This is the classes and functions reference of mne-python. Functions are grouped thematically by analysis stage. Functions and classes that are not below a module heading are found in the :py:mod:`mne` namespace.
- Classes
- Logging and Configuration
- Reading raw data
- File I/O
- Creating data objects from arrays
- Sample datasets
- Visualization
- Preprocessing
- Events
- Sensor Space Data
- Covariance
- MRI Processing
- Forward Modeling
- Inverse Solutions
- Source Space Data
- Time-Frequency
- Connectivity Estimation
- Statistics
- Simulation
- Decoding
- Realtime
- MNE-Report
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: class.rst io.Raw io.RawFIF Epochs Evoked SourceSpaces SourceEstimate VolSourceEstimate MixedSourceEstimate Covariance Dipole Label BiHemiLabel Transform preprocessing.ICA decoding.CSP decoding.Scaler decoding.ConcatenateChannels decoding.FilterEstimator decoding.PSDEstimator decoding.GeneralizationAcrossTime decoding.TimeDecoding realtime.RtEpochs realtime.RtClient realtime.MockRtClient realtime.StimServer realtime.StimClient report.Report
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst get_config_path get_config set_log_level set_log_file set_config
:py:mod:`mne.cuda`:
.. automodule:: mne.cuda :no-members: :no-inherited-members:
.. currentmodule:: mne.cuda
.. autosummary:: :toctree: generated/ :template: function.rst init_cuda
:py:mod:`mne.io`:
.. currentmodule:: mne.io
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst Raw
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst read_raw_bti read_raw_edf read_raw_kit read_raw_brainvision read_raw_egi read_raw_fif
.. currentmodule:: mne.io.kit
:py:mod:`mne.io.kit`:
.. autosummary:: :toctree: generated/ :template: function.rst read_mrk
.. currentmodule:: mne
Functions:
.. autosummary:: :toctree: generated :template: function.rst decimate_surface get_head_surf get_meg_helmet_surf get_volume_labels_from_aseg parse_config read_labels_from_annot read_bem_solution read_bem_surfaces read_cov read_dipole read_epochs read_epochs_kit read_events read_evokeds read_forward_solution read_label read_morph_map read_proj read_reject_parameters read_selection read_source_estimate read_source_spaces read_surface read_trans save_stc_as_volume write_labels_to_annot write_bem_solution write_bem_surfaces write_cov write_events write_evokeds write_forward_solution write_label write_proj write_source_spaces write_surface write_trans
Classes:
.. currentmodule:: mne
:py:mod:`mne`:
.. autosummary:: :toctree: generated/ :template: class.rst EvokedArray EpochsArray
.. currentmodule:: mne.io
:py:mod:`mne.io`:
.. autosummary:: :toctree: generated/ :template: class.rst RawArray
Functions:
.. currentmodule:: mne
:py:mod:`mne`:
.. autosummary:: :toctree: generated/ :template: function.rst create_info
:py:mod:`mne.datasets.sample`:
.. automodule:: mne.datasets.sample :no-members: :no-inherited-members:
.. currentmodule:: mne.datasets.sample
.. autosummary:: :toctree: generated/ :template: function.rst data_path
:py:mod:`mne.datasets.spm_face`:
.. automodule:: mne.datasets.spm_face :no-members: :no-inherited-members:
.. currentmodule:: mne.datasets.spm_face
.. autosummary:: :toctree: generated/ :template: function.rst data_path
:py:mod:`mne.datasets.brainstorm`:
.. automodule:: mne.datasets.brainstorm :no-members: :no-inherited-members:
.. currentmodule:: mne.datasets.brainstorm
.. autosummary:: :toctree: generated/ :template: function.rst bst_auditory.data_path bst_resting.data_path bst_raw.data_path
:py:mod:`mne.datasets.megsim`:
.. automodule:: mne.datasets.megsim :no-members: :no-inherited-members:
.. currentmodule:: mne.datasets.megsim
.. autosummary:: :toctree: generated/ :template: function.rst data_path load_data
:py:mod:`mne.viz`:
.. automodule:: mne.viz :no-members: :no-inherited-members:
.. currentmodule:: mne.viz
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst ClickableImage
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst circular_layout mne_analyze_colormap plot_connectivity_circle plot_cov plot_dipole_amplitudes plot_dipole_locations plot_drop_log plot_epochs plot_events plot_evoked plot_evoked_image plot_evoked_topomap plot_evoked_field plot_evoked_white plot_ica_sources plot_ica_components plot_ica_scores plot_ica_overlay plot_epochs_image plot_montage plot_projs_topomap plot_raw plot_raw_psd plot_snr_estimate plot_source_estimates plot_sparse_source_estimates plot_tfr_topomap plot_topo plot_topo_image_epochs plot_topomap compare_fiff add_background_image
.. currentmodule:: mne.io
.. autosummary:: :toctree: generated/ :template: function.rst show_fiff
Projections:
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst compute_proj_epochs compute_proj_evoked compute_proj_raw read_proj write_proj
Manipulate channels and set sensors locations for processing and plotting:
.. currentmodule:: mne.channels
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst Layout Montage DigMontage
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst fix_mag_coil_types read_montage read_dig_montage read_layout find_layout make_eeg_layout make_grid_layout read_ch_connectivity equalize_channels rename_channels generate_2d_layout
:py:mod:`mne.preprocessing`:
.. automodule:: mne.preprocessing :no-members: :no-inherited-members:
.. currentmodule:: mne.preprocessing
.. autosummary:: :toctree: generated/ :template: function.rst compute_proj_ecg compute_proj_eog create_ecg_epochs create_eog_epochs find_ecg_events find_eog_events ica_find_ecg_events ica_find_eog_events read_ica run_ica
EEG referencing:
.. currentmodule:: mne.io
.. autosummary:: :toctree: generated/ :template: function.rst add_reference_channels set_bipolar_reference set_eeg_reference
:py:mod:`mne.filter`:
.. automodule:: mne.filter :no-members: :no-inherited-members:
.. currentmodule:: mne.filter
.. autosummary:: :toctree: generated/ :template: function.rst band_pass_filter construct_iir_filter high_pass_filter low_pass_filter
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst concatenate_events find_events find_stim_steps make_fixed_length_events merge_events parse_config pick_events read_events write_events
.. currentmodule:: mne.event
.. autosummary:: :toctree: generated/ :template: function.rst define_target_events
.. currentmodule:: mne.epochs
.. autosummary:: :toctree: generated/ :template: function.rst combine_event_ids equalize_epoch_counts add_channels_epochs concatenate_epochs
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst combine_evoked concatenate_raws equalize_channels grand_average get_chpi_positions pick_channels pick_channels_cov pick_channels_forward pick_channels_regexp pick_types pick_types_forward read_epochs read_reject_parameters read_selection rename_channels
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst compute_covariance compute_raw_covariance make_ad_hoc_cov read_cov write_cov
.. currentmodule:: mne.cov
.. autosummary:: :toctree: generated/ :template: function.rst regularize
.. currentmodule:: mne
Step by step instructions for using :func:`gui.coregistration`:
.. autosummary:: :toctree: generated/ :template: function.rst gui.coregistration gui.fiducials create_default_subject scale_mri scale_bem scale_labels scale_source_space
:py:mod:`mne`:
.. currentmodule:: mne
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst add_source_space_distances apply_forward apply_forward_raw average_forward_solutions convert_forward_solution do_forward_solution make_bem_model make_bem_solution make_forward_solution make_field_map make_sphere_model morph_source_spaces read_bem_surfaces read_forward_solution read_trans read_source_spaces read_surface sensitivity_map setup_source_space setup_volume_source_space write_bem_surface write_trans
.. currentmodule:: mne.bem
.. autosummary:: :toctree: generated/ :template: function.rst make_watershed_bem make_flash_bem convert_flash_mris
.. currentmodule:: mne.forward
.. autosummary:: :toctree: generated/ :template: function.rst restrict_forward_to_label restrict_forward_to_stc
:py:mod:`mne.source_space`:
.. automodule:: mne.source_space :no-members: :no-inherited-members:
:py:mod:`mne.minimum_norm`:
.. automodule:: mne.minimum_norm :no-members: :no-inherited-members:
.. currentmodule:: mne.minimum_norm
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst InverseOperator
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst apply_inverse apply_inverse_epochs apply_inverse_raw compute_source_psd compute_source_psd_epochs compute_rank_inverse estimate_snr make_inverse_operator read_inverse_operator source_band_induced_power source_induced_power write_inverse_operator point_spread_function cross_talk_function
:py:mod:`mne.inverse_sparse`:
.. automodule:: mne.inverse_sparse :no-members: :no-inherited-members:
.. currentmodule:: mne.inverse_sparse
.. autosummary:: :toctree: generated/ :template: function.rst mixed_norm tf_mixed_norm gamma_map
:py:mod:`mne.beamformer`:
.. automodule:: mne.beamformer :no-members: :no-inherited-members:
.. currentmodule:: mne.beamformer
.. autosummary:: :toctree: generated/ :template: function.rst lcmv lcmv_epochs lcmv_raw dics dics_epochs dics_source_power rap_music
:py:mod:`mne`:
.. currentmodule:: mne
Functions:
.. autosummary:: :toctree: generated/ :template: function.rst fit_dipole
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst compute_morph_matrix extract_label_time_course grade_to_tris grade_to_vertices grow_labels label_sign_flip morph_data morph_data_precomputed read_labels_from_annot read_dipole read_label read_source_estimate save_stc_as_volume split_label stc_to_label transform_surface_to vertex_to_mni write_labels_to_annot write_label
:py:mod:`mne.time_frequency`:
.. automodule:: mne.time_frequency :no-members: :no-inherited-members:
.. currentmodule:: mne.time_frequency
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst AverageTFR
Functions that operate on mne-python objects:
.. autosummary:: :toctree: generated/ :template: function.rst compute_epochs_csd compute_epochs_psd compute_raw_psd fit_iir_model_raw tfr_morlet tfr_multitaper tfr_stockwell read_tfrs write_tfrs
Functions that operate on np.ndarray objects:
.. autosummary:: :toctree: generated/ :template: function.rst cwt_morlet dpss_windows morlet multitaper_psd single_trial_power stft istft stftfreq
:py:mod:`mne.time_frequency.tfr`:
.. automodule:: mne.time_frequency.tfr :no-members: :no-inherited-members:
.. currentmodule:: mne.time_frequency.tfr
.. autosummary:: :toctree: generated/ :template: function.rst cwt morlet
:py:mod:`mne.connectivity`:
.. automodule:: mne.connectivity :no-members: :no-inherited-members:
.. currentmodule:: mne.connectivity
.. autosummary:: :toctree: generated/ :template: function.rst seed_target_indices spectral_connectivity phase_slope_index
:py:mod:`mne.stats`:
.. automodule:: mne.stats :no-members: :no-inherited-members:
.. currentmodule:: mne.stats
.. autosummary:: :toctree: generated/ :template: function.rst bonferroni_correction fdr_correction permutation_cluster_test permutation_cluster_1samp_test permutation_t_test spatio_temporal_cluster_test spatio_temporal_cluster_1samp_test ttest_1samp_no_p linear_regression linear_regression_raw f_mway_rm
Functions to compute connectivity (adjacency) matrices for cluster-level statistics
.. currentmodule:: mne
.. autosummary:: :toctree: generated/ :template: function.rst spatial_dist_connectivity spatial_src_connectivity spatial_tris_connectivity spatio_temporal_src_connectivity spatio_temporal_tris_connectivity spatio_temporal_dist_connectivity
:py:mod:`mne.simulation`:
.. automodule:: mne.simulation :no-members: :no-inherited-members:
.. currentmodule:: mne.simulation
.. autosummary:: :toctree: generated/ :template: function.rst simulate_evoked simulate_raw simulate_stc simulate_sparse_stc select_source_in_label
:py:mod:`mne.decoding`:
.. automodule:: mne.decoding :no-members: :no-inherited-members:
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst Scaler ConcatenateChannels PSDEstimator FilterEstimator CSP GeneralizationAcrossTime
:py:mod:`mne.realtime`:
.. automodule:: mne.realtime :no-members: :no-inherited-members:
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst RtEpochs RtClient MockRtClient FieldTripClient StimServer StimClient
:py:mod:`mne.report`:
.. automodule:: mne.report :no-members: :no-inherited-members:
.. currentmodule:: mne.report
Classes:
.. autosummary:: :toctree: generated/ :template: class.rst Report