=============================================== Reference documentation: all nilearn functions =============================================== This is the class and function reference of nilearn. Please refer to the :ref:`user guide ` for more information and usage examples. .. contents:: **List of modules** :local: .. _connectome_ref: :mod:`nilearn.connectome`: Functional Connectivity ==================================================== .. automodule:: nilearn.connectome :no-members: :no-inherited-members: **Classes**: .. currentmodule:: nilearn.connectome .. autosummary:: :toctree: generated/ :template: class.rst ConnectivityMeasure GroupSparseCovariance GroupSparseCovarianceCV **Functions**: .. currentmodule:: nilearn.connectome .. autosummary:: :toctree: generated/ :template: function.rst sym_matrix_to_vec vec_to_sym_matrix group_sparse_covariance cov_to_corr prec_to_partial .. _datasets_ref: :mod:`nilearn.datasets`: Automatic Dataset Fetching =================================================== .. automodule:: nilearn.datasets :no-members: :no-inherited-members: **User guide:** See the :ref:`datasets` section for further details. Templates --------- **Functions**: .. currentmodule:: nilearn.datasets .. autosummary:: :toctree: generated/ :template: function.rst fetch_icbm152_2009 fetch_icbm152_brain_gm_mask fetch_surf_fsaverage load_mni152_brain_mask load_mni152_gm_mask load_mni152_gm_template load_mni152_template load_mni152_wm_mask load_mni152_wm_template Atlases ------- **Functions**: .. currentmodule:: nilearn.datasets .. autosummary:: :toctree: generated/ :template: function.rst fetch_atlas_aal fetch_atlas_allen_2011 fetch_atlas_basc_multiscale_2015 fetch_atlas_craddock_2012 fetch_atlas_destrieux_2009 fetch_atlas_difumo fetch_atlas_harvard_oxford fetch_atlas_juelich fetch_atlas_msdl fetch_atlas_pauli_2017 fetch_atlas_schaefer_2018 fetch_atlas_smith_2009 fetch_atlas_surf_destrieux fetch_atlas_talairach fetch_atlas_yeo_2011 fetch_coords_dosenbach_2010 fetch_coords_power_2011 fetch_coords_seitzman_2018 Preprocessed datasets --------------------- **Functions**: .. currentmodule:: nilearn.datasets .. autosummary:: :toctree: generated/ :template: function.rst fetch_abide_pcp fetch_adhd fetch_bids_langloc_dataset fetch_development_fmri fetch_fiac_first_level fetch_haxby fetch_language_localizer_demo_dataset fetch_localizer_first_level fetch_miyawaki2008 fetch_openneuro_dataset_index fetch_spm_auditory fetch_spm_multimodal_fmri fetch_surf_nki_enhanced Statistical maps/derivatives ---------------------------- **Functions**: .. currentmodule:: nilearn.datasets .. autosummary:: :toctree: generated/ :template: function.rst fetch_localizer_button_task fetch_localizer_calculation_task fetch_localizer_contrasts fetch_megatrawls_netmats fetch_mixed_gambles fetch_oasis_vbm fetch_neurovault_auditory_computation_task fetch_neurovault_motor_task General functions ----------------- **Functions**: .. currentmodule:: nilearn.datasets .. autosummary:: :toctree: generated/ :template: function.rst fetch_neurovault fetch_neurovault_ids fetch_openneuro_dataset get_data_dirs patch_openneuro_dataset select_from_index .. _decoding_ref: :mod:`nilearn.decoding`: Decoding ================================= .. automodule:: nilearn.decoding :no-members: :no-inherited-members: **Classes**: .. currentmodule:: nilearn.decoding .. autosummary:: :toctree: generated/ :template: class.rst Decoder DecoderRegressor FREMClassifier FREMRegressor SpaceNetClassifier SpaceNetRegressor SearchLight .. _decomposition_ref: :mod:`nilearn.decomposition`: Multivariate Decompositions ========================================================= .. automodule:: nilearn.decomposition :no-members: :no-inherited-members: **Classes**: .. currentmodule:: nilearn.decomposition .. autosummary:: :toctree: generated/ :template: class.rst CanICA DictLearning .. _image_ref: :mod:`nilearn.image`: Image Processing and Resampling Utilities =============================================================== .. automodule:: nilearn.image :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.image .. autosummary:: :toctree: generated/ :template: function.rst binarize_img clean_img concat_imgs coord_transform copy_img crop_img get_data high_variance_confounds index_img iter_img largest_connected_component_img load_img math_img mean_img new_img_like resample_img resample_to_img reorder_img smooth_img swap_img_hemispheres threshold_img .. _interfaces_ref: :mod:`nilearn.interfaces`: Loading components from interfaces ============================================================= .. automodule:: nilearn.interfaces :no-members: :no-inherited-members: :mod:`nilearn.interfaces.bids` ---------------------------------- .. automodule:: nilearn.interfaces.bids :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.interfaces.bids .. autosummary:: :toctree: generated/ :template: function.rst get_bids_files parse_bids_filename :mod:`nilearn.interfaces.fmriprep` ---------------------------------- .. automodule:: nilearn.interfaces.fmriprep :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.interfaces.fmriprep .. autosummary:: :toctree: generated/ :template: function.rst load_confounds load_confounds_strategy :mod:`nilearn.interfaces.fsl` ---------------------------------- .. automodule:: nilearn.interfaces.fsl :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.interfaces.fsl .. autosummary:: :toctree: generated/ :template: function.rst get_design_from_fslmat .. _maskers_ref: :mod:`nilearn.maskers`: Extracting Signals from Brain Images ============================================================ .. automodule:: nilearn.maskers :no-members: :no-inherited-members: **User guide:** See the :ref:`nifti_masker` section for further details. **Classes**: .. currentmodule:: nilearn.maskers .. autosummary:: :toctree: generated/ :template: class.rst BaseMasker NiftiMasker MultiNiftiMasker NiftiLabelsMasker NiftiMapsMasker NiftiSpheresMasker .. _masking_ref: :mod:`nilearn.masking`: Data Masking Utilities ============================================== .. automodule:: nilearn.masking :no-members: :no-inherited-members: **User guide:** See the :ref:`masking` section for further details. **Functions**: .. currentmodule:: nilearn.masking .. autosummary:: :toctree: generated/ :template: function.rst compute_epi_mask compute_multi_epi_mask compute_brain_mask compute_multi_brain_mask compute_background_mask compute_multi_background_mask intersect_masks apply_mask unmask :mod:`nilearn.regions`: Operating on Regions ============================================ .. automodule:: nilearn.regions :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.regions .. autosummary:: :toctree: generated/ :template: function.rst connected_regions connected_label_regions img_to_signals_labels signals_to_img_labels img_to_signals_maps signals_to_img_maps **Classes**: .. currentmodule:: nilearn.regions .. autosummary:: :toctree: generated/ :template: class.rst RegionExtractor Parcellations ReNA HierarchicalKMeans :mod:`nilearn.mass_univariate`: Mass-Univariate Analysis ========================================================= .. automodule:: nilearn.mass_univariate :no-members: :no-inherited-members: .. No relevant user manual section yet. **Functions**: .. currentmodule:: nilearn.mass_univariate .. autosummary:: :toctree: generated/ :template: function.rst permuted_ols .. _plotting_ref: :mod:`nilearn.plotting`: Plotting Brain Data ================================================ .. automodule:: nilearn.plotting :no-members: :no-inherited-members: .. No relevant user manual section yet. **Functions**: .. currentmodule:: nilearn.plotting .. autosummary:: :toctree: generated/ :template: function.rst find_cut_slices find_xyz_cut_coords find_parcellation_cut_coords find_probabilistic_atlas_cut_coords plot_anat plot_img plot_epi plot_matrix plot_roi plot_stat_map plot_glass_brain plot_connectome plot_markers plot_prob_atlas plot_carpet plot_surf plot_surf_roi plot_surf_contours plot_surf_stat_map plot_img_on_surf plot_img_comparison plot_design_matrix plot_event plot_contrast_matrix view_surf view_img_on_surf view_connectome view_markers view_img show :mod:`nilearn.plotting.displays`: Interacting with figures ---------------------------------------------------------- .. automodule:: nilearn.plotting.displays :no-members: :no-inherited-members: .. No relevant user manual section yet. **Functions**: .. currentmodule:: nilearn.plotting.displays .. autosummary:: :toctree: generated/ :template: function.rst get_projector get_slicer **Classes**: .. currentmodule:: nilearn.plotting.displays .. autosummary:: :toctree: generated/ :template: class.rst OrthoProjector XZProjector YZProjector YXProjector XProjector YProjector ZProjector LZRYProjector LYRZProjector LYRProjector LZRProjector LRProjector LProjector RProjector BaseAxes CutAxes GlassBrainAxes BaseSlicer OrthoSlicer PlotlySurfaceFigure TiledSlicer MosaicSlicer XZSlicer YZSlicer YXSlicer XSlicer YSlicer ZSlicer .. _signal_ref: :mod:`nilearn.signal`: Preprocessing Time Series ================================================ .. automodule:: nilearn.signal :no-members: :no-inherited-members: .. No relevant user manual section yet. **Functions**: .. currentmodule:: nilearn.signal .. autosummary:: :toctree: generated/ :template: function.rst butterworth clean high_variance_confounds .. _stats_ref: :mod:`nilearn.glm`: Generalized Linear Models ================================================ .. automodule:: nilearn.glm :no-members: :no-inherited-members: .. No relevant user manual section yet. **Classes**: .. currentmodule:: nilearn.glm .. autosummary:: :toctree: generated/ :template: class.rst Contrast FContrastResults TContrastResults ARModel OLSModel LikelihoodModelResults RegressionResults SimpleRegressionResults **Functions**: .. currentmodule:: nilearn.glm .. autosummary:: :toctree: generated/ :template: function.rst compute_contrast compute_fixed_effects expression_to_contrast_vector fdr_threshold cluster_level_inference threshold_stats_img :mod:`nilearn.glm.first_level` -------------------------------------- .. automodule:: nilearn.glm.first_level :no-members: :no-inherited-members: **Classes**: .. currentmodule:: nilearn.glm.first_level .. autosummary:: :toctree: generated/ :template: class.rst FirstLevelModel **Functions**: .. currentmodule:: nilearn.glm.first_level .. autosummary:: :toctree: generated/ :template: function.rst check_design_matrix compute_regressor first_level_from_bids glover_dispersion_derivative glover_hrf glover_time_derivative make_first_level_design_matrix mean_scaling run_glm spm_dispersion_derivative spm_hrf spm_time_derivative :mod:`nilearn.glm.second_level` --------------------------------------- .. automodule:: nilearn.glm.second_level :no-members: :no-inherited-members: **Classes**: .. currentmodule:: nilearn.glm.second_level .. autosummary:: :toctree: generated/ :template: class.rst SecondLevelModel **Functions**: .. currentmodule:: nilearn.glm.second_level .. autosummary:: :toctree: generated/ :template: function.rst make_second_level_design_matrix non_parametric_inference .. _reporting_ref: :mod:`nilearn.reporting`: Reporting Functions ============================================= .. automodule:: nilearn.reporting :no-members: :no-inherited-members: **Functions**: .. currentmodule:: nilearn.reporting .. autosummary:: :toctree: generated/ :template: function.rst get_clusters_table make_glm_report :mod:`nilearn.surface`: Manipulating Surface Data =================================================== .. automodule:: nilearn.surface :no-members: :no-inherited-members: .. No relevant user manual section yet. **Functions**: .. currentmodule:: nilearn.surface .. autosummary:: :toctree: generated/ :template: function.rst load_surf_data load_surf_mesh vol_to_surf