageformats.compat.NiftiImage method)

V

validate_coords() (in module nipy.neurospin.image.image) value_set() (nipy.io.imageformats.volumeutils.Recoder method) values (nipy.core.reference.array_coords.ArrayCoordMap attribute) values() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.minc.MincHeader method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method) (nipy.neurospin.image.image.Image method) (nipy.neurospin.image.image.MaskedImage method) values_in_world() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.xyz_image.XYZImage method) (nipy.neurospin.datasets.volumes.volume_data.VolumeData method) (nipy.neurospin.datasets.volumes.volume_field.VolumeField method) (nipy.neurospin.datasets.volumes.volume_grid.VolumeGrid method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method) var_feature_intra() (nipy.neurospin.spatial_models.parcellation.Parcellation method) variance() (nipy.neurospin.registration.spacetime_registration.Realign4d method) variance_inter() (nipy.neurospin.spatial_models.parcellation.Parcellation method) variance_intra() (nipy.neurospin.spatial_models.parcellation.Parcellation method) VBGMM (class in nipy.neurospin.clustering.bgmm) ve_step() (nipy.neurospin.segmentation.vem.VemTissueClassification method) vec12 (nipy.neurospin.registration.affine.Affine attribute) (nipy.neurospin.registration.affine.Rigid attribute) (nipy.neurospin.registration.affine.Similarity attribute) vector12() (in module nipy.neurospin.registration.affine) VemTissueClassification (class in nipy.neurospin.segmentation.vem) VersionedDatasource (class in nipy.utils.data) vm_step() (nipy.neurospin.segmentation.vem.VemTissueClassification method) vm_step_gauss() (in module nipy.neurospin.segmentation.vem)

vm_step_laplace() (in module nipy.neurospin.segmentation.vem) volume2ball() (in module nipy.algorithms.statistics.rft) VolumeData (class in nipy.neurospin.datasets.volumes.volume_data) VolumeField (class in nipy.neurospin.datasets.volumes.volume_field) VolumeGrid (class in nipy.neurospin.datasets.volumes.volume_grid) VolumeImg (class in nipy.neurospin.datasets.volumes.volume_img) voronoi() (in module nipy.neurospin.clustering.clustering) Voronoi_diagram() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) Voronoi_Labelling() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) VoxBo voxdim (nipy.io.imageformats.compat.NiftiImage attribute) voxel voxel_reproducibility() (in module nipy.neurospin.utils.reproducibility_measures) voxel_reproducibility_old() (in module nipy.neurospin.utils.reproducibility_measures) voxel_thresholded_ttest() (in module nipy.neurospin.utils.reproducibility_measures) voxel_transform() (nipy.neurospin.registration.iconic_registration.IconicRegistration method) vx2q() (nipy.io.imageformats.compat.NiftiImage method) vx2s() (nipy.io.imageformats.compat.NiftiImage method)

W

ward() (in module nipy.neurospin.clustering.hierarchical_clustering) (nipy.neurospin.graph.field.Field method) ward_field_segment() (in module nipy.neurospin.clustering.hierarchical_clustering) ward_msb() (in module nipy.neurospin.clustering.bootstrap_hc) ward_quick() (in module nipy.neurospin.clustering.hierarchical_clustering) ward_quick_segment() (in module nipy.neurospin.clustering.hierarchical_clustering) ward_segment() (in module nipy.neurospin.clustering.hierarchical_clustering) ward_simple() (in module nipy.neurospin.clustering.hierarchical_clustering) water activation PET WeightedDegree() (nipy.neurospin.clustering.hierarchical_clustering.WeightedForest method) (nipy.neurospin.graph.field.Field method) (nipy.neurospin.graph.forest.Forest method) (nipy.neurospin.graph.graph.BipartiteGraph method) (nipy.neurospin.graph.graph.WeightedGraph method) (nipy.neurospin.spatial_models.hroi.NROI method) (nipy.neurospin.spatial_models.structural_bfls.landmark_regions method) WeightedForest (class in nipy.neurospin.clustering.hierarchical_clustering) WeightedGraph (class in nipy.neurospin.graph.graph) WholeBrainNormalize (class in nipy.modalities.fmri.fmristat.utils)

Wishart_eval() (in module nipy.neurospin.clustering.bgmm) wmedian() (in module nipy.neurospin.segmentation.vem) world (nipy.neurospin.image.image.Image attribute) (nipy.neurospin.image.image.MaskedImage attribute) write_csv() (nipy.neurospin.utils.design_matrix.DesignMatrix method) write_data() (in module nipy.core.image.generators) (in module nipy.io.imageformats.header_ufuncs) write_raise() (nipy.io.imageformats.batteryrunners.Report method) write_scaled_data() (in module nipy.io.imageformats.header_ufuncs) write_screen_res() (in module nipy.algorithms.diagnostics.screens) write_to() (nipy.io.imageformats.analyze.AnalyzeHeader method) (nipy.io.imageformats.nifti1.Nifti1Extension method) (nipy.io.imageformats.nifti1.Nifti1Extensions method) (nipy.io.imageformats.nifti1.Nifti1Header method) (nipy.io.imageformats.spm2analyze.Spm2AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.Spm99AnalyzeHeader method) (nipy.io.imageformats.spm99analyze.SpmAnalyzeHeader method)

X

xslice() (in module nipy.core.reference.slices) xyz_ordered() (nipy.core.image.affine_image.AffineImage method) (nipy.core.image.xyz_image.XYZImage method) (nipy.neurospin.datasets.volumes.volume_img.VolumeImg method)

xyz_transform (nipy.core.image.xyz_image.XYZImage attribute) XYZImage (class in nipy.core.image.xyz_image) XYZTransform (class in nipy.core.image.xyz_image)

Y

yslice() (in module nipy.core.reference.slices)

Z

z_to_slice() (nipy.neurospin.registration.spacetime_registration.Image4d method) zscore() (in module nipy.neurospin.utils.zscore) (nipy.neurospin.glm.glm.contrast method) (nipy.neurospin.group.permutation_test.permutation_test method) (nipy.neurospin.group.permutation_test.permutation_test_onesample method) (nipy.neurospin.group.permutation_test.permutation_test_onesample_graph method) (nipy.neurospin.group.permutation_test.permutation_test_twosample method)

zslice() (in module nipy.core.reference.slices)