Index

_

__doc__ (in module osl_ephys.glm) (in module osl_ephys.maxfilter) (in module osl_ephys.preprocessing) (in module osl_ephys.report) (in module osl_ephys.source_recon) (in module osl_ephys.utils) __repr__() (osl_ephys.utils.spmio._data.Channel method) (osl_ephys.utils.spmio._data.Data method) (osl_ephys.utils.spmio._events.Event method) __str__() (osl_ephys.glm.glm_spectrum.GroupSensorGLMSpectrum method) (osl_ephys.glm.GroupSensorGLMSpectrum method) __version__ (in module osl_ephys) _add_autobad() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_autobad_dur() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_bad() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_badlimit() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_cal() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_ctc() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_force() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_frame() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_headpos() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_hpie() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_hpig() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_hpisubt() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_inorder() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_linefreq() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_movecomp() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_movecompinter() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_origin() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_outorder() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_scanner() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter)

_add_trans() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _add_tsss() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) _channel_property() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) _close() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) _compute_beamformer() (in module osl_ephys.source_recon.beamforming) _D (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) _draw_traces() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) _empty_to_val() (in module osl_ephys.utils.spmio._spmmeeg_utils) _event_property() (osl_ephys.utils.spmio._events.Trial method) _find_dat_file() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) _find_freesurfer_file() (in module osl_ephys.source_recon.parcellation) _find_outliers_in_dims() (in module osl_ephys.preprocessing.osl_wrappers) _find_outliers_in_segments() (in module osl_ephys.preprocessing.osl_wrappers) _find_package_file() (in module osl_ephys.source_recon.parcellation) _get_browser() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) _get_parc_chans() (in module osl_ephys.source_recon.sign_flipping) _get_parcel_timeseries() (in module osl_ephys.source_recon.parcellation) _get_trial_trigger_value() (in module osl_ephys.utils.spmio.spmmeeg) _init_browser() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) _keypress() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) _load_unicode_inputs() (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) _logger (in module osl_ephys.utils.spmio._events) _make_lcmv() (in module osl_ephys.source_recon.beamforming) _on_mouse_press() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) _parcel_timeseries2nii() (in module osl_ephys.source_recon.parcellation) _parse_condition() (in module osl_ephys.utils.version_utils) _plot_ica_sources_evoked() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) _plot_sources() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) _prepare_beamformer_input() (in module osl_ephys.source_recon.beamforming) _set_event_property() (osl_ephys.utils.spmio._events.Trial method) _update_picks() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) _update_vscroll() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method)

A

add_subdir() (in module osl_ephys.maxfilter) (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) add_to_data() (in module osl_ephys.report.src_report) adjacency (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorMaxStatPerm attribute) append_4d_parcellation() (in module osl_ephys.source_recon.nii) append_preproc_info() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch)

apply() (in module osl_ephys.preprocessing.ica_label) (osl_ephys.utils.spmio._data.Montage method) apply_flips() (in module osl_ephys.source_recon.sign_flipping) apply_flips_to_covariance() (in module osl_ephys.source_recon.sign_flipping) apply_inverse_operator_surf() (in module osl_ephys.source_recon.minimum_norm) apply_inverse_operator_vol() (in module osl_ephys.source_recon.minimum_norm) apply_lcmv() (in module osl_ephys.source_recon.beamforming) apply_lcmv_raw() (in module osl_ephys.source_recon.beamforming)

B

backend (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) backend_name (osl_ephys.preprocessing.osl_MNEBrowseFigure attribute) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure attribute) backends_to_try (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) bad (osl_ephys.utils.spmio._data.Channel attribute) (osl_ephys.utils.spmio._events.Trial attribute) bad_channels() (in module osl_ephys.preprocessing.osl_wrappers)

bad_segments() (in module osl_ephys.preprocessing.osl_wrappers) BaseSensorPerm (class in osl_ephys.glm.glm_base) be (osl_ephys.utils.spmio._data.Data attribute) beamform() (in module osl_ephys.source_recon.wrappers) beamform_and_parcellate() (in module osl_ephys.source_recon.wrappers) bem_display() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.coreg) best_fit_transform() (in module osl_ephys.source_recon.rhino.utils) binary_majority3d() (in module osl_ephys.source_recon.rhino.utils)

C

calc_noise_cov() (in module osl_ephys.source_recon.minimum_norm) calculate_samples() (osl_ephys.utils.spmio._events.Trial method) chan_types (in module osl_ephys.utils.spmio._data) Channel (class in osl_ephys.utils.spmio._data) channels (in module osl_ephys.utils.create_neuromag306_info) (osl_ephys.utils.spmio._data.Montage attribute) (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) chantype (osl_ephys.utils.spmio.SPMMEEG property) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG property) (osl_ephys.utils.SPMMEEG property) check_config_versions() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) check_freesurfer() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.freesurfer_utils) check_fsl() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.fsl_utils) check_if_already_computed() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.surfaces) check_lowered_string() (in module osl_ephys.utils.spmio._spmmeeg_utils) check_nii_for_nan() (in module osl_ephys.source_recon.rhino.utils) check_version() (in module osl_ephys.preprocessing) (in module osl_ephys.utils) (in module osl_ephys.utils.version_utils) closest_node() (in module osl_ephys.source_recon.rhino.utils) ClusterPermuteGLMSpectrum (class in osl_ephys.glm) (class in osl_ephys.glm.glm_spectrum) compute_cohens_f2() (osl_ephys.glm.glm_base.GLMBaseResult method) (osl_ephys.glm.GLMBaseResult method), [1] compute_surfaces() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.surfaces) (in module osl_ephys.source_recon.wrappers)

condlist (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) config (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.glm_spectrum.SensorGLMSpectrum attribute) (osl_ephys.glm.GroupGLMBaseResult attribute), [1] (osl_ephys.glm.SensorGLMSpectrum attribute) contrast_names (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.GroupGLMBaseResult attribute), [1] convert2mne_epochs() (in module osl_ephys.source_recon.parcellation) convert2mne_raw() (in module osl_ephys.source_recon.parcellation) convert2niftii() (in module osl_ephys.source_recon.parcellation) convert2source_estimate() (in module osl_ephys.source_recon.parcellation) convert_3dparc_to_4d() (in module osl_ephys.source_recon.nii) convert_4dparc_to_3d() (in module osl_ephys.source_recon.nii) convert_notts() (in module osl_ephys.utils) (in module osl_ephys.utils.opm) coreg() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.coreg) coreg_display() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.coreg) coreg_filenames (in module osl_ephys.utils) (in module osl_ephys.utils.opm) coreg_metrics() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.coreg) coregister() (in module osl_ephys.source_recon.wrappers) correct_mri() (in module osl_ephys.utils) (in module osl_ephys.utils.opm) covariance_matrix_correlation() (in module osl_ephys.source_recon.sign_flipping) create_freesurfer_mesh_from_bet_surface() (in module osl_ephys.source_recon.rhino.utils) create_freesurfer_meshes_from_bet_surfaces() (in module osl_ephys.source_recon.rhino.utils) create_inverse_operator() (in module osl_ephys.source_recon.minimum_norm) current_montage (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute)

D

dask_parallel_bag() (in module osl_ephys.preprocessing) (in module osl_ephys.utils) (in module osl_ephys.utils.parallel) Data (class in osl_ephys.utils.spmio._data) data (osl_ephys.glm.glm_base.GLMBaseResult attribute) (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.GLMBaseResult attribute), [1] (osl_ephys.glm.GroupGLMBaseResult attribute), [1] (osl_ephys.utils.spmio._data.Data attribute) (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) decorate_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) default_config (in module osl_ephys.utils.logger)

define_trial() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) delete_headshape_points() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) design (osl_ephys.glm.glm_base.GLMBaseResult attribute) (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.GLMBaseResult attribute), [1] (osl_ephys.glm.GroupGLMBaseResult attribute), [1] detect_artefacts() (in module osl_ephys.preprocessing.osl_wrappers) detect_bad_channels_psd() (in module osl_ephys.preprocessing.osl_wrappers) detect_maxfilt_zeros() (in module osl_ephys.preprocessing.osl_wrappers) downsample_headshape() (in module osl_ephys.source_recon.rhino.utils) drop_bad_epochs() (in module osl_ephys.preprocessing.osl_wrappers) dtype (osl_ephys.utils.spmio._data.Data attribute) duration (osl_ephys.utils.spmio._events.Event attribute) durations (osl_ephys.utils.spmio._events.Trial property)

E

empty_to_none() (in module osl_ephys.utils.spmio._spmmeeg_utils) empty_to_zero() (in module osl_ephys.utils.spmio._spmmeeg_utils) end_sample (osl_ephys.utils.spmio._events.Event attribute) end_samples (osl_ephys.utils.spmio._events.Trial property) end_time (osl_ephys.utils.spmio._events.Event attribute) end_times (osl_ephys.utils.spmio._events.Trial property) epoch_data() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) Event (class in osl_ephys.utils.spmio._events) event_type (osl_ephys.utils.spmio.spmmeeg.TrialParameters attribute) events (osl_ephys.utils.spmio._events.Trial attribute)

extract_fiducials_from_fif() (in module osl_ephys.source_recon.wrappers) extract_polhemus_from_elc() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) extract_polhemus_from_info() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) extract_polhemus_from_pos() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) extract_rhino_files() (in module osl_ephys.source_recon.rhino.utils) (in module osl_ephys.source_recon.wrappers)

F

f (osl_ephys.glm.glm_spectrum.GroupSensorGLMSpectrum attribute) (osl_ephys.glm.glm_spectrum.SensorGLMSpectrum attribute) (osl_ephys.glm.GroupSensorGLMSpectrum attribute) (osl_ephys.glm.SensorGLMSpectrum attribute) fiducials (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) fieldnames (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] fields (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] filename (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) find_file() (in module osl_ephys.source_recon.parcellation) find_flips() (in module osl_ephys.source_recon.sign_flipping) find_func() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.batch) find_run_id() (in module osl_ephys.preprocessing) (in module osl_ephys.source_recon) (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) find_template_subject() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.sign_flipping) (in module osl_ephys.source_recon.wrappers) fit_cbu_origin() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) fix_sign_ambiguity() (in module osl_ephys.source_recon.wrappers)

fl_con (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorMaxStatPerm attribute) fl_contrast_name (osl_ephys.glm.glm_base.SensorClusterPerm attribute) (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorClusterPerm attribute), [1] (osl_ephys.glm.SensorMaxStatPerm attribute) flatten_recursive() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) fname (in module osl_ephys.utils) (in module osl_ephys.utils.simulate) (osl_ephys.utils.spmio._data.Data attribute) (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) forward_model() (in module osl_ephys.source_recon.rhino.forward_model) (in module osl_ephys.source_recon.wrappers) from_dict() (osl_ephys.utils.spmio._data.Channel class method) (osl_ephys.utils.spmio._events.Event class method) fsample (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) fsleyes() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.fsl_utils) fsleyes_overlay() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.fsl_utils) full_index() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) fullpath (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute)

G

gen_html_data() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) (in module osl_ephys.report.src_report) gen_html_page() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) (in module osl_ephys.report.src_report) gen_html_summary() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) (in module osl_ephys.report.src_report) gen_report_from_fif() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) gen_summary_data() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) gesd() (in module osl_ephys.preprocessing.osl_wrappers) get() (osl_ephys.utils.Study method) (osl_ephys.utils.study.Study method) get_beamforming_filenames() (in module osl_ephys.source_recon.beamforming) get_channel_adjacency() (osl_ephys.glm.glm_base.GroupGLMBaseResult method) (osl_ephys.glm.GroupGLMBaseResult method), [1] get_config_from_fif() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) get_coreg_filenames() (in module osl_ephys.source_recon.freesurfer_utils) (in module osl_ephys.source_recon.rhino), [1] (in module osl_ephys.source_recon.rhino.coreg) get_data() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) get_evoked_contrast() (osl_ephys.glm.glm_epochs.GLMEpochsResult method) (osl_ephys.glm.glm_epochs.GroupGLMEpochs method) (osl_ephys.glm.GLMEpochsResult method) (osl_ephys.glm.GroupGLMEpochs method) get_fl_contrast() (osl_ephys.glm.glm_epochs.GroupGLMEpochs method) (osl_ephys.glm.glm_spectrum.GroupSensorGLMSpectrum method) (osl_ephys.glm.GroupGLMEpochs method) (osl_ephys.glm.GroupSensorGLMSpectrum method) get_flirt_xform_between_axes() (in module osl_ephys.source_recon.rhino.utils) get_flirtcoords2native_xform() (in module osl_ephys.source_recon.rhino.utils) get_freesurfer_filenames() (in module osl_ephys.source_recon.freesurfer_utils) get_gridstep() (in module osl_ephys.source_recon.rhino.utils) get_header_id() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) get_lcmv_weights() (in module osl_ephys.source_recon.beamforming) get_leadfields() (in module osl_ephys.source_recon.beamforming) get_level() (in module osl_ephys.utils.logger) get_mne_filenames() (in module osl_ephys.source_recon.minimum_norm) get_mne_sensor_cols() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) get_mne_xform_from_flirt_xform() (in module osl_ephys.source_recon.rhino.utils) get_orient() (in module osl_ephys.source_recon.rhino.utils) get_polhemus_from_info() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) get_rawdir() (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling)

get_recon_timeseries() (in module osl_ephys.source_recon.beamforming) get_rhino_filenames() (in module osl_ephys.source_recon.rhino.utils) get_sform() (in module osl_ephys.source_recon.rhino.utils) get_sig_clusters() (osl_ephys.glm.glm_base.SensorClusterPerm method) (osl_ephys.glm.glm_base.SensorMaxStatPerm method) (osl_ephys.glm.SensorClusterPerm method), [1] (osl_ephys.glm.SensorMaxStatPerm method) get_source_colors() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) get_surfaces_filenames() (in module osl_ephys.source_recon.rhino), [1], [2] (in module osl_ephys.source_recon.rhino.surfaces) get_vol_info_from_nii() (in module osl_ephys.source_recon.rhino.utils) get_vtk_mesh_native() (in module osl_ephys.source_recon.rhino.utils) gl_con (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorMaxStatPerm attribute) gl_contrast_name (osl_ephys.glm.glm_base.SensorClusterPerm attribute) (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorClusterPerm attribute), [1] (osl_ephys.glm.SensorMaxStatPerm attribute) glm_epochs() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_epochs) glm_irasa() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) glm_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) GLMBaseResult (class in osl_ephys.glm), [1] (class in osl_ephys.glm.glm_base) GLMEpochsResult (class in osl_ephys.glm) (class in osl_ephys.glm.glm_epochs) globdir (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] good_end_sample (osl_ephys.utils.spmio._events.Event attribute) good_end_samples (osl_ephys.utils.spmio._events.Trial property) good_index (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) good_sample (osl_ephys.utils.spmio._events.Event attribute) good_samples (osl_ephys.utils.spmio._events.Trial property) grid_average_downsample() (in module osl_ephys.source_recon.rhino.utils) group_glm_epochs() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_epochs) group_glm_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) group_glm_spectrum_from_array() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) GroupGLMBaseResult (class in osl_ephys.glm), [1] (class in osl_ephys.glm.glm_base) GroupGLMEpochs (class in osl_ephys.glm) (class in osl_ephys.glm.glm_epochs) GroupSensorGLMSpectrum (class in osl_ephys.glm) (class in osl_ephys.glm.glm_spectrum) guess_parcellation() (in module osl_ephys.source_recon.parcellation)

H

history (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute)

I

ica_label() (in module osl_ephys.preprocessing.ica_label) icp() (in module osl_ephys.source_recon.rhino.utils) import_data() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) indchantype() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) index (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) indsample() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method)

indtrial() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) info (osl_ephys.glm.glm_base.GLMBaseResult attribute) (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.glm_base.SensorClusterPerm attribute) (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.GLMBaseResult attribute), [1] (osl_ephys.glm.GroupGLMBaseResult attribute), [1] (osl_ephys.glm.SensorClusterPerm attribute), [1] (osl_ephys.glm.SensorMaxStatPerm attribute)

K

KNOWN_DTYPEIDS (in module osl_ephys.utils.spmio._data)

L

label (osl_ephys.utils.spmio._data.Channel attribute) (osl_ephys.utils.spmio._events.Trial attribute) labelnew (osl_ephys.utils.spmio._data.Montage attribute) labelorg (osl_ephys.utils.spmio._data.Montage attribute) load_config() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.batch) load_covariances() (in module osl_ephys.source_recon.sign_flipping) load_lcmv() (in module osl_ephys.source_recon.beamforming) load_parcellation() (in module osl_ephys.source_recon.parcellation) load_parcellation_description() (in module osl_ephys.source_recon.parcellation) load_template() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report)

local_orthogonalise() (in module osl_ephys.source_recon.parcellation) log_or_print() (in module osl_ephys.report) (in module osl_ephys.source_recon.rhino), [1], [2] (in module osl_ephys.utils.logger) logger (in module osl_ephys.preprocessing), [1] (in module osl_ephys.preprocessing.batch) (in module osl_ephys.preprocessing.ica_label) (in module osl_ephys.preprocessing.mne_wrappers) (in module osl_ephys.preprocessing.osl_wrappers) (in module osl_ephys.preprocessing.plot_ica) (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.batch) (in module osl_ephys.source_recon.minimum_norm) (in module osl_ephys.utils.misc) (in module osl_ephys.utils.package)

M

main() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) (in module osl_ephys.preprocessing.ica_label) (in module osl_ephys.utils.run_func) majority() (in module osl_ephys.source_recon.rhino.utils) make_fsaverage_src() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.freesurfer_utils) make_fwd_solution() (in module osl_ephys.source_recon.rhino.forward_model) make_lcmv() (in module osl_ephys.source_recon.beamforming) make_plots() (in module osl_ephys.source_recon.beamforming) make_watershed_bem() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.freesurfer_utils) (in module osl_ephys.source_recon.wrappers) mark_artefacts_as_bad() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) match_files (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] match_values (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] MaxStatPermuteGLMSpectrum (class in osl_ephys.glm) (class in osl_ephys.glm.glm_spectrum) minimum_norm() (in module osl_ephys.source_recon.wrappers) minimum_norm_and_parcellate() (in module osl_ephys.source_recon.wrappers) model (osl_ephys.glm.glm_base.GLMBaseResult attribute) (osl_ephys.glm.glm_base.GroupGLMBaseResult attribute) (osl_ephys.glm.GLMBaseResult attribute), [1] (osl_ephys.glm.GroupGLMBaseResult attribute), [1] module osl_ephys osl_ephys.glm osl_ephys.glm.glm_base osl_ephys.glm.glm_epochs osl_ephys.glm.glm_spectrum osl_ephys.maxfilter osl_ephys.maxfilter.maxfilter osl_ephys.preprocessing osl_ephys.preprocessing.batch osl_ephys.preprocessing.ica_label osl_ephys.preprocessing.mne_wrappers osl_ephys.preprocessing.osl_wrappers osl_ephys.preprocessing.plot_ica osl_ephys.report osl_ephys.report.preproc_report osl_ephys.report.src_report osl_ephys.source_recon osl_ephys.source_recon.batch osl_ephys.source_recon.beamforming osl_ephys.source_recon.freesurfer_utils osl_ephys.source_recon.minimum_norm osl_ephys.source_recon.nii osl_ephys.source_recon.parcellation osl_ephys.source_recon.rhino osl_ephys.source_recon.rhino.coreg osl_ephys.source_recon.rhino.forward_model osl_ephys.source_recon.rhino.fsl_utils osl_ephys.source_recon.rhino.polhemus osl_ephys.source_recon.rhino.surfaces osl_ephys.source_recon.rhino.utils osl_ephys.source_recon.sign_flipping osl_ephys.source_recon.wrappers osl_ephys.tests osl_ephys.tests.test_00_package_canary osl_ephys.tests.test_batch_api osl_ephys.tests.test_batch_preproc osl_ephys.tests.test_file_handling osl_ephys.tests.test_glm osl_ephys.tests.test_parallel osl_ephys.utils osl_ephys.utils.create_neuromag306_info osl_ephys.utils.file_handling osl_ephys.utils.logger osl_ephys.utils.misc osl_ephys.utils.opm osl_ephys.utils.package osl_ephys.utils.parallel osl_ephys.utils.run_func osl_ephys.utils.simulate osl_ephys.utils.simulation_config osl_ephys.utils.simulation_config.simulate osl_ephys.utils.spmio osl_ephys.utils.spmio._data osl_ephys.utils.spmio._events osl_ephys.utils.spmio._spmmeeg_utils osl_ephys.utils.spmio.spmmeeg osl_ephys.utils.study osl_ephys.utils.version_utils

Montage (class in osl_ephys.utils.spmio._data) montage (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) morph_surface() (in module osl_ephys.source_recon.minimum_norm)

N

n_good_samples (osl_ephys.utils.spmio.SPMMEEG property) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG property) (osl_ephys.utils.SPMMEEG property) name (osl_ephys.utils.spmio._data.Montage attribute) nchannels (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) nearest_neighbor() (in module osl_ephys.source_recon.rhino.utils)

niimask2indexpointcloud() (in module osl_ephys.source_recon.rhino.utils) niimask2mmpointcloud() (in module osl_ephys.source_recon.rhino.utils) nsamples (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) ntrials (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute)

O

offset (osl_ephys.utils.spmio._data.Data attribute) (osl_ephys.utils.spmio._events.Event attribute) offsets (osl_ephys.utils.spmio._events.Trial property) onset (osl_ephys.utils.spmio._events.Trial attribute) osl_ephys module osl_ephys.glm module osl_ephys.glm.glm_base module osl_ephys.glm.glm_epochs module osl_ephys.glm.glm_spectrum module osl_ephys.maxfilter module osl_ephys.maxfilter.maxfilter module osl_ephys.preprocessing module osl_ephys.preprocessing.batch module osl_ephys.preprocessing.ica_label module osl_ephys.preprocessing.mne_wrappers module osl_ephys.preprocessing.osl_wrappers module osl_ephys.preprocessing.plot_ica module osl_ephys.report module osl_ephys.report.preproc_report module osl_ephys.report.src_report module osl_ephys.source_recon module osl_ephys.source_recon.batch module osl_ephys.source_recon.beamforming module osl_ephys.source_recon.freesurfer_utils module osl_ephys.source_recon.minimum_norm module osl_ephys.source_recon.nii module osl_ephys.source_recon.parcellation module osl_ephys.source_recon.rhino module osl_ephys.source_recon.rhino.coreg module osl_ephys.source_recon.rhino.forward_model module osl_ephys.source_recon.rhino.fsl_utils module osl_ephys.source_recon.rhino.polhemus module osl_ephys.source_recon.rhino.surfaces module osl_ephys.source_recon.rhino.utils module osl_ephys.source_recon.sign_flipping module osl_ephys.source_recon.wrappers module

osl_ephys.tests module osl_ephys.tests.test_00_package_canary module osl_ephys.tests.test_batch_api module osl_ephys.tests.test_batch_preproc module osl_ephys.tests.test_file_handling module osl_ephys.tests.test_glm module osl_ephys.tests.test_parallel module osl_ephys.utils module osl_ephys.utils.create_neuromag306_info module osl_ephys.utils.file_handling module osl_ephys.utils.logger module osl_ephys.utils.misc module osl_ephys.utils.opm module osl_ephys.utils.package module osl_ephys.utils.parallel module osl_ephys.utils.run_func module osl_ephys.utils.simulate module osl_ephys.utils.simulation_config module osl_ephys.utils.simulation_config.simulate module osl_ephys.utils.spmio module osl_ephys.utils.spmio._data module osl_ephys.utils.spmio._events module osl_ephys.utils.spmio._spmmeeg_utils module osl_ephys.utils.spmio.spmmeeg module osl_ephys.utils.study module osl_ephys.utils.version_utils module osl_logger (in module osl_ephys) (in module osl_ephys.maxfilter) (in module osl_ephys.report) (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) (in module osl_ephys.utils.logger) (in module osl_ephys.utils.parallel) (in module osl_ephys.utils.version_utils) osl_MNEBrowseFigure (class in osl_ephys.preprocessing) (class in osl_ephys.preprocessing.plot_ica) osl_print() (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) other (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute)

P

parcel_centers() (in module osl_ephys.source_recon.parcellation) parcel_vector_to_voxel_grid() (in module osl_ephys.source_recon.parcellation) parcellate() (in module osl_ephys.source_recon.wrappers) parser (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) path (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) perm_data (osl_ephys.glm.glm_base.SensorClusterPerm attribute) (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorClusterPerm attribute), [1] (osl_ephys.glm.SensorMaxStatPerm attribute) permission (osl_ephys.utils.spmio._data.Data attribute) perms (osl_ephys.glm.glm_base.SensorClusterPerm attribute) (osl_ephys.glm.glm_base.SensorMaxStatPerm attribute) (osl_ephys.glm.SensorClusterPerm attribute), [1] (osl_ephys.glm.SensorMaxStatPerm attribute) plot_artefact_scan() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_bad_ica() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_channel_dists() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_channel_layout() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) plot_channel_time_series() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_config() (in module osl_ephys.report.src_report) plot_correlation() (in module osl_ephys.source_recon.parcellation) plot_custom_figures() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_digitisation_2d() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_ecg_summary() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_eog_summary() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_events() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_flowchart() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_freqbands() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_headmovement() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_ica() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.plot_ica) plot_joint_clusters() (in module osl_ephys.glm.glm_base) plot_joint_contrast() (osl_ephys.glm.glm_epochs.GLMEpochsResult method) (osl_ephys.glm.glm_epochs.GroupGLMEpochs method) (osl_ephys.glm.GLMEpochsResult method) (osl_ephys.glm.GroupGLMEpochs method) plot_joint_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) (osl_ephys.glm.glm_spectrum.GroupSensorGLMSpectrum method) (osl_ephys.glm.glm_spectrum.SensorGLMSpectrum method) (osl_ephys.glm.GroupSensorGLMSpectrum method) (osl_ephys.glm.SensorGLMSpectrum method) plot_joint_spectrum_clusters() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) plot_parcellation() (in module osl_ephys.report.src_report) (in module osl_ephys.source_recon.parcellation)

plot_polhemus_points() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) plot_preproc_flowchart() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) plot_psd() (in module osl_ephys.source_recon.parcellation) plot_rawdata() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_sensor_data() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) plot_sensor_erp() (in module osl_ephys.glm.glm_base) plot_sensor_proj() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) plot_sensor_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) (osl_ephys.glm.glm_spectrum.SensorGLMSpectrum method) (osl_ephys.glm.SensorGLMSpectrum method) plot_sensors() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_sig_clusters() (osl_ephys.glm.ClusterPermuteGLMSpectrum method) (osl_ephys.glm.glm_base.SensorClusterPerm method) (osl_ephys.glm.glm_base.SensorMaxStatPerm method) (osl_ephys.glm.glm_spectrum.ClusterPermuteGLMSpectrum method) (osl_ephys.glm.glm_spectrum.MaxStatPermuteGLMSpectrum method) (osl_ephys.glm.MaxStatPermuteGLMSpectrum method) (osl_ephys.glm.SensorClusterPerm method), [1] (osl_ephys.glm.SensorMaxStatPerm method) plot_sign_flipping_results() (in module osl_ephys.report.src_report) plot_source_topo() (in module osl_ephys.glm.glm_base) (in module osl_ephys.report) (in module osl_ephys.source_recon.parcellation) plot_spectra() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_summary_bad_chans() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_summary_bad_segs() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) plot_surfaces() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.surfaces) plot_topos() (osl_ephys.preprocessing.osl_MNEBrowseFigure method) (osl_ephys.preprocessing.plot_ica.osl_MNEBrowseFigure method) plot_with_cols() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_base) (in module osl_ephys.glm.glm_spectrum) pos (osl_ephys.utils.spmio._data.Data attribute) post_stim (osl_ephys.utils.spmio.spmmeeg.TrialParameters attribute) pre_stim (osl_ephys.utils.spmio.spmmeeg.TrialParameters attribute) prep_scaled_freq() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) print_custom_func_info() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) print_info() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) print_scan_summary() (in module osl_ephys.report) (in module osl_ephys.report.preproc_report) process_file_inputs() (in module osl_ephys.maxfilter) (in module osl_ephys.preprocessing) (in module osl_ephys.report) (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling)

Q

quick_load_dig() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter)

R

randomly_flip() (in module osl_ephys.source_recon.sign_flipping) read_dataset() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) read_glm_epochs() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_epochs) read_glm_spectrum() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_spectrum) read_mne_epochs() (in module osl_ephys.glm) (in module osl_ephys.glm.glm_epochs) recon_all() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.freesurfer_utils) recon_timeseries2niftii() (in module osl_ephys.source_recon.rhino.utils) refresh() (osl_ephys.utils.Study method) (osl_ephys.utils.study.Study method) reindex_event_samples() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) reindex_good_samples() (osl_ephys.utils.spmio.SPMMEEG method) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG method) (osl_ephys.utils.SPMMEEG method) remove_stray_headshape_points() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) repl (osl_ephys.utils.spmio._events.Trial attribute) replace_headshape() (in module osl_ephys.source_recon.rhino.utils) resample_parcellation() (in module osl_ephys.source_recon.parcellation) rescale_sensor_positions() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) rhino_icp() (in module osl_ephys.source_recon.rhino.utils) rigid_transform_3D() (in module osl_ephys.source_recon.rhino.utils) rotate_pointcloud() (in module osl_ephys.source_recon.rhino.utils) run_cbu_3stage_maxfilter() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) run_maxfilter() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) run_maxfilter_batch() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) run_mne_annotate_amplitude() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_annotate_muscle_zscore() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_anonymous() (in module osl_ephys.preprocessing.mne_wrappers)

run_mne_apply_baseline() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_apply_ica() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_compute_current_source_density() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_drop_bad() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_epochs() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_find_bad_channels_maxwell() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_find_events() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_ica_autoreject() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_ica_raw() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_interpolate_bads() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_maxwell_filter() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_notch_filter() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_pick() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_pick_channels() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_pick_types() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_resample() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_set_channel_types() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_tfr_morlet() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_tfr_multitaper() (in module osl_ephys.preprocessing.mne_wrappers) run_mne_tfr_stockwell() (in module osl_ephys.preprocessing.mne_wrappers) run_multistage_maxfilter() (in module osl_ephys.maxfilter) (in module osl_ephys.maxfilter.maxfilter) run_osl_bad_channels() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_bad_segments() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_drop_bad_epochs() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_glm_add_contrast() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_glm_add_regressor() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_glm_fit() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_glm_permutations() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_read_dataset() (in module osl_ephys.preprocessing.osl_wrappers) run_osl_zscore_present_data() (in module osl_ephys.preprocessing.osl_wrappers) run_package_tests() (in module osl_ephys.utils) (in module osl_ephys.utils.package) run_proc_batch() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) run_proc_chain() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch) run_src_batch() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.batch) run_src_chain() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.batch)

S

sample (osl_ephys.utils.spmio._events.Event attribute) samples (osl_ephys.utils.spmio._events.Trial property) sanitise_filepath() (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling) save_mni_fiducials() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.polhemus) (in module osl_ephys.source_recon.wrappers) save_or_show_renderer() (in module osl_ephys.source_recon.rhino.utils) save_pkl() (osl_ephys.glm.glm_base.BaseSensorPerm method) (osl_ephys.glm.glm_base.GLMBaseResult method) (osl_ephys.glm.glm_epochs.GLMEpochsResult method) (osl_ephys.glm.glm_epochs.GroupGLMEpochs method) (osl_ephys.glm.glm_spectrum.GroupSensorGLMSpectrum method) (osl_ephys.glm.GLMBaseResult method), [1] (osl_ephys.glm.GLMEpochsResult method) (osl_ephys.glm.GroupGLMEpochs method) (osl_ephys.glm.GroupSensorGLMSpectrum method) save_polhemus_fif() (in module osl_ephys.source_recon.rhino.utils) scl_inter (osl_ephys.utils.spmio._data.Data attribute) scl_slope (osl_ephys.utils.spmio._data.Data attribute) SensorClusterPerm (class in osl_ephys.glm), [1] (class in osl_ephys.glm.glm_base) SensorGLMSpectrum (class in osl_ephys.glm) (class in osl_ephys.glm.glm_spectrum) SensorMaxStatPerm (class in osl_ephys.glm) (class in osl_ephys.glm.glm_base) sensors (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) set_level() (in module osl_ephys.utils.logger) set_random_seed() (in module osl_ephys.preprocessing) (in module osl_ephys.source_recon) (in module osl_ephys.utils.misc) set_up() (in module osl_ephys.utils.logger) setup_freesurfer() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.freesurfer_utils) setup_fsl() (in module osl_ephys.source_recon) (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.fsl_utils)

setup_volume_source_space() (in module osl_ephys.source_recon.rhino.forward_model) setUpClass() (osl_ephys.tests.test_00_package_canary.TestPackageData class method) (osl_ephys.tests.test_batch_preproc.TestPreprocessingBatch class method) (osl_ephys.tests.test_batch_preproc.TestPreprocessingChain class method) (osl_ephys.tests.test_file_handling.TestFileInputs class method) (osl_ephys.tests.test_file_handling.TestStudyClass class method) (osl_ephys.tests.test_glm.TestGLMSpectrum class method) (osl_ephys.tests.test_parallel.TestSimpleDask class method) shape (osl_ephys.utils.spmio._data.Data attribute) simulate_data() (in module osl_ephys.utils) (in module osl_ephys.utils.simulate) (in module osl_ephys.utils.simulation_config.simulate) simulate_raw_from_template() (in module osl_ephys.utils) (in module osl_ephys.utils.simulate) (in module osl_ephys.utils.simulation_config) (in module osl_ephys.utils.simulation_config.simulate) simulate_rest_mvar() (in module osl_ephys.utils) (in module osl_ephys.utils.simulate) (in module osl_ephys.utils.simulation_config.simulate) size (osl_ephys.utils.spmio.SPMMEEG property) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG property) (osl_ephys.utils.SPMMEEG property) soft_import() (in module osl_ephys.utils) (in module osl_ephys.utils.package) spatial_dist_adjacency() (in module osl_ephys.source_recon.parcellation) spatially_downsample() (in module osl_ephys.source_recon.nii) SPMMEEG (class in osl_ephys.utils) (class in osl_ephys.utils.spmio) (class in osl_ephys.utils.spmio.spmmeeg) std_data() (in module osl_ephys.source_recon.sign_flipping) Study (class in osl_ephys.utils) (class in osl_ephys.utils.study) studydir (osl_ephys.utils.Study attribute), [1] (osl_ephys.utils.study.Study attribute), [1] surf_parcellate_timeseries() (in module osl_ephys.source_recon.parcellation) surfaces_display() (in module osl_ephys.source_recon.rhino) (in module osl_ephys.source_recon.rhino.surfaces) symmetric_orthogonalise() (in module osl_ephys.source_recon.parcellation) system_call() (in module osl_ephys.source_recon.rhino.utils)

T

tag (osl_ephys.utils.spmio._events.Trial attribute) tearDownClass() (osl_ephys.tests.test_batch_preproc.TestPreprocessingBatch class method) (osl_ephys.tests.test_batch_preproc.TestPreprocessingChain class method) (osl_ephys.tests.test_file_handling.TestFileInputs class method) (osl_ephys.tests.test_file_handling.TestStudyClass class method) (osl_ephys.tests.test_glm.TestGLMSpectrum class method) (osl_ephys.tests.test_parallel.TestSimpleDask class method) test_channel_data() (osl_ephys.tests.test_00_package_canary.TestPackageData method) test_dask_batch() (osl_ephys.tests.test_batch_preproc.TestPreprocessingBatch method) test_find_files() (osl_ephys.tests.test_file_handling.TestFileInputs method) test_find_func_from_userlist() (osl_ephys.tests.test_batch_api.TestFunctionFinding method) test_find_func_in_mne_object() (osl_ephys.tests.test_batch_api.TestFunctionFinding method) test_find_func_in_mne_wrapper() (osl_ephys.tests.test_batch_api.TestFunctionFinding method) test_find_func_in_osl_wrapper() (osl_ephys.tests.test_batch_api.TestFunctionFinding method) test_glm_irasa() (osl_ephys.tests.test_glm.TestGLMSpectrum method) test_glm_spectrum() (osl_ephys.tests.test_glm.TestGLMSpectrum method) test_module_structure() (osl_ephys.tests.test_00_package_canary.TestModuleStructure method) test_parcellation_data() (osl_ephys.tests.test_00_package_canary.TestPackageData method) test_process_file_inputs() (osl_ephys.tests.test_file_handling.TestFileInputs method) test_process_file_inputs_with_missing() (osl_ephys.tests.test_file_handling.TestFileInputs method) test_process_file_inputs_with_regular_expression() (osl_ephys.tests.test_file_handling.TestFileInputs method) test_process_file_inputs_with_single_path() (osl_ephys.tests.test_file_handling.TestFileInputs method) test_simple_batch() (osl_ephys.tests.test_batch_preproc.TestPreprocessingBatch method) test_simple_chain() (osl_ephys.tests.test_batch_preproc.TestPreprocessingChain method) (osl_ephys.tests.test_batch_preproc.TestVersions method) test_simple_func() (osl_ephys.tests.test_parallel.TestSimpleDask method) test_simple_func_multiple_inputs() (osl_ephys.tests.test_parallel.TestSimpleDask method) test_simple_func_with_everything() (osl_ephys.tests.test_parallel.TestSimpleDask method) test_simple_func_with_fixed_args() (osl_ephys.tests.test_parallel.TestSimpleDask method) test_simple_func_with_fixed_kwargs() (osl_ephys.tests.test_parallel.TestSimpleDask method) test_simple_study() (osl_ephys.tests.test_file_handling.TestStudyClass method) test_simulatons_data() (osl_ephys.tests.test_00_package_canary.TestPackageData method) TestFileInputs (class in osl_ephys.tests.test_file_handling) TestFunctionFinding (class in osl_ephys.tests.test_batch_api) TestGLMSpectrum (class in osl_ephys.tests.test_glm) TestModuleStructure (class in osl_ephys.tests.test_00_package_canary) TestPackageData (class in osl_ephys.tests.test_00_package_canary) TestPreprocessingBatch (class in osl_ephys.tests.test_batch_preproc) TestPreprocessingChain (class in osl_ephys.tests.test_batch_preproc) TestSimpleDask (class in osl_ephys.tests.test_parallel) TestStudyClass (class in osl_ephys.tests.test_file_handling)

TestVersions (class in osl_ephys.tests.test_batch_preproc) time (osl_ephys.utils.spmio._events.Event attribute) (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) time_embed() (in module osl_ephys.source_recon.sign_flipping) time_onset (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) times (osl_ephys.glm.glm_epochs.GLMEpochsResult attribute) (osl_ephys.glm.glm_epochs.GroupGLMEpochs attribute) (osl_ephys.glm.GLMEpochsResult attribute) (osl_ephys.glm.GroupGLMEpochs attribute) (osl_ephys.utils.spmio._events.Trial property) timeseries2nii() (in module osl_ephys.source_recon.rhino.utils) tmin (osl_ephys.glm.glm_epochs.GLMEpochsResult attribute) (osl_ephys.glm.glm_epochs.GroupGLMEpochs attribute) (osl_ephys.glm.GLMEpochsResult attribute) (osl_ephys.glm.GroupGLMEpochs attribute) to_dict() (osl_ephys.utils.spmio._events.Event method) tra (osl_ephys.utils.spmio._data.Montage attribute) transform (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) transform_bet_surfaces() (in module osl_ephys.source_recon.rhino.utils) transform_recon_timeseries() (in module osl_ephys.source_recon.beamforming) transform_vtk_mesh() (in module osl_ephys.source_recon.rhino.utils) Trial (class in osl_ephys.utils.spmio._events) trial_definition (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) trial_end (osl_ephys.utils.spmio._events.Event attribute) trial_start (osl_ephys.utils.spmio._events.Event attribute) trial_starts (osl_ephys.utils.spmio._events.Trial property) TrialParameters (class in osl_ephys.utils.spmio.spmmeeg) type (osl_ephys.utils.spmio._data.Channel attribute) (osl_ephys.utils.spmio._events.Event attribute) (osl_ephys.utils.spmio.SPMMEEG attribute) (osl_ephys.utils.spmio.spmmeeg.SPMMEEG attribute) (osl_ephys.utils.SPMMEEG attribute) types (osl_ephys.utils.spmio._events.Trial property)

U

units (osl_ephys.utils.spmio._data.Channel attribute)

update_config() (in module osl_ephys.report.src_report)

V

validate_outdir() (in module osl_ephys.maxfilter) (in module osl_ephys.preprocessing) (in module osl_ephys.report) (in module osl_ephys.source_recon) (in module osl_ephys.utils) (in module osl_ephys.utils.file_handling)

value (osl_ephys.utils.spmio._events.Event attribute) values (osl_ephys.utils.spmio._events.Trial property) vol_parcellate_timeseries() (in module osl_ephys.source_recon.parcellation) voxel_timeseries() (in module osl_ephys.source_recon.beamforming)

W

write_dataset() (in module osl_ephys.preprocessing) (in module osl_ephys.preprocessing.batch)

X

x (osl_ephys.utils.spmio._data.Channel attribute)

xform_points() (in module osl_ephys.source_recon.rhino.utils)

Y

y (osl_ephys.utils.spmio._data.Channel attribute)