API

Release:

0.6.1

Date:

March 02, 2026

• algorithms.clustering.bgmm
  • Module: algorithms.clustering.bgmm
  • Classes
    • BGMM
      • BGMM
        • BGMM.__init__()
        • BGMM.average_log_like()
        • BGMM.bayes_factor()
        • BGMM.bic()
        • BGMM.check()
        • BGMM.check_x()
        • BGMM.conditional_posterior_proba()
        • BGMM.estimate()
        • BGMM.evidence()
        • BGMM.guess_priors()
        • BGMM.guess_regularizing()
        • BGMM.initialize()
        • BGMM.initialize_and_estimate()
        • BGMM.likelihood()
        • BGMM.map_label()
        • BGMM.mixture_likelihood()
        • BGMM.plugin()
        • BGMM.pop()
        • BGMM.probability_under_prior()
        • BGMM.sample()
        • BGMM.sample_and_average()
        • BGMM.sample_indicator()
        • BGMM.set_priors()
        • BGMM.show()
        • BGMM.show_components()
        • BGMM.test()
        • BGMM.train()
        • BGMM.unweighted_likelihood()
        • BGMM.unweighted_likelihood_()
        • BGMM.update()
        • BGMM.update_means()
        • BGMM.update_precisions()
        • BGMM.update_weights()
    • VBGMM
      • VBGMM
        • VBGMM.__init__()
        • VBGMM.average_log_like()
        • VBGMM.bayes_factor()
        • VBGMM.bic()
        • VBGMM.check()
        • VBGMM.check_x()
        • VBGMM.conditional_posterior_proba()
        • VBGMM.estimate()
        • VBGMM.evidence()
        • VBGMM.guess_priors()
        • VBGMM.guess_regularizing()
        • VBGMM.initialize()
        • VBGMM.initialize_and_estimate()
        • VBGMM.likelihood()
        • VBGMM.map_label()
        • VBGMM.mixture_likelihood()
        • VBGMM.plugin()
        • VBGMM.pop()
        • VBGMM.probability_under_prior()
        • VBGMM.sample()
        • VBGMM.sample_and_average()
        • VBGMM.sample_indicator()
        • VBGMM.set_priors()
        • VBGMM.show()
        • VBGMM.show_components()
        • VBGMM.test()
        • VBGMM.train()
        • VBGMM.unweighted_likelihood()
        • VBGMM.unweighted_likelihood_()
        • VBGMM.update()
        • VBGMM.update_means()
        • VBGMM.update_precisions()
        • VBGMM.update_weights()
  • Functions
    • detsh()
    • dirichlet_eval()
    • dkl_dirichlet()
    • dkl_gaussian()
    • dkl_wishart()
    • generate_Wishart()
    • generate_normals()
    • generate_perm()
    • multinomial()
    • normal_eval()
    • wishart_eval()
• algorithms.clustering.ggmixture
  • Module: algorithms.clustering.ggmixture
  • Classes
    • GGGM
      • GGGM
        • GGGM.__init__()
        • GGGM.Estep()
        • GGGM.Mstep()
        • GGGM.component_likelihood()
        • GGGM.estimate()
        • GGGM.init()
        • GGGM.init_fdr()
        • GGGM.parameters()
        • GGGM.posterior()
        • GGGM.show()
    • GGM
      • GGM
        • GGM.__init__()
        • GGM.Estep()
        • GGM.Mstep()
        • GGM.estimate()
        • GGM.parameters()
        • GGM.posterior()
        • GGM.show()
    • Gamma
      • Gamma
        • Gamma.__init__()
        • Gamma.check()
        • Gamma.estimate()
        • Gamma.parameters()
• algorithms.clustering.gmm
  • Module: algorithms.clustering.gmm
  • Classes
    • GMM
      • GMM
        • GMM.__init__()
        • GMM.average_log_like()
        • GMM.bic()
        • GMM.check()
        • GMM.check_x()
        • GMM.estimate()
        • GMM.evidence()
        • GMM.guess_regularizing()
        • GMM.initialize()
        • GMM.initialize_and_estimate()
        • GMM.likelihood()
        • GMM.map_label()
        • GMM.mixture_likelihood()
        • GMM.plugin()
        • GMM.pop()
        • GMM.show()
        • GMM.show_components()
        • GMM.test()
        • GMM.train()
        • GMM.unweighted_likelihood()
        • GMM.unweighted_likelihood_()
        • GMM.update()
    • GridDescriptor
      • GridDescriptor
        • GridDescriptor.__init__()
        • GridDescriptor.make_grid()
        • GridDescriptor.set()
  • Functions
    • best_fitting_GMM()
    • plot2D()
• algorithms.clustering.hierarchical_clustering
  • Module: algorithms.clustering.hierarchical_clustering
  • Class
  • WeightedForest
    • WeightedForest
      • WeightedForest.__init__()
      • WeightedForest.adjacency()
      • WeightedForest.all_distances()
      • WeightedForest.anti_symmeterize()
      • WeightedForest.cc()
      • WeightedForest.check()
      • WeightedForest.check_compatible_height()
      • WeightedForest.cliques()
      • WeightedForest.compact_neighb()
      • WeightedForest.compute_children()
      • WeightedForest.copy()
      • WeightedForest.cut_redundancies()
      • WeightedForest.define_graph_attributes()
      • WeightedForest.degrees()
      • WeightedForest.depth_from_leaves()
      • WeightedForest.dijkstra()
      • WeightedForest.floyd()
      • WeightedForest.from_3d_grid()
      • WeightedForest.get_E()
      • WeightedForest.get_V()
      • WeightedForest.get_children()
      • WeightedForest.get_descendants()
      • WeightedForest.get_edges()
      • WeightedForest.get_height()
      • WeightedForest.get_vertices()
      • WeightedForest.get_weights()
      • WeightedForest.is_connected()
      • WeightedForest.isleaf()
      • WeightedForest.isroot()
      • WeightedForest.kruskal()
      • WeightedForest.leaves_of_a_subtree()
      • WeightedForest.left_incidence()
      • WeightedForest.list_of_neighbors()
      • WeightedForest.list_of_subtrees()
      • WeightedForest.main_cc()
      • WeightedForest.merge_simple_branches()
      • WeightedForest.normalize()
      • WeightedForest.partition()
      • WeightedForest.plot()
      • WeightedForest.plot_height()
      • WeightedForest.propagate_upward()
      • WeightedForest.propagate_upward_and()
      • WeightedForest.remove_edges()
      • WeightedForest.remove_trivial_edges()
      • WeightedForest.reorder_from_leaves_to_roots()
      • WeightedForest.right_incidence()
      • WeightedForest.set_edges()
      • WeightedForest.set_euclidian()
      • WeightedForest.set_gaussian()
      • WeightedForest.set_height()
      • WeightedForest.set_weights()
      • WeightedForest.show()
      • WeightedForest.split()
      • WeightedForest.subforest()
      • WeightedForest.subgraph()
      • WeightedForest.symmeterize()
      • WeightedForest.to_coo_matrix()
      • WeightedForest.tree_depth()
      • WeightedForest.voronoi_diagram()
      • WeightedForest.voronoi_labelling()
  • Functions
    • average_link_graph()
    • average_link_graph_segment()
    • fusion()
    • ward()
    • ward_field_segment()
    • ward_quick()
    • ward_quick_segment()
    • ward_segment()
• algorithms.clustering.imm
  • Module: algorithms.clustering.imm
  • Classes
    • IMM
      • IMM
        • IMM.__init__()
        • IMM.average_log_like()
        • IMM.bayes_factor()
        • IMM.bic()
        • IMM.check()
        • IMM.check_x()
        • IMM.conditional_posterior_proba()
        • IMM.cross_validated_update()
        • IMM.estimate()
        • IMM.evidence()
        • IMM.guess_priors()
        • IMM.guess_regularizing()
        • IMM.initialize()
        • IMM.initialize_and_estimate()
        • IMM.likelihood()
        • IMM.likelihood_under_the_prior()
        • IMM.map_label()
        • IMM.mixture_likelihood()
        • IMM.plugin()
        • IMM.pop()
        • IMM.probability_under_prior()
        • IMM.reduce()
        • IMM.sample()
        • IMM.sample_and_average()
        • IMM.sample_indicator()
        • IMM.set_constant_densities()
        • IMM.set_priors()
        • IMM.show()
        • IMM.show_components()
        • IMM.simple_update()
        • IMM.test()
        • IMM.train()
        • IMM.unweighted_likelihood()
        • IMM.unweighted_likelihood_()
        • IMM.update()
        • IMM.update_means()
        • IMM.update_precisions()
        • IMM.update_weights()
    • MixedIMM
      • MixedIMM
        • MixedIMM.__init__()
        • MixedIMM.average_log_like()
        • MixedIMM.bayes_factor()
        • MixedIMM.bic()
        • MixedIMM.check()
        • MixedIMM.check_x()
        • MixedIMM.conditional_posterior_proba()
        • MixedIMM.cross_validated_update()
        • MixedIMM.estimate()
        • MixedIMM.evidence()
        • MixedIMM.guess_priors()
        • MixedIMM.guess_regularizing()
        • MixedIMM.initialize()
        • MixedIMM.initialize_and_estimate()
        • MixedIMM.likelihood()
        • MixedIMM.likelihood_under_the_prior()
        • MixedIMM.map_label()
        • MixedIMM.mixture_likelihood()
        • MixedIMM.plugin()
        • MixedIMM.pop()
        • MixedIMM.probability_under_prior()
        • MixedIMM.reduce()
        • MixedIMM.sample()
        • MixedIMM.sample_and_average()
        • MixedIMM.sample_indicator()
        • MixedIMM.set_constant_densities()
        • MixedIMM.set_priors()
        • MixedIMM.show()
        • MixedIMM.show_components()
        • MixedIMM.simple_update()
        • MixedIMM.test()
        • MixedIMM.train()
        • MixedIMM.unweighted_likelihood()
        • MixedIMM.unweighted_likelihood_()
        • MixedIMM.update()
        • MixedIMM.update_means()
        • MixedIMM.update_precisions()
        • MixedIMM.update_weights()
  • Functions
    • co_labelling()
    • main()
• algorithms.clustering.utils
  • Module: algorithms.clustering.utils
  • Functions
    • kmeans()
    • voronoi()
• algorithms.clustering.von_mises_fisher_mixture
  • Module: algorithms.clustering.von_mises_fisher_mixture
  • Class
  • VonMisesMixture
    • VonMisesMixture
      • VonMisesMixture.__init__()
      • VonMisesMixture.density_per_component()
      • VonMisesMixture.estimate()
      • VonMisesMixture.estimate_means()
      • VonMisesMixture.estimate_weights()
      • VonMisesMixture.log_density_per_component()
      • VonMisesMixture.log_weighted_density()
      • VonMisesMixture.mixture_density()
      • VonMisesMixture.responsibilities()
      • VonMisesMixture.show()
      • VonMisesMixture.weighted_density()
  • Functions
    • estimate_robust_vmm()
    • example_cv_nonoise()
    • example_noisy()
    • select_vmm()
    • select_vmm_cv()
    • sphere_density()
• algorithms.diagnostics.commands
  • Module: algorithms.diagnostics.commands
  • Functions
    • diagnose()
    • parse_fname_axes()
    • tsdiffana()
• algorithms.diagnostics.screens
  • Module: algorithms.diagnostics.screens
  • Functions
    • screen()
    • write_screen_res()
• algorithms.diagnostics.timediff
  • Module: algorithms.diagnostics.timediff
  • Functions
    • time_slice_diffs()
    • time_slice_diffs_image()
• algorithms.diagnostics.tsdiffplot
  • Module: algorithms.diagnostics.tsdiffplot
  • Functions
    • plot_tsdiffs()
    • plot_tsdiffs_image()
• algorithms.fwhm
  • Module: algorithms.fwhm
  • Classes
    • ReselImage
      • ReselImage
        • ReselImage.__init__()
        • ReselImage.fwhm2resel()
        • ReselImage.integrate()
        • ReselImage.resel2fwhm()
    • Resels
      • Resels
        • Resels.__init__()
        • Resels.fwhm2resel()
        • Resels.integrate()
        • Resels.resel2fwhm()
• algorithms.graph.bipartite_graph
  • Module: algorithms.graph.bipartite_graph
  • Class
  • BipartiteGraph
    • BipartiteGraph
      • BipartiteGraph.__init__()
      • BipartiteGraph.copy()
      • BipartiteGraph.set_edges()
      • BipartiteGraph.set_weights()
      • BipartiteGraph.subgraph_left()
      • BipartiteGraph.subgraph_right()
  • Functions
    • bipartite_graph_from_adjacency()
    • bipartite_graph_from_coo_matrix()
    • check_feature_matrices()
    • cross_eps()
    • cross_knn()
• algorithms.graph.field
  • Module: algorithms.graph.field
  • Class
  • Field
    • Field
      • Field.__init__()
      • Field.adjacency()
      • Field.anti_symmeterize()
      • Field.cc()
      • Field.cliques()
      • Field.closing()
      • Field.compact_neighb()
      • Field.constrained_voronoi()
      • Field.copy()
      • Field.custom_watershed()
      • Field.cut_redundancies()
      • Field.degrees()
      • Field.diffusion()
      • Field.dijkstra()
      • Field.dilation()
      • Field.erosion()
      • Field.floyd()
      • Field.from_3d_grid()
      • Field.geodesic_kmeans()
      • Field.get_E()
      • Field.get_V()
      • Field.get_edges()
      • Field.get_field()
      • Field.get_local_maxima()
      • Field.get_vertices()
      • Field.get_weights()
      • Field.highest_neighbor()
      • Field.is_connected()
      • Field.kruskal()
      • Field.left_incidence()
      • Field.list_of_neighbors()
      • Field.local_maxima()
      • Field.main_cc()
      • Field.normalize()
      • Field.opening()
      • Field.remove_edges()
      • Field.remove_trivial_edges()
      • Field.right_incidence()
      • Field.set_edges()
      • Field.set_euclidian()
      • Field.set_field()
      • Field.set_gaussian()
      • Field.set_weights()
      • Field.show()
      • Field.subfield()
      • Field.subgraph()
      • Field.symmeterize()
      • Field.threshold_bifurcations()
      • Field.to_coo_matrix()
      • Field.voronoi_diagram()
      • Field.voronoi_labelling()
      • Field.ward()
  • Functions
    • field_from_coo_matrix_and_data()
    • field_from_graph_and_data()
• algorithms.graph.forest
  • Module: algorithms.graph.forest
  • Forest
    • Forest
      • Forest.__init__()
      • Forest.adjacency()
      • Forest.all_distances()
      • Forest.anti_symmeterize()
      • Forest.cc()
      • Forest.check()
      • Forest.cliques()
      • Forest.compact_neighb()
      • Forest.compute_children()
      • Forest.copy()
      • Forest.cut_redundancies()
      • Forest.define_graph_attributes()
      • Forest.degrees()
      • Forest.depth_from_leaves()
      • Forest.dijkstra()
      • Forest.floyd()
      • Forest.from_3d_grid()
      • Forest.get_E()
      • Forest.get_V()
      • Forest.get_children()
      • Forest.get_descendants()
      • Forest.get_edges()
      • Forest.get_vertices()
      • Forest.get_weights()
      • Forest.is_connected()
      • Forest.isleaf()
      • Forest.isroot()
      • Forest.kruskal()
      • Forest.leaves_of_a_subtree()
      • Forest.left_incidence()
      • Forest.list_of_neighbors()
      • Forest.main_cc()
      • Forest.merge_simple_branches()
      • Forest.normalize()
      • Forest.propagate_upward()
      • Forest.propagate_upward_and()
      • Forest.remove_edges()
      • Forest.remove_trivial_edges()
      • Forest.reorder_from_leaves_to_roots()
      • Forest.right_incidence()
      • Forest.set_edges()
      • Forest.set_euclidian()
      • Forest.set_gaussian()
      • Forest.set_weights()
      • Forest.show()
      • Forest.subforest()
      • Forest.subgraph()
      • Forest.symmeterize()
      • Forest.to_coo_matrix()
      • Forest.tree_depth()
      • Forest.voronoi_diagram()
      • Forest.voronoi_labelling()
• algorithms.graph.graph
  • Module: algorithms.graph.graph
  • Classes
    • Graph
      • Graph
        • Graph.__init__()
        • Graph.adjacency()
        • Graph.cc()
        • Graph.degrees()
        • Graph.get_E()
        • Graph.get_V()
        • Graph.get_edges()
        • Graph.get_vertices()
        • Graph.main_cc()
        • Graph.set_edges()
        • Graph.show()
        • Graph.to_coo_matrix()
    • WeightedGraph
      • WeightedGraph
        • WeightedGraph.__init__()
        • WeightedGraph.adjacency()
        • WeightedGraph.anti_symmeterize()
        • WeightedGraph.cc()
        • WeightedGraph.cliques()
        • WeightedGraph.compact_neighb()
        • WeightedGraph.copy()
        • WeightedGraph.cut_redundancies()
        • WeightedGraph.degrees()
        • WeightedGraph.dijkstra()
        • WeightedGraph.floyd()
        • WeightedGraph.from_3d_grid()
        • WeightedGraph.get_E()
        • WeightedGraph.get_V()
        • WeightedGraph.get_edges()
        • WeightedGraph.get_vertices()
        • WeightedGraph.get_weights()
        • WeightedGraph.is_connected()
        • WeightedGraph.kruskal()
        • WeightedGraph.left_incidence()
        • WeightedGraph.list_of_neighbors()
        • WeightedGraph.main_cc()
        • WeightedGraph.normalize()
        • WeightedGraph.remove_edges()
        • WeightedGraph.remove_trivial_edges()
        • WeightedGraph.right_incidence()
        • WeightedGraph.set_edges()
        • WeightedGraph.set_euclidian()
        • WeightedGraph.set_gaussian()
        • WeightedGraph.set_weights()
        • WeightedGraph.show()
        • WeightedGraph.subgraph()
        • WeightedGraph.symmeterize()
        • WeightedGraph.to_coo_matrix()
        • WeightedGraph.voronoi_diagram()
        • WeightedGraph.voronoi_labelling()
  • Functions
    • complete_graph()
    • concatenate_graphs()
    • eps_nn()
    • graph_3d_grid()
    • knn()
    • lil_cc()
    • mst()
    • wgraph_from_3d_grid()
    • wgraph_from_adjacency()
    • wgraph_from_coo_matrix()
• algorithms.group.parcel_analysis
  • Module: algorithms.group.parcel_analysis
  • ParcelAnalysis
    • ParcelAnalysis
      • ParcelAnalysis.__init__()
      • ParcelAnalysis.dump_results()
      • ParcelAnalysis.parcel_maps()
      • ParcelAnalysis.t_map()
    • parcel_analysis()
• algorithms.interpolation
  • Module: algorithms.interpolation
  • ImageInterpolator
    • ImageInterpolator
      • ImageInterpolator.__init__()
      • ImageInterpolator.evaluate()
      • ImageInterpolator.mode
      • ImageInterpolator.n_prepad_if_needed
      • ImageInterpolator.order
• algorithms.kernel_smooth
  • Module: algorithms.kernel_smooth
  • Class
  • LinearFilter
    • LinearFilter
      • LinearFilter.__init__()
      • LinearFilter.normalization
      • LinearFilter.smooth()
  • Functions
    • fwhm2sigma()
    • sigma2fwhm()
• algorithms.optimize
  • Module: algorithms.optimize
    • fmin_steepest()
• algorithms.registration.affine
  • Module: algorithms.registration.affine
  • Classes
    • Affine
      • Affine
        • Affine.__init__()
        • Affine.apply()
        • Affine.as_affine()
        • Affine.compose()
        • Affine.copy()
        • Affine.from_matrix44()
        • Affine.inv()
        • Affine.is_direct
        • Affine.param
        • Affine.param_inds
        • Affine.pre_rotation
        • Affine.precond
        • Affine.rotation
        • Affine.scaling
        • Affine.translation
    • Affine2D
      • Affine2D
        • Affine2D.__init__()
        • Affine2D.apply()
        • Affine2D.as_affine()
        • Affine2D.compose()
        • Affine2D.copy()
        • Affine2D.from_matrix44()
        • Affine2D.inv()
        • Affine2D.is_direct
        • Affine2D.param
        • Affine2D.param_inds
        • Affine2D.pre_rotation
        • Affine2D.precond
        • Affine2D.rotation
        • Affine2D.scaling
        • Affine2D.translation
    • Rigid
      • Rigid
        • Rigid.__init__()
        • Rigid.apply()
        • Rigid.as_affine()
        • Rigid.compose()
        • Rigid.copy()
        • Rigid.from_matrix44()
        • Rigid.inv()
        • Rigid.is_direct
        • Rigid.param
        • Rigid.param_inds
        • Rigid.pre_rotation
        • Rigid.precond
        • Rigid.rotation
        • Rigid.scaling
        • Rigid.translation
    • Rigid2D
      • Rigid2D
        • Rigid2D.__init__()
        • Rigid2D.apply()
        • Rigid2D.as_affine()
        • Rigid2D.compose()
        • Rigid2D.copy()
        • Rigid2D.from_matrix44()
        • Rigid2D.inv()
        • Rigid2D.is_direct
        • Rigid2D.param
        • Rigid2D.param_inds
        • Rigid2D.pre_rotation
        • Rigid2D.precond
        • Rigid2D.rotation
        • Rigid2D.scaling
        • Rigid2D.translation
    • Similarity
      • Similarity
        • Similarity.__init__()
        • Similarity.apply()
        • Similarity.as_affine()
        • Similarity.compose()
        • Similarity.copy()
        • Similarity.from_matrix44()
        • Similarity.inv()
        • Similarity.is_direct
        • Similarity.param
        • Similarity.param_inds
        • Similarity.pre_rotation
        • Similarity.precond
        • Similarity.rotation
        • Similarity.scaling
        • Similarity.translation
    • Similarity2D
      • Similarity2D
        • Similarity2D.__init__()
        • Similarity2D.apply()
        • Similarity2D.as_affine()
        • Similarity2D.compose()
        • Similarity2D.copy()
        • Similarity2D.from_matrix44()
        • Similarity2D.inv()
        • Similarity2D.is_direct
        • Similarity2D.param
        • Similarity2D.param_inds
        • Similarity2D.pre_rotation
        • Similarity2D.precond
        • Similarity2D.rotation
        • Similarity2D.scaling
        • Similarity2D.translation
  • Functions
    • inverse_affine()
    • preconditioner()
    • rotation_mat2vec()
    • rotation_vec2mat()
    • slices2aff()
    • subgrid_affine()
    • threshold()
    • to_matrix44()
• algorithms.registration.chain_transform
  • Module: algorithms.registration.chain_transform
  • ChainTransform
    • ChainTransform
      • ChainTransform.__init__()
      • ChainTransform.apply()
      • ChainTransform.param
• algorithms.registration.groupwise_registration
  • Module: algorithms.registration.groupwise_registration
  • Classes
    • FmriRealign4d
      • FmriRealign4d
        • FmriRealign4d.__init__()
        • FmriRealign4d.estimate()
        • FmriRealign4d.resample()
    • Image4d
      • Image4d
        • Image4d.__init__()
        • Image4d.free_data()
        • Image4d.get_fdata()
        • Image4d.get_shape()
        • Image4d.scanner_time()
        • Image4d.z_to_slice()
    • Realign4d
      • Realign4d
        • Realign4d.__init__()
        • Realign4d.estimate()
        • Realign4d.resample()
    • Realign4dAlgorithm
      • Realign4dAlgorithm
        • Realign4dAlgorithm.__init__()
        • Realign4dAlgorithm.align_to_refscan()
        • Realign4dAlgorithm.estimate_instant_motion()
        • Realign4dAlgorithm.estimate_motion()
        • Realign4dAlgorithm.init_instant_motion()
        • Realign4dAlgorithm.resample()
        • Realign4dAlgorithm.resample_full_data()
        • Realign4dAlgorithm.set_fmin()
        • Realign4dAlgorithm.set_transform()
    • SpaceRealign
      • SpaceRealign
        • SpaceRealign.__init__()
        • SpaceRealign.estimate()
        • SpaceRealign.resample()
    • SpaceTimeRealign
      • SpaceTimeRealign
        • SpaceTimeRealign.__init__()
        • SpaceTimeRealign.estimate()
        • SpaceTimeRealign.resample()
  • Functions
    • adjust_subsampling()
    • guess_slice_axis_and_direction()
    • interp_slice_times()
    • make_grid()
    • realign4d()
    • resample4d()
    • scanner_coords()
    • single_run_realign4d()
    • tr_from_header()
• algorithms.registration.histogram_registration
  • Module: algorithms.registration.histogram_registration
  • Class
  • HistogramRegistration
    • HistogramRegistration
      • HistogramRegistration.__init__()
      • HistogramRegistration.eval()
      • HistogramRegistration.eval_gradient()
      • HistogramRegistration.eval_hessian()
      • HistogramRegistration.explore()
      • HistogramRegistration.interp
      • HistogramRegistration.optimize()
      • HistogramRegistration.set_fov()
      • HistogramRegistration.similarity
      • HistogramRegistration.subsample()
  • Functions
    • approx_gradient()
    • approx_hessian()
    • approx_hessian_diag()
    • clamp()
    • ideal_spacing()
    • smallest_bounding_box()
    • smooth_image()
• algorithms.registration.optimizer
  • Module: algorithms.registration.optimizer
  • Functions
    • configure_optimizer()
    • subdict()
    • use_derivatives()
• algorithms.registration.polyaffine
  • Module: algorithms.registration.polyaffine
  • PolyAffine
    • PolyAffine
      • PolyAffine.__init__()
      • PolyAffine.affine()
      • PolyAffine.affines()
      • PolyAffine.apply()
      • PolyAffine.compose()
      • PolyAffine.left_compose()
      • PolyAffine.param
• algorithms.registration.resample
  • Module: algorithms.registration.resample
  • Functions
    • cast_array()
    • resample()
• algorithms.registration.scripting
  • Module: algorithms.registration.scripting
  • Functions
    • aff2euler()
    • aff2rot_zooms()
    • space_time_realign()
• algorithms.registration.similarity_measures
  • Module: algorithms.registration.similarity_measures
  • Classes
    • CorrelationCoefficient
      • CorrelationCoefficient
        • CorrelationCoefficient.__init__()
        • CorrelationCoefficient.loss()
        • CorrelationCoefficient.npoints()
    • CorrelationRatio
      • CorrelationRatio
        • CorrelationRatio.__init__()
        • CorrelationRatio.loss()
        • CorrelationRatio.npoints()
    • CorrelationRatioL1
      • CorrelationRatioL1
        • CorrelationRatioL1.__init__()
        • CorrelationRatioL1.loss()
        • CorrelationRatioL1.npoints()
    • DiscreteParzenMutualInformation
      • DiscreteParzenMutualInformation
        • DiscreteParzenMutualInformation.__init__()
        • DiscreteParzenMutualInformation.loss()
        • DiscreteParzenMutualInformation.npoints()
    • MutualInformation
      • MutualInformation
        • MutualInformation.__init__()
        • MutualInformation.loss()
        • MutualInformation.npoints()
    • NormalizedMutualInformation
      • NormalizedMutualInformation
        • NormalizedMutualInformation.__init__()
        • NormalizedMutualInformation.loss()
        • NormalizedMutualInformation.npoints()
    • ParzenMutualInformation
      • ParzenMutualInformation
        • ParzenMutualInformation.__init__()
        • ParzenMutualInformation.loss()
        • ParzenMutualInformation.npoints()
    • SimilarityMeasure
      • SimilarityMeasure
        • SimilarityMeasure.__init__()
        • SimilarityMeasure.loss()
        • SimilarityMeasure.npoints()
    • SupervisedLikelihoodRatio
      • SupervisedLikelihoodRatio
        • SupervisedLikelihoodRatio.__init__()
        • SupervisedLikelihoodRatio.loss()
        • SupervisedLikelihoodRatio.npoints()
  • Functions
    • correlation2loglikelihood()
    • dist2loss()
• algorithms.registration.transform
  • Module: algorithms.registration.transform
  • Transform
    • Transform
      • Transform.__init__()
      • Transform.apply()
      • Transform.compose()
      • Transform.param
• algorithms.registration.type_check
  • Module: algorithms.registration.type_check
  • Functions
    • check_type()
    • check_type_and_shape()
• algorithms.resample
  • Module: algorithms.resample
  • Functions
    • resample()
    • resample_img2img()
• algorithms.segmentation.brain_segmentation
  • Module: algorithms.segmentation.brain_segmentation
  • BrainT1Segmentation
    • BrainT1Segmentation
      • BrainT1Segmentation.__init__()
      • BrainT1Segmentation.convert()
• algorithms.segmentation.segmentation
  • Module: algorithms.segmentation.segmentation
  • Class
  • Segmentation
    • Segmentation
      • Segmentation.__init__()
      • Segmentation.free_energy()
      • Segmentation.log_external_field()
      • Segmentation.map()
      • Segmentation.normalized_external_field()
      • Segmentation.run()
      • Segmentation.set_markov_prior()
      • Segmentation.ve_step()
      • Segmentation.vm_step()
  • Functions
    • binarize_ppm()
    • map_from_ppm()
    • moment_matching()
• algorithms.slicetiming.timefuncs
  • Module: algorithms.slicetiming.timefuncs
  • Functions
    • st_01234()
    • st_02413()
    • st_03142()
    • st_13024()
    • st_41302()
    • st_42031()
    • st_43210()
    • st_odd0_even1()
• algorithms.statistics.bayesian_mixed_effects
  • Module: algorithms.statistics.bayesian_mixed_effects
    • two_level_glm()
• algorithms.statistics.bench.bench_intvol
  • Module: algorithms.statistics.bench.bench_intvol
  • Functions
    • bench_lips1d()
    • bench_lips2d()
    • bench_lips3d()
• algorithms.statistics.empirical_pvalue
  • Module: algorithms.statistics.empirical_pvalue
  • Class
  • NormalEmpiricalNull
    • NormalEmpiricalNull
      • NormalEmpiricalNull.__init__()
      • NormalEmpiricalNull.fdr()
      • NormalEmpiricalNull.fdrcurve()
      • NormalEmpiricalNull.learn()
      • NormalEmpiricalNull.plot()
      • NormalEmpiricalNull.threshold()
      • NormalEmpiricalNull.uncorrected_threshold()
  • Functions
    • check_p_values()
    • fdr()
    • fdr_threshold()
    • gamma_gaussian_fit()
    • gaussian_fdr()
    • gaussian_fdr_threshold()
    • smoothed_histogram_from_samples()
    • three_classes_GMM_fit()
• algorithms.statistics.formula.formulae
  • Module: algorithms.statistics.formula.formulae
    • Formula objects
  • Classes
    • Beta
      • Beta
        • Beta.__init__()
        • Beta.adjoint()
        • Beta.apart()
        • Beta.args
        • Beta.args_cnc()
        • Beta.as_base_exp()
        • Beta.as_coeff_Add()
        • Beta.as_coeff_Mul()
        • Beta.as_coeff_add()
        • Beta.as_coeff_exponent()
        • Beta.as_coeff_mul()
        • Beta.as_coefficient()
        • Beta.as_coefficients_dict()
        • Beta.as_content_primitive()
        • Beta.as_dummy()
        • Beta.as_expr()
        • Beta.as_independent()
        • Beta.as_leading_term()
        • Beta.as_numer_denom()
        • Beta.as_ordered_factors()
        • Beta.as_ordered_terms()
        • Beta.as_poly()
        • Beta.as_powers_dict()
        • Beta.as_real_imag()
        • Beta.as_set()
        • Beta.as_terms()
        • Beta.aseries()
        • Beta.assumptions0
        • Beta.atoms()
        • Beta.binary_symbols
        • Beta.cancel()
        • Beta.canonical_variables
        • Beta.class_key()
        • Beta.coeff()
        • Beta.collect()
        • Beta.combsimp()
        • Beta.compare()
        • Beta.conjugate()
        • Beta.copy()
        • Beta.could_extract_minus_sign()
        • Beta.count()
        • Beta.count_ops()
        • Beta.default_assumptions
        • Beta.diff()
        • Beta.dir()
        • Beta.doit()
        • Beta.dummy_eq()
        • Beta.dummy_index
        • Beta.equals()
        • Beta.evalf()
        • Beta.expand()
        • Beta.expr_free_symbols
        • Beta.extract_additively()
        • Beta.extract_branch_factor()
        • Beta.extract_multiplicatively()
        • Beta.factor()
        • Beta.find()
        • Beta.fourier_series()
        • Beta.fps()
        • Beta.free_symbols
        • Beta.fromiter()
        • Beta.func
        • Beta.gammasimp()
        • Beta.getO()
        • Beta.getn()
        • Beta.has()
        • Beta.has_free()
        • Beta.has_xfree()
        • Beta.integrate()
        • Beta.invert()
        • Beta.is_Add
        • Beta.is_AlgebraicNumber
        • Beta.is_Atom
        • Beta.is_Boolean
        • Beta.is_Derivative
        • Beta.is_Dummy
        • Beta.is_Equality
        • Beta.is_Float
        • Beta.is_Function
        • Beta.is_Indexed
        • Beta.is_Integer
        • Beta.is_MatAdd
        • Beta.is_MatMul
        • Beta.is_Matrix
        • Beta.is_Mul
        • Beta.is_Not
        • Beta.is_Number
        • Beta.is_NumberSymbol
        • Beta.is_Order
        • Beta.is_Piecewise
        • Beta.is_Point
        • Beta.is_Poly
        • Beta.is_Pow
        • Beta.is_Rational
        • Beta.is_Relational
        • Beta.is_Symbol
        • Beta.is_Vector
        • Beta.is_Wild
        • Beta.is_algebraic
        • Beta.is_algebraic_expr()
        • Beta.is_antihermitian
        • Beta.is_commutative
        • Beta.is_comparable
        • Beta.is_complex
        • Beta.is_composite
        • Beta.is_constant()
        • Beta.is_even
        • Beta.is_extended_negative
        • Beta.is_extended_nonnegative
        • Beta.is_extended_nonpositive
        • Beta.is_extended_nonzero
        • Beta.is_extended_positive
        • Beta.is_extended_real
        • Beta.is_finite
        • Beta.is_hermitian
        • Beta.is_hypergeometric()
        • Beta.is_imaginary
        • Beta.is_infinite
        • Beta.is_integer
        • Beta.is_irrational
        • Beta.is_meromorphic()
        • Beta.is_negative
        • Beta.is_noninteger
        • Beta.is_nonnegative
        • Beta.is_nonpositive
        • Beta.is_nonzero
        • Beta.is_number
        • Beta.is_odd
        • Beta.is_polar
        • Beta.is_polynomial()
        • Beta.is_positive
        • Beta.is_prime
        • Beta.is_rational
        • Beta.is_rational_function()
        • Beta.is_real
        • Beta.is_same()
        • Beta.is_scalar
        • Beta.is_symbol
        • Beta.is_transcendental
        • Beta.is_zero
        • Beta.kind
        • Beta.leadterm()
        • Beta.limit()
        • Beta.lseries()
        • Beta.match()
        • Beta.matches()
        • Beta.n()
        • Beta.name
        • Beta.normal()
        • Beta.nseries()
        • Beta.nsimplify()
        • Beta.powsimp()
        • Beta.primitive()
        • Beta.radsimp()
        • Beta.ratsimp()
        • Beta.rcall()
        • Beta.refine()
        • Beta.removeO()
        • Beta.replace()
        • Beta.rewrite()
        • Beta.round()
        • Beta.separate()
        • Beta.series()
        • Beta.simplify()
        • Beta.sort_key()
        • Beta.subs()
        • Beta.taylor_term()
        • Beta.to_nnf()
        • Beta.together()
        • Beta.transpose()
        • Beta.trigsimp()
        • Beta.xreplace()
    • Factor
      • Factor
        • Factor.__init__()
        • Factor.coefs
        • Factor.design()
        • Factor.design_expr
        • Factor.dtype
        • Factor.fromcol()
        • Factor.fromrec()
        • Factor.get_term()
        • Factor.main_effect
        • Factor.mean
        • Factor.params
        • Factor.stratify()
        • Factor.subs()
        • Factor.terms
    • FactorTerm
      • FactorTerm
        • FactorTerm.__init__()
        • FactorTerm.adjoint()
        • FactorTerm.apart()
        • FactorTerm.args
        • FactorTerm.args_cnc()
        • FactorTerm.as_base_exp()
        • FactorTerm.as_coeff_Add()
        • FactorTerm.as_coeff_Mul()
        • FactorTerm.as_coeff_add()
        • FactorTerm.as_coeff_exponent()
        • FactorTerm.as_coeff_mul()
        • FactorTerm.as_coefficient()
        • FactorTerm.as_coefficients_dict()
        • FactorTerm.as_content_primitive()
        • FactorTerm.as_dummy()
        • FactorTerm.as_expr()
        • FactorTerm.as_independent()
        • FactorTerm.as_leading_term()
        • FactorTerm.as_numer_denom()
        • FactorTerm.as_ordered_factors()
        • FactorTerm.as_ordered_terms()
        • FactorTerm.as_poly()
        • FactorTerm.as_powers_dict()
        • FactorTerm.as_real_imag()
        • FactorTerm.as_set()
        • FactorTerm.as_terms()
        • FactorTerm.aseries()
        • FactorTerm.assumptions0
        • FactorTerm.atoms()
        • FactorTerm.binary_symbols
        • FactorTerm.cancel()
        • FactorTerm.canonical_variables
        • FactorTerm.class_key()
        • FactorTerm.coeff()
        • FactorTerm.collect()
        • FactorTerm.combsimp()
        • FactorTerm.compare()
        • FactorTerm.conjugate()
        • FactorTerm.copy()
        • FactorTerm.could_extract_minus_sign()
        • FactorTerm.count()
        • FactorTerm.count_ops()
        • FactorTerm.default_assumptions
        • FactorTerm.diff()
        • FactorTerm.dir()
        • FactorTerm.doit()
        • FactorTerm.dummy_eq()
        • FactorTerm.equals()
        • FactorTerm.evalf()
        • FactorTerm.expand()
        • FactorTerm.expr_free_symbols
        • FactorTerm.extract_additively()
        • FactorTerm.extract_branch_factor()
        • FactorTerm.extract_multiplicatively()
        • FactorTerm.factor()
        • FactorTerm.find()
        • FactorTerm.formula
        • FactorTerm.fourier_series()
        • FactorTerm.fps()
        • FactorTerm.free_symbols
        • FactorTerm.fromiter()
        • FactorTerm.func
        • FactorTerm.gammasimp()
        • FactorTerm.getO()
        • FactorTerm.getn()
        • FactorTerm.has()
        • FactorTerm.has_free()
        • FactorTerm.has_xfree()
        • FactorTerm.integrate()
        • FactorTerm.invert()
        • FactorTerm.is_Add
        • FactorTerm.is_AlgebraicNumber
        • FactorTerm.is_Atom
        • FactorTerm.is_Boolean
        • FactorTerm.is_Derivative
        • FactorTerm.is_Dummy
        • FactorTerm.is_Equality
        • FactorTerm.is_Float
        • FactorTerm.is_Function
        • FactorTerm.is_Indexed
        • FactorTerm.is_Integer
        • FactorTerm.is_MatAdd
        • FactorTerm.is_MatMul
        • FactorTerm.is_Matrix
        • FactorTerm.is_Mul
        • FactorTerm.is_Not
        • FactorTerm.is_Number
        • FactorTerm.is_NumberSymbol
        • FactorTerm.is_Order
        • FactorTerm.is_Piecewise
        • FactorTerm.is_Point
        • FactorTerm.is_Poly
        • FactorTerm.is_Pow
        • FactorTerm.is_Rational
        • FactorTerm.is_Relational
        • FactorTerm.is_Symbol
        • FactorTerm.is_Vector
        • FactorTerm.is_Wild
        • FactorTerm.is_algebraic
        • FactorTerm.is_algebraic_expr()
        • FactorTerm.is_antihermitian
        • FactorTerm.is_commutative
        • FactorTerm.is_comparable
        • FactorTerm.is_complex
        • FactorTerm.is_composite
        • FactorTerm.is_constant()
        • FactorTerm.is_even
        • FactorTerm.is_extended_negative
        • FactorTerm.is_extended_nonnegative
        • FactorTerm.is_extended_nonpositive
        • FactorTerm.is_extended_nonzero
        • FactorTerm.is_extended_positive
        • FactorTerm.is_extended_real
        • FactorTerm.is_finite
        • FactorTerm.is_hermitian
        • FactorTerm.is_hypergeometric()
        • FactorTerm.is_imaginary
        • FactorTerm.is_infinite
        • FactorTerm.is_integer
        • FactorTerm.is_irrational
        • FactorTerm.is_meromorphic()
        • FactorTerm.is_negative
        • FactorTerm.is_noninteger
        • FactorTerm.is_nonnegative
        • FactorTerm.is_nonpositive
        • FactorTerm.is_nonzero
        • FactorTerm.is_number
        • FactorTerm.is_odd
        • FactorTerm.is_polar
        • FactorTerm.is_polynomial()
        • FactorTerm.is_positive
        • FactorTerm.is_prime
        • FactorTerm.is_rational
        • FactorTerm.is_rational_function()
        • FactorTerm.is_real
        • FactorTerm.is_same()
        • FactorTerm.is_scalar
        • FactorTerm.is_symbol
        • FactorTerm.is_transcendental
        • FactorTerm.is_zero
        • FactorTerm.kind
        • FactorTerm.leadterm()
        • FactorTerm.limit()
        • FactorTerm.lseries()
        • FactorTerm.match()
        • FactorTerm.matches()
        • FactorTerm.n()
        • FactorTerm.name
        • FactorTerm.normal()
        • FactorTerm.nseries()
        • FactorTerm.nsimplify()
        • FactorTerm.powsimp()
        • FactorTerm.primitive()
        • FactorTerm.radsimp()
        • FactorTerm.ratsimp()
        • FactorTerm.rcall()
        • FactorTerm.refine()
        • FactorTerm.removeO()
        • FactorTerm.replace()
        • FactorTerm.rewrite()
        • FactorTerm.round()
        • FactorTerm.separate()
        • FactorTerm.series()
        • FactorTerm.simplify()
        • FactorTerm.sort_key()
        • FactorTerm.subs()
        • FactorTerm.taylor_term()
        • FactorTerm.to_nnf()
        • FactorTerm.together()
        • FactorTerm.transpose()
        • FactorTerm.trigsimp()
        • FactorTerm.xreplace()
    • Formula
      • Formula
        • Formula.__init__()
        • Formula.coefs
        • Formula.design()
        • Formula.design_expr
        • Formula.dtype
        • Formula.fromrec()
        • Formula.mean
        • Formula.params
        • Formula.subs()
        • Formula.terms
    • RandomEffects
      • RandomEffects
        • RandomEffects.__init__()
        • RandomEffects.coefs
        • RandomEffects.cov()
        • RandomEffects.design()
        • RandomEffects.design_expr
        • RandomEffects.dtype
        • RandomEffects.fromrec()
        • RandomEffects.mean
        • RandomEffects.params
        • RandomEffects.subs()
        • RandomEffects.terms
    • Term
      • Term
        • Term.__init__()
        • Term.adjoint()
        • Term.apart()
        • Term.args
        • Term.args_cnc()
        • Term.as_base_exp()
        • Term.as_coeff_Add()
        • Term.as_coeff_Mul()
        • Term.as_coeff_add()
        • Term.as_coeff_exponent()
        • Term.as_coeff_mul()
        • Term.as_coefficient()
        • Term.as_coefficients_dict()
        • Term.as_content_primitive()
        • Term.as_dummy()
        • Term.as_expr()
        • Term.as_independent()
        • Term.as_leading_term()
        • Term.as_numer_denom()
        • Term.as_ordered_factors()
        • Term.as_ordered_terms()
        • Term.as_poly()
        • Term.as_powers_dict()
        • Term.as_real_imag()
        • Term.as_set()
        • Term.as_terms()
        • Term.aseries()
        • Term.assumptions0
        • Term.atoms()
        • Term.binary_symbols
        • Term.cancel()
        • Term.canonical_variables
        • Term.class_key()
        • Term.coeff()
        • Term.collect()
        • Term.combsimp()
        • Term.compare()
        • Term.conjugate()
        • Term.copy()
        • Term.could_extract_minus_sign()
        • Term.count()
        • Term.count_ops()
        • Term.default_assumptions
        • Term.diff()
        • Term.dir()
        • Term.doit()
        • Term.dummy_eq()
        • Term.equals()
        • Term.evalf()
        • Term.expand()
        • Term.expr_free_symbols
        • Term.extract_additively()
        • Term.extract_branch_factor()
        • Term.extract_multiplicatively()
        • Term.factor()
        • Term.find()
        • Term.formula
        • Term.fourier_series()
        • Term.fps()
        • Term.free_symbols
        • Term.fromiter()
        • Term.func
        • Term.gammasimp()
        • Term.getO()
        • Term.getn()
        • Term.has()
        • Term.has_free()
        • Term.has_xfree()
        • Term.integrate()
        • Term.invert()
        • Term.is_Add
        • Term.is_AlgebraicNumber
        • Term.is_Atom
        • Term.is_Boolean
        • Term.is_Derivative
        • Term.is_Dummy
        • Term.is_Equality
        • Term.is_Float
        • Term.is_Function
        • Term.is_Indexed
        • Term.is_Integer
        • Term.is_MatAdd
        • Term.is_MatMul
        • Term.is_Matrix
        • Term.is_Mul
        • Term.is_Not
        • Term.is_Number
        • Term.is_NumberSymbol
        • Term.is_Order
        • Term.is_Piecewise
        • Term.is_Point
        • Term.is_Poly
        • Term.is_Pow
        • Term.is_Rational
        • Term.is_Relational
        • Term.is_Symbol
        • Term.is_Vector
        • Term.is_Wild
        • Term.is_algebraic
        • Term.is_algebraic_expr()
        • Term.is_antihermitian
        • Term.is_commutative
        • Term.is_comparable
        • Term.is_complex
        • Term.is_composite
        • Term.is_constant()
        • Term.is_even
        • Term.is_extended_negative
        • Term.is_extended_nonnegative
        • Term.is_extended_nonpositive
        • Term.is_extended_nonzero
        • Term.is_extended_positive
        • Term.is_extended_real
        • Term.is_finite
        • Term.is_hermitian
        • Term.is_hypergeometric()
        • Term.is_imaginary
        • Term.is_infinite
        • Term.is_integer
        • Term.is_irrational
        • Term.is_meromorphic()
        • Term.is_negative
        • Term.is_noninteger
        • Term.is_nonnegative
        • Term.is_nonpositive
        • Term.is_nonzero
        • Term.is_number
        • Term.is_odd
        • Term.is_polar
        • Term.is_polynomial()
        • Term.is_positive
        • Term.is_prime
        • Term.is_rational
        • Term.is_rational_function()
        • Term.is_real
        • Term.is_same()
        • Term.is_scalar
        • Term.is_symbol
        • Term.is_transcendental
        • Term.is_zero
        • Term.kind
        • Term.leadterm()
        • Term.limit()
        • Term.lseries()
        • Term.match()
        • Term.matches()
        • Term.n()
        • Term.name
        • Term.normal()
        • Term.nseries()
        • Term.nsimplify()
        • Term.powsimp()
        • Term.primitive()
        • Term.radsimp()
        • Term.ratsimp()
        • Term.rcall()
        • Term.refine()
        • Term.removeO()
        • Term.replace()
        • Term.rewrite()
        • Term.round()
        • Term.separate()
        • Term.series()
        • Term.simplify()
        • Term.sort_key()
        • Term.subs()
        • Term.taylor_term()
        • Term.to_nnf()
        • Term.together()
        • Term.transpose()
        • Term.trigsimp()
        • Term.xreplace()
  • Functions
    • contrast_from_cols_or_rows()
    • define()
    • getparams()
    • getterms()
    • is_factor()
    • is_factor_term()
    • is_formula()
    • is_term()
    • make_dummy()
    • make_recarray()
    • natural_spline()
    • terms()
• algorithms.statistics.mixed_effects_stat
  • Module: algorithms.statistics.mixed_effects_stat
  • Class
  • MixedEffectsModel
    • MixedEffectsModel
      • MixedEffectsModel.__init__()
      • MixedEffectsModel.fit()
      • MixedEffectsModel.log_like()
      • MixedEffectsModel.predict()
      • MixedEffectsModel.score()
  • Functions
    • check_arrays()
    • generate_data()
    • mfx_stat()
    • one_sample_ftest()
    • one_sample_ttest()
    • t_stat()
    • two_sample_ftest()
    • two_sample_ttest()
• algorithms.statistics.models.family.family
  • Module: algorithms.statistics.models.family.family
  • Classes
    • Binomial
      • Binomial
        • Binomial.__init__()
        • Binomial.deviance()
        • Binomial.devresid()
        • Binomial.fitted()
        • Binomial.link
        • Binomial.links
        • Binomial.predict()
        • Binomial.tol
        • Binomial.valid
        • Binomial.variance
        • Binomial.weights()
    • Family
      • Family
        • Family.__init__()
        • Family.deviance()
        • Family.devresid()
        • Family.fitted()
        • Family.link
        • Family.links
        • Family.predict()
        • Family.tol
        • Family.valid
        • Family.weights()
    • Gamma
      • Gamma
        • Gamma.__init__()
        • Gamma.deviance()
        • Gamma.devresid()
        • Gamma.fitted()
        • Gamma.link
        • Gamma.links
        • Gamma.predict()
        • Gamma.tol
        • Gamma.valid
        • Gamma.variance
        • Gamma.weights()
    • Gaussian
      • Gaussian
        • Gaussian.__init__()
        • Gaussian.deviance()
        • Gaussian.devresid()
        • Gaussian.fitted()
        • Gaussian.link
        • Gaussian.links
        • Gaussian.predict()
        • Gaussian.tol
        • Gaussian.valid
        • Gaussian.variance
        • Gaussian.weights()
    • InverseGaussian
      • InverseGaussian
        • InverseGaussian.__init__()
        • InverseGaussian.deviance()
        • InverseGaussian.devresid()
        • InverseGaussian.fitted()
        • InverseGaussian.link
        • InverseGaussian.links
        • InverseGaussian.predict()
        • InverseGaussian.tol
        • InverseGaussian.valid
        • InverseGaussian.variance
        • InverseGaussian.weights()
    • Poisson
      • Poisson
        • Poisson.__init__()
        • Poisson.deviance()
        • Poisson.devresid()
        • Poisson.fitted()
        • Poisson.link
        • Poisson.links
        • Poisson.predict()
        • Poisson.tol
        • Poisson.valid
        • Poisson.variance
        • Poisson.weights()
• algorithms.statistics.models.family.links
  • Module: algorithms.statistics.models.family.links
  • Classes
    • CDFLink
      • CDFLink
        • CDFLink.__init__()
        • CDFLink.clean()
        • CDFLink.deriv()
        • CDFLink.initialize()
        • CDFLink.inverse()
        • CDFLink.tol
    • CLogLog
      • CLogLog
        • CLogLog.__init__()
        • CLogLog.clean()
        • CLogLog.deriv()
        • CLogLog.initialize()
        • CLogLog.inverse()
        • CLogLog.tol
    • Link
      • Link
        • Link.__init__()
        • Link.deriv()
        • Link.initialize()
        • Link.inverse()
    • Log
      • Log
        • Log.__init__()
        • Log.clean()
        • Log.deriv()
        • Log.initialize()
        • Log.inverse()
        • Log.tol
    • Logit
      • Logit
        • Logit.__init__()
        • Logit.clean()
        • Logit.deriv()
        • Logit.initialize()
        • Logit.inverse()
        • Logit.tol
    • Power
      • Power
        • Power.__init__()
        • Power.deriv()
        • Power.initialize()
        • Power.inverse()
• algorithms.statistics.models.family.varfuncs
  • Module: algorithms.statistics.models.family.varfuncs
  • Classes
    • Binomial
      • Binomial
        • Binomial.__init__()
        • Binomial.clean()
        • Binomial.tol
    • Power
      • Power
        • Power.__init__()
    • VarianceFunction
      • VarianceFunction
        • VarianceFunction.__init__()
• algorithms.statistics.models.glm
  • Module: algorithms.statistics.models.glm
    • General linear models
  • Model
    • Model
      • Model.__init__()
      • Model.cont()
      • Model.deviance()
      • Model.estimate_scale()
      • Model.fit()
      • Model.has_intercept
      • Model.information()
      • Model.initialize()
      • Model.logL()
      • Model.niter
      • Model.predict()
      • Model.rank
      • Model.score()
      • Model.whiten()
• algorithms.statistics.models.model
  • Module: algorithms.statistics.models.model
  • Classes
    • FContrastResults
      • FContrastResults
        • FContrastResults.__init__()
    • LikelihoodModel
      • LikelihoodModel
        • LikelihoodModel.__init__()
        • LikelihoodModel.fit()
        • LikelihoodModel.information()
        • LikelihoodModel.initialize()
        • LikelihoodModel.logL()
        • LikelihoodModel.predict()
        • LikelihoodModel.score()
    • LikelihoodModelResults
      • LikelihoodModelResults
        • LikelihoodModelResults.__init__()
        • LikelihoodModelResults.AIC
        • LikelihoodModelResults.BIC
        • LikelihoodModelResults.Fcontrast()
        • LikelihoodModelResults.Tcontrast()
        • LikelihoodModelResults.conf_int()
        • LikelihoodModelResults.logL
        • LikelihoodModelResults.t()
        • LikelihoodModelResults.vcov()
    • Model
      • Model
        • Model.__init__()
        • Model.fit()
        • Model.initialize()
        • Model.predict()
    • TContrastResults
      • TContrastResults
        • TContrastResults.__init__()
• algorithms.statistics.models.nlsmodel
  • Module: algorithms.statistics.models.nlsmodel
  • NLSModel
    • NLSModel
      • NLSModel.__init__()
      • NLSModel.SSE()
      • NLSModel.fit()
      • NLSModel.getZ()
      • NLSModel.getomega()
      • NLSModel.initialize()
      • NLSModel.predict()
• algorithms.statistics.models.regression
  • Module: algorithms.statistics.models.regression
  • Classes
    • AREstimator
      • AREstimator
        • AREstimator.__init__()
    • ARModel
      • ARModel
        • ARModel.__init__()
        • ARModel.fit()
        • ARModel.has_intercept
        • ARModel.information()
        • ARModel.initialize()
        • ARModel.iterative_fit()
        • ARModel.logL()
        • ARModel.predict()
        • ARModel.rank
        • ARModel.score()
        • ARModel.whiten()
    • GLSModel
      • GLSModel
        • GLSModel.__init__()
        • GLSModel.fit()
        • GLSModel.has_intercept
        • GLSModel.information()
        • GLSModel.initialize()
        • GLSModel.logL()
        • GLSModel.predict()
        • GLSModel.rank
        • GLSModel.score()
        • GLSModel.whiten()
    • OLSModel
      • OLSModel
        • OLSModel.__init__()
        • OLSModel.fit()
        • OLSModel.has_intercept
        • OLSModel.information()
        • OLSModel.initialize()
        • OLSModel.logL()
        • OLSModel.predict()
        • OLSModel.rank
        • OLSModel.score()
        • OLSModel.whiten()
    • RegressionResults
      • RegressionResults
        • RegressionResults.__init__()
        • RegressionResults.AIC
        • RegressionResults.BIC
        • RegressionResults.F_overall
        • RegressionResults.Fcontrast()
        • RegressionResults.MSE
        • RegressionResults.MSR
        • RegressionResults.MST
        • RegressionResults.R2
        • RegressionResults.R2_adj
        • RegressionResults.SSE
        • RegressionResults.SSR
        • RegressionResults.SST
        • RegressionResults.Tcontrast()
        • RegressionResults.conf_int()
        • RegressionResults.logL
        • RegressionResults.norm_resid
        • RegressionResults.predicted
        • RegressionResults.resid
        • RegressionResults.t()
        • RegressionResults.vcov()
    • WLSModel
      • WLSModel
        • WLSModel.__init__()
        • WLSModel.fit()
        • WLSModel.has_intercept
        • WLSModel.information()
        • WLSModel.initialize()
        • WLSModel.logL()
        • WLSModel.predict()
        • WLSModel.rank
        • WLSModel.score()
        • WLSModel.whiten()
  • Functions
    • ar_bias_correct()
    • ar_bias_corrector()
    • isestimable()
    • yule_walker()
• algorithms.statistics.models.utils
  • Module: algorithms.statistics.models.utils
  • Class
  • StepFunction
    • StepFunction
      • StepFunction.__init__()
  • Functions
    • ECDF()
    • mad()
    • monotone_fn_inverter()
• algorithms.statistics.onesample
  • Module: algorithms.statistics.onesample
  • Functions
    • estimate_mean()
    • estimate_varatio()
• algorithms.statistics.rft
  • Module: algorithms.statistics.rft
  • Classes
    • ChiBarSquared
      • ChiBarSquared
        • ChiBarSquared.__init__()
        • ChiBarSquared.density()
        • ChiBarSquared.integ()
        • ChiBarSquared.pvalue()
        • ChiBarSquared.quasi()
    • ChiSquared
      • ChiSquared
        • ChiSquared.__init__()
        • ChiSquared.density()
        • ChiSquared.integ()
        • ChiSquared.pvalue()
        • ChiSquared.quasi()
    • ECcone
      • ECcone
        • ECcone.__init__()
        • ECcone.density()
        • ECcone.integ()
        • ECcone.pvalue()
        • ECcone.quasi()
    • ECquasi
      • ECquasi
        • ECquasi.__init__()
        • ECquasi.c
        • ECquasi.change_exponent()
        • ECquasi.coef
        • ECquasi.coefficients
        • ECquasi.coeffs
        • ECquasi.compatible()
        • ECquasi.denom_poly()
        • ECquasi.deriv()
        • ECquasi.integ()
        • ECquasi.o
        • ECquasi.order
        • ECquasi.r
        • ECquasi.roots
        • ECquasi.variable
    • FStat
      • FStat
        • FStat.__init__()
        • FStat.density()
        • FStat.integ()
        • FStat.pvalue()
        • FStat.quasi()
    • Hotelling
      • Hotelling
        • Hotelling.__init__()
        • Hotelling.density()
        • Hotelling.integ()
        • Hotelling.pvalue()
        • Hotelling.quasi()
    • IntrinsicVolumes
      • IntrinsicVolumes
        • IntrinsicVolumes.__init__()
    • MultilinearForm
      • MultilinearForm
        • MultilinearForm.__init__()
        • MultilinearForm.density()
        • MultilinearForm.integ()
        • MultilinearForm.pvalue()
        • MultilinearForm.quasi()
    • OneSidedF
      • OneSidedF
        • OneSidedF.__init__()
        • OneSidedF.density()
        • OneSidedF.integ()
        • OneSidedF.pvalue()
        • OneSidedF.quasi()
    • Roy
      • Roy
        • Roy.__init__()
        • Roy.density()
        • Roy.integ()
        • Roy.pvalue()
        • Roy.quasi()
    • TStat
      • TStat
        • TStat.__init__()
        • TStat.density()
        • TStat.integ()
        • TStat.pvalue()
        • TStat.quasi()
    • fnsum
      • fnsum
        • fnsum.__init__()
  • Functions
    • Q()
    • ball_search()
    • binomial()
    • mu_ball()
    • mu_sphere()
    • scale_space()
    • spherical_search()
    • volume2ball()
• algorithms.statistics.utils
  • Module: algorithms.statistics.utils
  • Functions
    • check_cast_bin8()
    • complex()
    • cube_with_strides_center()
    • decompose2d()
    • decompose3d()
    • join_complexes()
    • multiple_fast_inv()
    • multiple_mahalanobis()
    • test_EC2()
    • test_EC3()
    • z_score()
• algorithms.utils.fast_distance
  • Module: algorithms.utils.fast_distance
    • euclidean_distance()
• algorithms.utils.matrices
  • Module: algorithms.utils.matrices
  • Functions
    • full_rank()
    • matrix_rank()
    • pos_recipr()
    • recipr0()
• algorithms.utils.pca
  • Module: algorithms.utils.pca
  • Functions
    • pca()
    • pca_image()
• cli.diagnose
  • Module: cli.diagnose
    • main()
• cli.img3dto4d
  • Module: cli.img3dto4d
  • Functions
    • do_3d_to_4d()
    • main()
• cli.img4dto3d
  • Module: cli.img4dto3d
    • main()
• cli.realign4d
  • Module: cli.realign4d
    • main()
• cli.tsdiffana
  • Module: cli.tsdiffana
    • main()
• conftest
  • Module: conftest
  • Functions
    • add_np()
    • in_tmp_path()
    • mpl_imports()
• core.image.image
  • Module: core.image.image
  • Classes
    • Image
      • Image
        • Image.__init__()
        • Image.affine
        • Image.axes
        • Image.coordmap
        • Image.from_image()
        • Image.get_fdata()
        • Image.header
        • Image.metadata
        • Image.ndim
        • Image.reference
        • Image.renamed_axes()
        • Image.renamed_reference()
        • Image.reordered_axes()
        • Image.reordered_reference()
        • Image.shape
    • SliceMaker
      • SliceMaker
        • SliceMaker.__init__()
  • Functions
    • fromarray()
    • is_image()
    • iter_axis()
    • rollaxis()
    • rollimg()
    • subsample()
    • synchronized_order()
• core.image.image_list
  • Module: core.image.image_list
  • ImageList
    • ImageList
      • ImageList.__init__()
      • ImageList.from_image()
      • ImageList.get_list_data()
• core.image.image_spaces
  • Module: core.image.image_spaces
  • Functions
    • as_xyz_image()
    • is_xyz_affable()
    • make_xyz_image()
    • xyz_affine()
• core.reference.array_coords
  • Module: core.reference.array_coords
  • Classes
    • ArrayCoordMap
      • ArrayCoordMap
        • ArrayCoordMap.__init__()
        • ArrayCoordMap.from_shape()
        • ArrayCoordMap.transposed_values
        • ArrayCoordMap.values
    • Grid
      • Grid
        • Grid.__init__()
• core.reference.coordinate_map
  • Module: core.reference.coordinate_map
    • Common API
    • Operations on mappings (module level functions)
  • Classes
    • AffineTransform
      • AffineTransform
        • AffineTransform.__init__()
        • AffineTransform.affine
        • AffineTransform.from_params()
        • AffineTransform.from_start_step()
        • AffineTransform.function_domain
        • AffineTransform.function_range
        • AffineTransform.identity()
        • AffineTransform.inverse()
        • AffineTransform.ndims
        • AffineTransform.renamed_domain()
        • AffineTransform.renamed_range()
        • AffineTransform.reordered_domain()
        • AffineTransform.reordered_range()
        • AffineTransform.similar_to()
    • AxisError
      • AxisError
        • AxisError.__init__()
        • AxisError.add_note()
        • AxisError.args
        • AxisError.with_traceback()
    • CoordMapMaker
      • CoordMapMaker
        • CoordMapMaker.__init__()
        • CoordMapMaker.affine_maker
        • CoordMapMaker.generic_maker
        • CoordMapMaker.make_affine()
        • CoordMapMaker.make_cmap()
    • CoordMapMakerError
      • CoordMapMakerError
        • CoordMapMakerError.__init__()
        • CoordMapMakerError.add_note()
        • CoordMapMakerError.args
        • CoordMapMakerError.with_traceback()
    • CoordinateMap
      • CoordinateMap
        • CoordinateMap.__init__()
        • CoordinateMap.function
        • CoordinateMap.function_domain
        • CoordinateMap.function_range
        • CoordinateMap.inverse()
        • CoordinateMap.inverse_function
        • CoordinateMap.ndims
        • CoordinateMap.renamed_domain()
        • CoordinateMap.renamed_range()
        • CoordinateMap.reordered_domain()
        • CoordinateMap.reordered_range()
        • CoordinateMap.similar_to()
  • Functions
    • append_io_dim()
    • axmap()
    • compose()
    • drop_io_dim()
    • equivalent()
    • input_axis_index()
    • io_axis_indices()
    • orth_axes()
    • product()
    • renamed_domain()
    • renamed_range()
    • reordered_domain()
    • reordered_range()
    • shifted_domain_origin()
    • shifted_range_origin()
• core.reference.coordinate_system
  • Module: core.reference.coordinate_system
  • Classes
    • CoordSysMaker
      • CoordSysMaker
        • CoordSysMaker.__init__()
        • CoordSysMaker.coord_sys_klass
    • CoordSysMakerError
      • CoordSysMakerError
        • CoordSysMakerError.__init__()
        • CoordSysMakerError.add_note()
        • CoordSysMakerError.args
        • CoordSysMakerError.with_traceback()
    • CoordinateSystem
      • CoordinateSystem
        • CoordinateSystem.__init__()
        • CoordinateSystem.coord_dtype
        • CoordinateSystem.coord_names
        • CoordinateSystem.dtype
        • CoordinateSystem.index()
        • CoordinateSystem.name
        • CoordinateSystem.ndim
        • CoordinateSystem.similar_to()
    • CoordinateSystemError
      • CoordinateSystemError
        • CoordinateSystemError.__init__()
        • CoordinateSystemError.add_note()
        • CoordinateSystemError.args
        • CoordinateSystemError.with_traceback()
  • Functions
    • is_coordsys()
    • is_coordsys_maker()
    • product()
    • safe_dtype()
• core.reference.slices
  • Module: core.reference.slices
  • Functions
    • bounding_box()
    • xslice()
    • yslice()
    • zslice()
• core.reference.spaces
  • Module: core.reference.spaces
  • Classes
    • AffineError
      • AffineError
        • AffineError.__init__()
        • AffineError.add_note()
        • AffineError.args
        • AffineError.with_traceback()
    • AxesError
      • AxesError
        • AxesError.__init__()
        • AxesError.add_note()
        • AxesError.args
        • AxesError.with_traceback()
    • SpaceError
      • SpaceError
        • SpaceError.__init__()
        • SpaceError.add_note()
        • SpaceError.args
        • SpaceError.with_traceback()
    • SpaceTypeError
      • SpaceTypeError
        • SpaceTypeError.__init__()
        • SpaceTypeError.add_note()
        • SpaceTypeError.args
        • SpaceTypeError.with_traceback()
    • XYZSpace
      • XYZSpace
        • XYZSpace.__init__()
        • XYZSpace.as_map()
        • XYZSpace.as_tuple()
        • XYZSpace.register_to()
        • XYZSpace.to_coordsys_maker()
        • XYZSpace.x
        • XYZSpace.x_suffix
        • XYZSpace.y
        • XYZSpace.y_suffix
        • XYZSpace.z
        • XYZSpace.z_suffix
  • Functions
    • get_world_cs()
    • is_xyz_affable()
    • is_xyz_space()
    • known_space()
    • xyz_affine()
    • xyz_order()
• core.utils.generators
  • Module: core.utils.generators
  • Functions
    • data_generator()
    • f_generator()
    • matrix_generator()
    • parcels()
    • shape_generator()
    • slice_generator()
    • slice_parcels()
    • write_data()
• interfaces.matlab
  • Module: interfaces.matlab
  • Functions
    • mlab_tempfile()
    • run_matlab()
    • run_matlab_script()
• interfaces.spm
  • Module: interfaces.spm
  • Class
  • SpmInfo
    • SpmInfo
      • SpmInfo.__init__()
      • SpmInfo.spm_path
      • SpmInfo.spm_ver
  • Functions
    • fltcols()
    • fname_presuffix()
    • fnames_presuffix()
    • make_job()
    • run_jobdef()
    • scans_for_fname()
    • scans_for_fnames()
• io.files
  • Module: io.files
    • Examples
  • Functions
    • as_image()
    • load()
    • save()
• io.nibcompat
  • Module: io.nibcompat
  • Functions
    • get_affine()
    • get_dataobj()
    • get_header()
    • get_unscaled_data()
• io.nifti_ref
  • Module: io.nifti_ref
    • Background
      • NIFTI input coordinate system
      • NIFTI output coordinate system
      • NIFTI input / output mapping
      • Time-like axes
      • Does this NIFTI image have a time-like axis?
    • What we do about all this
  • Class
  • NiftiError
    • NiftiError
      • NiftiError.__init__()
      • NiftiError.add_note()
      • NiftiError.args
      • NiftiError.with_traceback()
  • Functions
    • nifti2nipy()
    • nipy2nifti()
• labs.datasets.converters
  • Module: labs.datasets.converters
  • Functions
    • as_volume_img()
    • save()
• labs.datasets.transforms.affine_transform
  • Module: labs.datasets.transforms.affine_transform
  • AffineTransform
    • AffineTransform
      • AffineTransform.__init__()
      • AffineTransform.affine
      • AffineTransform.composed_with()
      • AffineTransform.get_inverse()
      • AffineTransform.input_space
      • AffineTransform.inverse_mapping()
      • AffineTransform.mapping()
      • AffineTransform.output_space
• labs.datasets.transforms.affine_utils
  • Module: labs.datasets.transforms.affine_utils
  • Functions
    • apply_affine()
    • from_matrix_vector()
    • get_bounds()
    • to_matrix_vector()
• labs.datasets.transforms.transform
  • Module: labs.datasets.transforms.transform
  • Classes
    • CompositionError
      • CompositionError
        • CompositionError.__init__()
        • CompositionError.add_note()
        • CompositionError.args
        • CompositionError.with_traceback()
    • Transform
      • Transform
        • Transform.__init__()
        • Transform.composed_with()
        • Transform.get_inverse()
        • Transform.input_space
        • Transform.inverse_mapping
        • Transform.mapping
        • Transform.output_space
• labs.datasets.volumes.volume_data
  • Module: labs.datasets.volumes.volume_data
  • VolumeData
    • VolumeData
      • VolumeData.__init__()
      • VolumeData.as_volume_img()
      • VolumeData.composed_with_transform()
      • VolumeData.get_fdata()
      • VolumeData.get_transform()
      • VolumeData.interpolation
      • VolumeData.like_from_data()
      • VolumeData.metadata
      • VolumeData.resampled_to_img()
      • VolumeData.values_in_world()
      • VolumeData.world_space
• labs.datasets.volumes.volume_field
  • Module: labs.datasets.volumes.volume_field
  • VolumeField
    • VolumeField
      • VolumeField.__init__()
      • VolumeField.as_volume_img()
      • VolumeField.composed_with_transform()
      • VolumeField.get_transform()
      • VolumeField.metadata
      • VolumeField.resampled_to_img()
      • VolumeField.values_in_world()
      • VolumeField.world_space
• labs.datasets.volumes.volume_grid
  • Module: labs.datasets.volumes.volume_grid
  • VolumeGrid
    • VolumeGrid
      • VolumeGrid.__init__()
      • VolumeGrid.as_volume_img()
      • VolumeGrid.composed_with_transform()
      • VolumeGrid.get_fdata()
      • VolumeGrid.get_transform()
      • VolumeGrid.get_world_coords()
      • VolumeGrid.interpolation
      • VolumeGrid.like_from_data()
      • VolumeGrid.metadata
      • VolumeGrid.resampled_to_img()
      • VolumeGrid.values_in_world()
      • VolumeGrid.world_space
• labs.datasets.volumes.volume_img
  • Module: labs.datasets.volumes.volume_img
  • VolumeImg
    • VolumeImg
      • VolumeImg.__init__()
      • VolumeImg.affine
      • VolumeImg.as_volume_img()
      • VolumeImg.composed_with_transform()
      • VolumeImg.get_affine()
      • VolumeImg.get_fdata()
      • VolumeImg.get_transform()
      • VolumeImg.get_world_coords()
      • VolumeImg.interpolation
      • VolumeImg.like_from_data()
      • VolumeImg.metadata
      • VolumeImg.resampled_to_img()
      • VolumeImg.values_in_world()
      • VolumeImg.world_space
      • VolumeImg.xyz_ordered()
• labs.glm.glm
  • Module: labs.glm.glm
  • Classes
    • contrast
      • contrast
        • contrast.__init__()
        • contrast.pvalue()
        • contrast.stat()
        • contrast.summary()
        • contrast.zscore()
    • glm
      • glm
        • glm.__init__()
        • glm.contrast()
        • glm.fit()
        • glm.save()
  • Functions
    • load()
    • ols()
• labs.group.permutation_test
  • Module: labs.group.permutation_test
  • Classes
    • permutation_test
      • permutation_test
        • permutation_test.__init__()
        • permutation_test.calibrate()
        • permutation_test.height_threshold()
        • permutation_test.pvalue()
        • permutation_test.zscore()
    • permutation_test_onesample
      • permutation_test_onesample
        • permutation_test_onesample.__init__()
        • permutation_test_onesample.calibrate()
        • permutation_test_onesample.height_threshold()
        • permutation_test_onesample.pvalue()
        • permutation_test_onesample.zscore()
    • permutation_test_onesample_graph
      • permutation_test_onesample_graph
        • permutation_test_onesample_graph.__init__()
        • permutation_test_onesample_graph.calibrate()
        • permutation_test_onesample_graph.height_threshold()
        • permutation_test_onesample_graph.pvalue()
        • permutation_test_onesample_graph.zscore()
    • permutation_test_twosample
      • permutation_test_twosample
        • permutation_test_twosample.__init__()
        • permutation_test_twosample.calibrate()
        • permutation_test_twosample.height_threshold()
        • permutation_test_twosample.pvalue()
        • permutation_test_twosample.zscore()
  • Functions
    • compute_cluster_stats()
    • compute_region_stat()
    • extract_clusters_from_diam()
    • extract_clusters_from_graph()
    • extract_clusters_from_thresh()
    • max_dist()
    • onesample_stat()
    • peak_XYZ()
    • sorted_values()
    • twosample_stat()
• labs.mask
  • Module: labs.mask
  • Functions
    • compute_mask()
    • compute_mask_files()
    • compute_mask_sessions()
    • intersect_masks()
    • largest_cc()
    • series_from_mask()
    • threshold_connect_components()
• labs.spatial_models.bayesian_structural_analysis
  • Module: labs.spatial_models.bayesian_structural_analysis
    • compute_landmarks()
• labs.spatial_models.bsa_io
  • Module: labs.spatial_models.bsa_io
    • make_bsa_image()
• labs.spatial_models.discrete_domain
  • Module: labs.spatial_models.discrete_domain
  • Classes
    • DiscreteDomain
      • DiscreteDomain
        • DiscreteDomain.__init__()
        • DiscreteDomain.connected_components()
        • DiscreteDomain.copy()
        • DiscreteDomain.get_coord()
        • DiscreteDomain.get_feature()
        • DiscreteDomain.get_volume()
        • DiscreteDomain.integrate()
        • DiscreteDomain.mask()
        • DiscreteDomain.representative_feature()
        • DiscreteDomain.set_feature()
    • MeshDomain
      • MeshDomain
        • MeshDomain.__init__()
        • MeshDomain.area()
        • MeshDomain.topology()
    • NDGridDomain
      • NDGridDomain
        • NDGridDomain.__init__()
        • NDGridDomain.connected_components()
        • NDGridDomain.copy()
        • NDGridDomain.get_coord()
        • NDGridDomain.get_feature()
        • NDGridDomain.get_volume()
        • NDGridDomain.integrate()
        • NDGridDomain.make_feature_from_image()
        • NDGridDomain.mask()
        • NDGridDomain.representative_feature()
        • NDGridDomain.set_feature()
        • NDGridDomain.to_image()
    • StructuredDomain
      • StructuredDomain
        • StructuredDomain.__init__()
        • StructuredDomain.connected_components()
        • StructuredDomain.copy()
        • StructuredDomain.get_coord()
        • StructuredDomain.get_feature()
        • StructuredDomain.get_volume()
        • StructuredDomain.integrate()
        • StructuredDomain.mask()
        • StructuredDomain.representative_feature()
        • StructuredDomain.set_feature()
  • Functions
    • array_affine_coord()
    • domain_from_binary_array()
    • domain_from_image()
    • domain_from_mesh()
    • grid_domain_from_binary_array()
    • grid_domain_from_image()
    • grid_domain_from_shape()
    • idx_affine_coord()
    • reduce_coo_matrix()
    • smatrix_from_3d_array()
    • smatrix_from_3d_idx()
    • smatrix_from_nd_array()
    • smatrix_from_nd_idx()
• labs.spatial_models.hierarchical_parcellation
  • Module: labs.spatial_models.hierarchical_parcellation
  • Functions
    • hparcel()
    • perm_prfx()
• labs.spatial_models.hroi
  • Module: labs.spatial_models.hroi
  • Class
  • HierarchicalROI
    • HierarchicalROI
      • HierarchicalROI.__init__()
      • HierarchicalROI.copy()
      • HierarchicalROI.feature_to_voxel_map()
      • HierarchicalROI.get_coord()
      • HierarchicalROI.get_feature()
      • HierarchicalROI.get_id()
      • HierarchicalROI.get_leaves_id()
      • HierarchicalROI.get_local_volume()
      • HierarchicalROI.get_parents()
      • HierarchicalROI.get_roi_feature()
      • HierarchicalROI.get_size()
      • HierarchicalROI.get_volume()
      • HierarchicalROI.integrate()
      • HierarchicalROI.make_forest()
      • HierarchicalROI.make_graph()
      • HierarchicalROI.merge_ascending()
      • HierarchicalROI.merge_descending()
      • HierarchicalROI.plot_feature()
      • HierarchicalROI.recompute_labels()
      • HierarchicalROI.reduce_to_leaves()
      • HierarchicalROI.remove_feature()
      • HierarchicalROI.remove_roi_feature()
      • HierarchicalROI.representative_feature()
      • HierarchicalROI.select_id()
      • HierarchicalROI.select_roi()
      • HierarchicalROI.set_feature()
      • HierarchicalROI.set_roi_feature()
      • HierarchicalROI.to_image()
  • Functions
    • HROI_as_discrete_domain_blobs()
    • HROI_from_watershed()
    • hroi_agglomeration()
    • make_hroi_from_subdomain()
• labs.spatial_models.mroi
  • Module: labs.spatial_models.mroi
  • Class
  • SubDomains
    • SubDomains
      • SubDomains.__init__()
      • SubDomains.copy()
      • SubDomains.feature_to_voxel_map()
      • SubDomains.get_coord()
      • SubDomains.get_feature()
      • SubDomains.get_id()
      • SubDomains.get_local_volume()
      • SubDomains.get_roi_feature()
      • SubDomains.get_size()
      • SubDomains.get_volume()
      • SubDomains.integrate()
      • SubDomains.plot_feature()
      • SubDomains.recompute_labels()
      • SubDomains.remove_feature()
      • SubDomains.remove_roi_feature()
      • SubDomains.representative_feature()
      • SubDomains.select_id()
      • SubDomains.select_roi()
      • SubDomains.set_feature()
      • SubDomains.set_roi_feature()
      • SubDomains.to_image()
  • Functions
    • subdomain_from_array()
    • subdomain_from_balls()
    • subdomain_from_image()
    • subdomain_from_position_and_image()
• labs.spatial_models.parcel_io
  • Module: labs.spatial_models.parcel_io
  • Functions
    • fixed_parcellation()
    • mask_parcellation()
    • parcel_input()
    • parcellation_based_analysis()
    • write_parcellation_images()
• labs.spatial_models.parcellation
  • Module: labs.spatial_models.parcellation
  • MultiSubjectParcellation
    • MultiSubjectParcellation
      • MultiSubjectParcellation.__init__()
      • MultiSubjectParcellation.check()
      • MultiSubjectParcellation.copy()
      • MultiSubjectParcellation.get_feature()
      • MultiSubjectParcellation.make_feature()
      • MultiSubjectParcellation.population()
      • MultiSubjectParcellation.set_feature()
      • MultiSubjectParcellation.set_individual_labels()
      • MultiSubjectParcellation.set_template_labels()
• labs.spatial_models.structural_bfls
  • Module: labs.spatial_models.structural_bfls
  • LandmarkRegions
    • LandmarkRegions
      • LandmarkRegions.__init__()
      • LandmarkRegions.centers()
      • LandmarkRegions.kernel_density()
      • LandmarkRegions.map_label()
      • LandmarkRegions.roi_prevalence()
      • LandmarkRegions.show()
    • build_landmarks()
• labs.statistical_mapping
  • Module: labs.statistical_mapping
  • Class
  • LinearModel
    • LinearModel
      • LinearModel.__init__()
      • LinearModel.contrast()
      • LinearModel.def_model
      • LinearModel.def_niter
      • LinearModel.dump()
  • Functions
    • bonferroni()
    • cluster_stats()
    • get_3d_peaks()
    • linear_model_fit()
    • onesample_test()
    • prepare_arrays()
    • simulated_pvalue()
    • twosample_test()
• labs.utils.reproducibility_measures
  • Module: labs.utils.reproducibility_measures
  • Functions
    • bootstrap_group()
    • cluster_reproducibility()
    • cluster_threshold()
    • conjunction()
    • coord_bsa()
    • draw_samples()
    • fttest()
    • get_cluster_position_from_thresholded_map()
    • get_peak_position_from_thresholded_map()
    • group_reproducibility_metrics()
    • histo_repro()
    • map_reproducibility()
    • mfx_ttest()
    • peak_reproducibility()
    • split_group()
    • statistics_from_position()
    • ttest()
    • voxel_reproducibility()
    • voxel_thresholded_ttest()
• labs.utils.simul_multisubject_fmri_dataset
  • Module: labs.utils.simul_multisubject_fmri_dataset
  • Functions
    • surrogate_2d_dataset()
    • surrogate_3d_dataset()
    • surrogate_4d_dataset()
• labs.utils.zscore
  • Module: labs.utils.zscore
    • zscore()
• labs.viz_tools.activation_maps
  • Module: labs.viz_tools.activation_maps
  • Functions
    • demo_plot_map()
    • plot_anat()
    • plot_map()
• labs.viz_tools.anat_cache
  • Module: labs.viz_tools.anat_cache
    • find_mni_template()
• labs.viz_tools.cm
  • Module: labs.viz_tools.cm
  • Functions
    • alpha_cmap()
    • dim_cmap()
    • replace_inside()
• labs.viz_tools.coord_tools
  • Module: labs.viz_tools.coord_tools
  • Functions
    • coord_transform()
    • find_cut_coords()
    • find_maxsep_cut_coords()
    • get_mask_bounds()
• labs.viz_tools.maps_3d
  • Module: labs.viz_tools.maps_3d
  • Functions
    • affine_img_src()
    • autocrop_img()
    • demo_plot_map_3d()
    • m2screenshot()
    • plot_anat_3d()
    • plot_map_3d()
• labs.viz_tools.slicers
  • Module: labs.viz_tools.slicers
  • Classes
    • BaseSlicer
      • BaseSlicer
        • BaseSlicer.__init__()
        • BaseSlicer.annotate()
        • BaseSlicer.contour_map()
        • BaseSlicer.edge_map()
        • BaseSlicer.find_cut_coords()
        • BaseSlicer.init_with_figure()
        • BaseSlicer.plot_map()
        • BaseSlicer.title()
    • BaseStackedSlicer
      • BaseStackedSlicer
        • BaseStackedSlicer.__init__()
        • BaseStackedSlicer.annotate()
        • BaseStackedSlicer.contour_map()
        • BaseStackedSlicer.draw_cross()
        • BaseStackedSlicer.edge_map()
        • BaseStackedSlicer.find_cut_coords()
        • BaseStackedSlicer.init_with_figure()
        • BaseStackedSlicer.plot_map()
        • BaseStackedSlicer.title()
    • CutAxes
      • CutAxes
        • CutAxes.__init__()
        • CutAxes.do_cut()
        • CutAxes.draw_cut()
        • CutAxes.draw_left_right()
        • CutAxes.draw_position()
        • CutAxes.get_object_bounds()
    • OrthoSlicer
      • OrthoSlicer
        • OrthoSlicer.__init__()
        • OrthoSlicer.annotate()
        • OrthoSlicer.contour_map()
        • OrthoSlicer.draw_cross()
        • OrthoSlicer.edge_map()
        • OrthoSlicer.find_cut_coords()
        • OrthoSlicer.init_with_figure()
        • OrthoSlicer.plot_map()
        • OrthoSlicer.title()
    • XSlicer
      • XSlicer
        • XSlicer.__init__()
        • XSlicer.annotate()
        • XSlicer.contour_map()
        • XSlicer.draw_cross()
        • XSlicer.edge_map()
        • XSlicer.find_cut_coords()
        • XSlicer.init_with_figure()
        • XSlicer.plot_map()
        • XSlicer.title()
    • YSlicer
      • YSlicer
        • YSlicer.__init__()
        • YSlicer.annotate()
        • YSlicer.contour_map()
        • YSlicer.draw_cross()
        • YSlicer.edge_map()
        • YSlicer.find_cut_coords()
        • YSlicer.init_with_figure()
        • YSlicer.plot_map()
        • YSlicer.title()
    • ZSlicer
      • ZSlicer
        • ZSlicer.__init__()
        • ZSlicer.annotate()
        • ZSlicer.contour_map()
        • ZSlicer.draw_cross()
        • ZSlicer.edge_map()
        • ZSlicer.find_cut_coords()
        • ZSlicer.init_with_figure()
        • ZSlicer.plot_map()
        • ZSlicer.title()
  • Function
    • demo_ortho_slicer()
• labs.viz_tools.test.test_activation_maps
  • Module: labs.viz_tools.test.test_activation_maps
  • Functions
    • test_anat_cache()
    • test_demo_plot_map()
    • test_plot_anat()
    • test_plot_anat_kwargs()
    • test_plot_map_empty()
    • test_plot_map_with_auto_cut_coords()
• labs.viz_tools.test.test_cm
  • Module: labs.viz_tools.test.test_cm
  • Functions
    • test_dim_cmap()
    • test_replace_inside()
• labs.viz_tools.test.test_coord_tools
  • Module: labs.viz_tools.test.test_coord_tools
  • Functions
    • test_coord_transform_trivial()
    • test_find_cut_coords()
    • test_find_maxsep_cut_coords()
• labs.viz_tools.test.test_edge_detect
  • Module: labs.viz_tools.test.test_edge_detect
  • Functions
    • test_edge_detect()
    • test_fast_abs_percentile()
• labs.viz_tools.test.test_slicers
  • Module: labs.viz_tools.test.test_slicers
    • test_demo_ortho_slicer()
• modalities.fmri.design
  • Module: modalities.fmri.design
  • Functions
    • block_amplitudes()
    • block_design()
    • event_design()
    • fourier_basis()
    • natural_spline()
    • openfmri2nipy()
    • stack2designs()
    • stack_contrasts()
    • stack_designs()
• modalities.fmri.design_matrix
  • Module: modalities.fmri.design_matrix
  • Class
  • DesignMatrix
    • DesignMatrix
      • DesignMatrix.__init__()
      • DesignMatrix.show()
      • DesignMatrix.show_contrast()
      • DesignMatrix.write_csv()
  • Functions
    • dmtx_from_csv()
    • dmtx_light()
    • make_dmtx()
• modalities.fmri.experimental_paradigm
  • Module: modalities.fmri.experimental_paradigm
    • Notes
  • Classes
    • BlockParadigm
      • BlockParadigm
        • BlockParadigm.__init__()
        • BlockParadigm.write_to_csv()
    • EventRelatedParadigm
      • EventRelatedParadigm
        • EventRelatedParadigm.__init__()
        • EventRelatedParadigm.write_to_csv()
    • Paradigm
      • Paradigm
        • Paradigm.__init__()
        • Paradigm.write_to_csv()
  • Function
    • load_paradigm_from_csv_file()
• modalities.fmri.fmri
  • Module: modalities.fmri.fmri
  • FmriImageList
    • FmriImageList
      • FmriImageList.__init__()
      • FmriImageList.from_image()
      • FmriImageList.get_list_data()
    • axis0_generator()
• modalities.fmri.fmristat.hrf
  • Module: modalities.fmri.fmristat.hrf
    • References
  • Functions
    • spectral_decomposition()
    • taylor_approx()
• modalities.fmri.fmristat.invert
  • Module: modalities.fmri.fmristat.invert
    • invertR()
• modalities.fmri.fmristat.model
  • Module: modalities.fmri.fmristat.model
  • Classes
    • AR1
      • AR1
        • AR1.__init__()
        • AR1.execute()
    • ModelOutputImage
      • ModelOutputImage
        • ModelOutputImage.__init__()
        • ModelOutputImage.save()
    • OLS
      • OLS
        • OLS.__init__()
        • OLS.execute()
  • Functions
    • estimateAR()
    • generate_output()
    • model_generator()
    • output_AR1()
    • output_F()
    • output_T()
    • output_resid()
    • results_generator()
• modalities.fmri.fmristat.outputters
  • Module: modalities.fmri.fmristat.outputters
  • Classes
    • RegressionOutput
      • RegressionOutput
        • RegressionOutput.__init__()
    • RegressionOutputList
      • RegressionOutputList
        • RegressionOutputList.__init__()
    • TOutput
      • TOutput
        • TOutput.__init__()
  • Functions
    • output_AR1()
    • output_F()
    • output_T()
    • output_resid()
• modalities.fmri.glm
  • Module: modalities.fmri.glm
    • Examples
  • Classes
    • Contrast
      • Contrast
        • Contrast.__init__()
        • Contrast.p_value()
        • Contrast.stat()
        • Contrast.z_score()
    • FMRILinearModel
      • FMRILinearModel
        • FMRILinearModel.__init__()
        • FMRILinearModel.contrast()
        • FMRILinearModel.fit()
    • GeneralLinearModel
      • GeneralLinearModel
        • GeneralLinearModel.__init__()
        • GeneralLinearModel.contrast()
        • GeneralLinearModel.fit()
        • GeneralLinearModel.get_beta()
        • GeneralLinearModel.get_logL()
        • GeneralLinearModel.get_mse()
  • Function
    • data_scaling()
• modalities.fmri.hemodynamic_models
  • Module: modalities.fmri.hemodynamic_models
  • Functions
    • compute_regressor()
    • glover_hrf()
    • glover_time_derivative()
    • spm_dispersion_derivative()
    • spm_hrf()
    • spm_time_derivative()
• modalities.fmri.hrf
  • Module: modalities.fmri.hrf
  • Functions
    • ddspmt()
    • dspmt()
    • gamma_expr()
    • gamma_params()
    • spm_hrf_compat()
    • spmt()
• modalities.fmri.realfuncs
  • Module: modalities.fmri.realfuncs
  • Functions
    • dct_ii_basis()
    • dct_ii_cut_basis()
• modalities.fmri.spm.correlation
  • Module: modalities.fmri.spm.correlation
  • Functions
    • ARcomponents()
    • ARcovariance()
• modalities.fmri.spm.model
  • Module: modalities.fmri.spm.model
  • Class
  • SecondStage
    • SecondStage
      • SecondStage.__init__()
      • SecondStage.execute()
  • Functions
    • Fmask()
    • estimate_pooled_covariance()
• modalities.fmri.spm.reml
  • Module: modalities.fmri.spm.reml
  • Functions
    • orth()
    • reml()
• modalities.fmri.spm.trace
  • Module: modalities.fmri.spm.trace
    • trRV()
• modalities.fmri.utils
  • Module: modalities.fmri.utils
  • Classes
    • Interp1dNumeric
      • Interp1dNumeric
        • Interp1dNumeric.__init__()
        • Interp1dNumeric.dtype
        • Interp1dNumeric.fill_value
    • TimeConvolver
      • TimeConvolver
        • TimeConvolver.__init__()
        • TimeConvolver.convolve()
  • Functions
    • blocks()
    • convolve_functions()
    • define()
    • events()
    • fourier_basis()
    • interp()
    • lambdify_t()
    • linear_interp()
    • step_function()
• pkg_info
  • Module: pkg_info
  • Functions
    • get_pkg_info()
    • pkg_commit_hash()
• testing.decorators
  • Module: testing.decorators
  • Functions
    • if_datasource()
    • if_example_data()
    • if_templates()
    • make_label_dec()
    • needs_mpl_agg()
    • needs_review()
• utils
  • Module: utils
  • VisibleDeprecationWarning
    • VisibleDeprecationWarning
      • VisibleDeprecationWarning.__init__()
      • VisibleDeprecationWarning.add_note()
      • VisibleDeprecationWarning.args
      • VisibleDeprecationWarning.with_traceback()
    • deprecate_with_doc()
• utils.arrays
  • Module: utils.arrays
    • strides_from()
• utils.perlpie
  • Module: utils.perlpie
    • Parameters
    • Requires
    • Examples
  • Functions
    • check_deps()
    • main()
    • perl_dash_pie()
    • print_extended_help()
• utils.utilities
  • Module: utils.utilities
  • Functions
    • is_iterable()
    • is_numlike()
    • seq_prod()