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mne-python doc python_reference.rst

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Python API Reference

This is the reference for classes (CamelCase names) and functions (underscore_case names) of MNE-Python, grouped thematically by analysis stage. Functions and classes that are not below a module heading are found in the mne namespace.

MNE-Python also provides multiple command-line scripts that can be called directly from a terminal, see :ref:`python_commands`.

:py:mod:`mne`:

.. automodule:: mne
 :no-members:
 :no-inherited-members:

Most-used classes

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 io.Raw
 Epochs
 Evoked
 Info

Reading raw data

:py:mod:`mne.io`:

.. currentmodule:: mne.io

.. automodule:: mne.io
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 anonymize_info
 read_raw
 read_raw_artemis123
 read_raw_bti
 read_raw_cnt
 read_raw_ctf
 read_raw_curry
 read_raw_edf
 read_raw_bdf
 read_raw_gdf
 read_raw_kit
 read_raw_nicolet
 read_raw_nirx
 read_raw_eeglab
 read_raw_brainvision
 read_raw_egi
 read_raw_fif
 read_raw_eximia
 read_raw_fieldtrip

Base class:

.. autosummary::
 :toctree: generated

 BaseRaw

:py:mod:`mne.io.kit`:

.. currentmodule:: mne.io.kit

.. automodule:: mne.io.kit
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 read_mrk

File I/O

.. currentmodule:: mne

.. autosummary::
 :toctree: generated

 channel_type
 channel_indices_by_type
 get_head_surf
 get_meg_helmet_surf
 get_volume_labels_from_aseg
 get_volume_labels_from_src
 parse_config
 read_labels_from_annot
 read_bem_solution
 read_bem_surfaces
 read_cov
 read_dipole
 read_epochs
 read_epochs_kit
 read_epochs_eeglab
 read_epochs_fieldtrip
 read_events
 read_evokeds
 read_evoked_fieldtrip
 read_freesurfer_lut
 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
 read_tri
 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
 what
 io.read_info
 io.show_fiff

Base class:

.. autosummary::
 :toctree: generated

 BaseEpochs

Creating data objects from arrays

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 EvokedArray
 EpochsArray
 io.RawArray
 create_info

Datasets

.. currentmodule:: mne.datasets

:py:mod:`mne.datasets`:

.. automodule:: mne.datasets
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 brainstorm.bst_auditory.data_path
 brainstorm.bst_resting.data_path
 brainstorm.bst_raw.data_path
 eegbci.load_data
 eegbci.standardize
 fetch_aparc_sub_parcellation
 fetch_fsaverage
 fetch_hcp_mmp_parcellation
 fnirs_motor.data_path
 hf_sef.data_path
 kiloword.data_path
 limo.load_data
 misc.data_path
 mtrf.data_path
 multimodal.data_path
 opm.data_path
 sleep_physionet.age.fetch_data
 sleep_physionet.temazepam.fetch_data
 sample.data_path
 somato.data_path
 spm_face.data_path
 visual_92_categories.data_path
 phantom_4dbti.data_path
 refmeg_noise.data_path

Visualization

.. currentmodule:: mne.viz

:py:mod:`mne.viz`:

.. automodule:: mne.viz
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 ClickableImage
 add_background_image
 centers_to_edges
 compare_fiff
 circular_layout
 iter_topography
 mne_analyze_colormap
 plot_bem
 plot_brain_colorbar
 plot_connectivity_circle
 plot_cov
 plot_csd
 plot_dipole_amplitudes
 plot_dipole_locations
 plot_drop_log
 plot_epochs
 plot_epochs_psd_topomap
 plot_events
 plot_evoked
 plot_evoked_image
 plot_evoked_topo
 plot_evoked_topomap
 plot_evoked_joint
 plot_evoked_field
 plot_evoked_white
 plot_filter
 plot_head_positions
 plot_ideal_filter
 plot_compare_evokeds
 plot_ica_sources
 plot_ica_components
 plot_ica_properties
 plot_ica_scores
 plot_ica_overlay
 plot_epochs_image
 plot_layout
 plot_montage
 plot_projs_topomap
 plot_raw
 plot_raw_psd
 plot_sensors
 plot_sensors_connectivity
 plot_snr_estimate
 plot_source_estimates
 link_brains
 plot_volume_source_estimates
 plot_vector_source_estimates
 plot_sparse_source_estimates
 plot_tfr_topomap
 plot_topo_image_epochs
 plot_topomap
 plot_alignment
 snapshot_brain_montage
 plot_arrowmap
 set_3d_backend
 get_3d_backend
 use_3d_backend
 set_3d_options
 set_3d_view
 set_3d_title
 create_3d_figure
 get_brain_class

Preprocessing

Projections:

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Projection
 compute_proj_epochs
 compute_proj_evoked
 compute_proj_raw
 read_proj
 write_proj

:py:mod:`mne.channels`:

.. currentmodule:: mne.channels

.. automodule:: mne.channels
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 Layout
 DigMontage
 fix_mag_coil_types
 read_polhemus_fastscan
 get_builtin_montages
 make_dig_montage
 read_dig_polhemus_isotrak
 read_dig_captrak
 read_dig_dat
 read_dig_egi
 read_dig_fif
 read_dig_hpts
 make_standard_montage
 read_custom_montage
 compute_dev_head_t
 read_layout
 find_layout
 make_eeg_layout
 make_grid_layout
 find_ch_adjacency
 read_ch_adjacency
 equalize_channels
 rename_channels
 generate_2d_layout
 make_1020_channel_selections

:py:mod:`mne.preprocessing`:

.. currentmodule:: mne.preprocessing

.. automodule:: mne.preprocessing
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 ICA
 Xdawn
 annotate_movement
 annotate_muscle_zscore
 compute_average_dev_head_t
 compute_current_source_density
 compute_proj_ecg
 compute_proj_eog
 create_ecg_epochs
 create_eog_epochs
 find_bad_channels_maxwell
 find_ecg_events
 find_eog_events
 fix_stim_artifact
 ica_find_ecg_events
 ica_find_eog_events
 infomax
 mark_flat
 maxwell_filter
 oversampled_temporal_projection
 peak_finder
 read_ica
 corrmap
 read_ica_eeglab

:py:mod:`mne.preprocessing.nirs`:

.. currentmodule:: mne.preprocessing.nirs

.. automodule:: mne.preprocessing.nirs
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 optical_density
 beer_lambert_law
 source_detector_distances
 short_channels
 scalp_coupling_index
 temporal_derivative_distribution_repair

EEG referencing:

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 add_reference_channels
 set_bipolar_reference
 set_eeg_reference

:py:mod:`mne.filter`:

.. currentmodule:: mne.filter

.. automodule:: mne.filter
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 construct_iir_filter
 create_filter
 estimate_ringing_samples
 filter_data
 notch_filter
 resample

:py:mod:`mne.chpi`

.. currentmodule:: mne.chpi

.. automodule:: mne.chpi
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 compute_chpi_amplitudes
 compute_chpi_locs
 compute_head_pos
 extract_chpi_locs_ctf
 filter_chpi
 head_pos_to_trans_rot_t
 read_head_pos
 write_head_pos

:py:mod:`mne.transforms`

.. currentmodule:: mne.transforms

.. automodule:: mne.transforms
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 Transform
 quat_to_rot
 rot_to_quat
 read_ras_mni_t

Events

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Annotations
 AcqParserFIF
 concatenate_events
 find_events
 find_stim_steps
 make_fixed_length_events
 make_fixed_length_epochs
 merge_events
 parse_config
 pick_events
 read_annotations
 read_events
 write_events
 concatenate_epochs
 events_from_annotations
 annotations_from_events

:py:mod:`mne.event`:

.. automodule:: mne.event
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.event

.. autosummary::
 :toctree: generated/

 define_target_events
 shift_time_events

:py:mod:`mne.epochs`:

.. automodule:: mne.epochs
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.epochs

.. autosummary::
 :toctree: generated/

 add_channels_epochs
 average_movements
 combine_event_ids
 equalize_epoch_counts

Sensor Space Data

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 combine_evoked
 concatenate_raws
 equalize_channels
 grand_average
 pick_channels
 pick_channels_cov
 pick_channels_forward
 pick_channels_regexp
 pick_types
 pick_types_forward
 pick_info
 read_epochs
 read_reject_parameters
 read_selection
 rename_channels

Covariance computation

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Covariance
 compute_covariance
 compute_raw_covariance
 cov.compute_whitener
 cov.prepare_noise_cov
 cov.regularize
 compute_rank
 make_ad_hoc_cov
 read_cov
 write_cov

MRI Processing

.. currentmodule:: mne

Step by step instructions for using :func:`gui.coregistration`:

• Scaling a template MRI for subjects for which no MRI is available

.. autosummary::
 :toctree: generated/

 coreg.get_mni_fiducials
 gui.coregistration
 gui.fiducials
 create_default_subject
 scale_mri
 scale_bem
 scale_labels
 scale_source_space

Forward Modeling

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Forward
 SourceSpaces
 add_source_space_distances
 apply_forward
 apply_forward_raw
 average_forward_solutions
 convert_forward_solution
 decimate_surface
 dig_mri_distances
 forward.compute_depth_prior
 forward.compute_orient_prior
 forward.restrict_forward_to_label
 forward.restrict_forward_to_stc
 make_bem_model
 make_bem_solution
 make_forward_dipole
 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
 surface.complete_surface_info
 surface.read_curvature
 use_coil_def
 write_bem_surfaces
 write_trans

:py:mod:`mne.bem`:

.. automodule:: mne.bem
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.bem

.. autosummary::
 :toctree: generated/

 ConductorModel
 fit_sphere_to_headshape
 get_fitting_dig
 make_watershed_bem
 make_flash_bem
 convert_flash_mris

Inverse Solutions

:py:mod:`mne.minimum_norm`:

.. automodule:: mne.minimum_norm
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.minimum_norm

.. autosummary::
 :toctree: generated/

 InverseOperator
 apply_inverse
 apply_inverse_cov
 apply_inverse_epochs
 apply_inverse_raw
 compute_source_psd
 compute_source_psd_epochs
 compute_rank_inverse
 estimate_snr
 make_inverse_operator
 prepare_inverse_operator
 read_inverse_operator
 source_band_induced_power
 source_induced_power
 write_inverse_operator
 make_inverse_resolution_matrix
 resolution_metrics
 get_cross_talk
 get_point_spread

:py:mod:`mne.inverse_sparse`:

.. automodule:: mne.inverse_sparse
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.inverse_sparse

.. autosummary::
 :toctree: generated/

 mixed_norm
 tf_mixed_norm
 gamma_map
 make_stc_from_dipoles

:py:mod:`mne.beamformer`:

.. automodule:: mne.beamformer
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.beamformer

.. autosummary::
 :toctree: generated/

 Beamformer
 read_beamformer
 make_lcmv
 apply_lcmv
 apply_lcmv_epochs
 apply_lcmv_raw
 apply_lcmv_cov
 make_dics
 apply_dics
 apply_dics_csd
 apply_dics_epochs
 rap_music
 tf_dics
 tf_lcmv
 make_lcmv_resolution_matrix

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Dipole
 DipoleFixed
 fit_dipole

:py:mod:`mne.dipole`:

.. automodule:: mne.dipole
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.dipole

.. autosummary::
 :toctree: generated/

 get_phantom_dipoles

Source Space Data

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 BiHemiLabel
 Label
 MixedSourceEstimate
 MixedVectorSourceEstimate
 SourceEstimate
 VectorSourceEstimate
 VolSourceEstimate
 VolVectorSourceEstimate
 SourceMorph
 compute_source_morph
 head_to_mni
 head_to_mri
 extract_label_time_course
 grade_to_tris
 grade_to_vertices
 label.select_sources
 grow_labels
 label_sign_flip
 labels_to_stc
 morph_labels
 random_parcellation
 read_labels_from_annot
 read_dipole
 read_label
 read_source_estimate
 read_source_morph
 split_label
 stc_to_label
 transform_surface_to
 vertex_to_mni
 write_labels_to_annot
 write_label

Time-Frequency

:py:mod:`mne.time_frequency`:

.. automodule:: mne.time_frequency
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.time_frequency

.. autosummary::
 :toctree: generated/

 AverageTFR
 EpochsTFR
 CrossSpectralDensity

Functions that operate on mne-python objects:

.. autosummary::
 :toctree: generated/

 csd_fourier
 csd_multitaper
 csd_morlet
 pick_channels_csd
 read_csd
 fit_iir_model_raw
 psd_welch
 psd_multitaper
 tfr_morlet
 tfr_multitaper
 tfr_stockwell
 read_tfrs
 write_tfrs

Functions that operate on np.ndarray objects:

.. autosummary::
 :toctree: generated/

 csd_array_fourier
 csd_array_multitaper
 csd_array_morlet
 dpss_windows
 morlet
 stft
 istft
 stftfreq
 psd_array_multitaper
 psd_array_welch
 tfr_array_morlet
 tfr_array_multitaper
 tfr_array_stockwell

:py:mod:`mne.time_frequency.tfr`:

.. automodule:: mne.time_frequency.tfr
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.time_frequency.tfr

.. autosummary::
 :toctree: generated/

 cwt
 morlet

Connectivity Estimation

:py:mod:`mne.connectivity`:

.. automodule:: mne.connectivity
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.connectivity

.. autosummary::
 :toctree: generated/

 degree
 envelope_correlation
 phase_slope_index
 seed_target_indices
 spectral_connectivity

Statistics

:py:mod:`mne.stats`:

.. automodule:: mne.stats
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.stats

Parametric statistics (see :mod:`scipy.stats` and :mod:`statsmodels` for more options):

.. autosummary::
 :toctree: generated/

 ttest_1samp_no_p
 ttest_ind_no_p
 f_oneway
 f_mway_rm
 f_threshold_mway_rm
 linear_regression
 linear_regression_raw

Mass-univariate multiple comparison correction:

.. autosummary::
 :toctree: generated/

 bonferroni_correction
 fdr_correction

Non-parametric (clustering) resampling methods:

.. autosummary::
 :toctree: generated/

 combine_adjacency
 permutation_cluster_test
 permutation_cluster_1samp_test
 permutation_t_test
 spatio_temporal_cluster_test
 spatio_temporal_cluster_1samp_test
 summarize_clusters_stc
 bootstrap_confidence_interval

Compute adjacency matrices for cluster-level statistics:

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 channels.find_ch_adjacency
 channels.read_ch_adjacency
 spatial_dist_adjacency
 spatial_src_adjacency
 spatial_tris_adjacency
 spatial_inter_hemi_adjacency
 spatio_temporal_src_adjacency
 spatio_temporal_tris_adjacency
 spatio_temporal_dist_adjacency

Simulation

:py:mod:`mne.simulation`:

.. automodule:: mne.simulation
 :no-members:
 :no-inherited-members:

.. currentmodule:: mne.simulation

.. autosummary::
 :toctree: generated/

 add_chpi
 add_ecg
 add_eog
 add_noise
 simulate_evoked
 simulate_raw
 simulate_stc
 simulate_sparse_stc
 select_source_in_label
 SourceSimulator

Decoding

:py:mod:`mne.decoding`:

.. automodule:: mne.decoding
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 CSP
 EMS
 FilterEstimator
 LinearModel
 PSDEstimator
 Scaler
 TemporalFilter
 TimeFrequency
 UnsupervisedSpatialFilter
 Vectorizer
 ReceptiveField
 TimeDelayingRidge
 SlidingEstimator
 GeneralizingEstimator
 SPoC

Functions that assist with decoding and model fitting:

.. autosummary::
 :toctree: generated/

 compute_ems
 cross_val_multiscore
 get_coef

Realtime

Realtime functionality has moved to the standalone module :mod:`mne_realtime`.

MNE-Report

:py:mod:`mne`:

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 Report
 open_report

Logging and Configuration

.. currentmodule:: mne

.. autosummary::
 :toctree: generated/

 get_config_path
 get_config
 open_docs
 set_log_level
 set_log_file
 set_config
 set_cache_dir
 sys_info
 verbose

:py:mod:`mne.utils`:

.. currentmodule:: mne.utils

.. automodule:: mne.utils
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 deprecated
 warn

:py:mod:`mne.cuda`:

.. currentmodule:: mne.cuda

.. automodule:: mne.cuda
 :no-members:
 :no-inherited-members:

.. autosummary::
 :toctree: generated/

 get_cuda_memory
 init_cuda
 set_cuda_device

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