Index

A

abs_canonical_power() (in module meganorm.src.featureExtraction) abs_individual_power() (in module meganorm.src.featureExtraction) add_feature() (in module meganorm.src.featureExtraction) add_specific_layout() (in module meganorm.layouts.layouts) annotate_noisy_raw() (in module meganorm.src.preprocess) aperiodic_mode (meganorm.utils.IO.Config attribute) apply_auto_ica_pipeline() (in module meganorm.src.preprocess) apply_chpi() (in module meganorm.src.preprocess) apply_chpi_filter (meganorm.utils.IO.Config attribute) apply_empty_room_recording (meganorm.utils.IO.Config attribute) apply_environmental_noise_correction (meganorm.utils.IO.Config attribute) apply_environmental_noise_ica_with_ref_meg (meganorm.utils.IO.Config attribute) apply_environmental_noise_ssp_with_eroom (meganorm.utils.IO.Config attribute) apply_gedai (meganorm.utils.IO.Config attribute) apply_gradient_comp() (in module meganorm.src.preprocess) apply_Head_movement_correction (meganorm.utils.IO.Config attribute) apply_ica (meganorm.utils.IO.Config attribute)

apply_ica_elbow_detection (meganorm.utils.IO.Config attribute) apply_morphing (meganorm.utils.IO.Config attribute) apply_mri_QC (meganorm.utils.IO.Config attribute) apply_mri_template (meganorm.utils.IO.Config attribute) apply_oversampled_temporal_projection (meganorm.utils.IO.Config attribute) apply_source_localization (meganorm.utils.IO.Config attribute) apply_tsss() (in module meganorm.src.preprocess) auto_ica_corr_thr (meganorm.utils.IO.Config attribute) auto_ica_with_corr() (in module meganorm.src.preprocess) auto_ica_with_mean() (in module meganorm.src.preprocess) auto_parallel_feature_extraction() (in module meganorm.utils.parallel) auto_reject_segmentation() (in module meganorm.src.preprocess) AutoIca_with_IcaLabel() (in module meganorm.src.preprocess) autoreject_consensus_percs (meganorm.utils.IO.Config attribute) autoreject_cv (meganorm.utils.IO.Config attribute) autoreject_n_interpolates (meganorm.utils.IO.Config attribute) autoreject_thresh_method (meganorm.utils.IO.Config attribute)

B

bad_segment_removal_method (meganorm.utils.IO.Config attribute) band_power_ratio() (in module meganorm.src.featureExtraction) BandRatio (class in meganorm.utils.IO)

beamforme_depth (meganorm.utils.IO.Config attribute) beamformer_arg_check() (meganorm.utils.IO.Config method) beamformer_pick_ori (meganorm.utils.IO.Config attribute) beamformer_weight_norm (meganorm.utils.IO.Config attribute)

C

cal_stats_for_INOCs() (in module meganorm.utils.nm) calculate_PNOCs() (in module meganorm.utils.nm) center_head_bias_scale_check() (meganorm.utils.IO.Config method) check_jobs_status() (in module meganorm.utils.parallel) check_log_for_success() (in module meganorm.utils.freesurfer) check_user_jobs() (in module meganorm.utils.parallel) classify_subject_status() (in module meganorm.utils.freesurfer) clean_nan_columns() (in module meganorm.utils.IO) collect_results() (in module meganorm.utils.parallel) compute_hemispheric_asymmetry() (in module meganorm.src.featureExtraction) computePsd() (in module meganorm.src.psdParameterize)

Config (class in meganorm.utils.IO) coregisteration_final_n_iterations (meganorm.utils.IO.Config attribute) coregisteration_final_nasion_weight (meganorm.utils.IO.Config attribute) coregisteration_scale_mode (meganorm.utils.IO.Config attribute) covariance_method (meganorm.utils.IO.Config attribute) create_feature_container() (in module meganorm.src.featureExtraction) create_layouts() (in module meganorm.layouts.layouts) create_slurm_script() (in module meganorm.utils.freesurfer) ctf_gradient_comp_level (meganorm.utils.IO.Config attribute) cutoffFreqHigh (meganorm.utils.IO.Config attribute) cutoffFreqLow (meganorm.utils.IO.Config attribute)

D

denominator (meganorm.utils.IO.BandRatio attribute) digital_filter (meganorm.utils.IO.Config attribute) discover_subjects() (in module meganorm.utils.freesurfer)

drop_mag_or_grad() (in module meganorm.src.preprocess) drop_noisy_flat_channel (meganorm.utils.IO.Config attribute) drop_noisy_meg_channels() (in module meganorm.src.preprocess) drop_noisy_segments() (in module meganorm.src.preprocess)

E

eeg_flat_threshold (meganorm.utils.IO.Config attribute) eeg_var_threshold (meganorm.utils.IO.Config attribute) either_template_mri_or_mri_qc() (meganorm.utils.IO.Config method) env_noise_removal_same() (meganorm.utils.IO.Config method) environmental_noise_ica_with_ref_meg_measure (meganorm.utils.IO.Config attribute)

environmental_noise_ica_with_ref_meg_method (meganorm.utils.IO.Config attribute) environmental_noise_ica_with_ref_meg_thr (meganorm.utils.IO.Config attribute) estimate_centiles() (in module meganorm.utils.nm) evaluate_mace() (in module meganorm.utils.nm) extract_rs_blocks() (in module meganorm.src.preprocess)

F

feature_categories (meganorm.utils.IO.Config attribute) feature_extract() (in module meganorm.src.featureExtraction) find_bids_t1w_files() (in module meganorm.utils.freesurfer) find_failed_meg_subjects() (in module meganorm.utils.IO) find_ica_component() (in module meganorm.src.preprocess) find_other_meg_session() (in module meganorm.utils.IO) find_other_mri_session() (in module meganorm.utils.IO) find_ref_meg_artifact() (in module meganorm.src.preprocess) fooof() (in module meganorm.src.psdParameterize) fooof_freq_range_high (meganorm.utils.IO.Config attribute)

fooof_freq_range_low (meganorm.utils.IO.Config attribute) fooof_min_peak_height (meganorm.utils.IO.Config attribute) fooof_peak_threshold (meganorm.utils.IO.Config attribute) fooof_peak_width_limits (meganorm.utils.IO.Config attribute) fooof_res_save_path (meganorm.utils.IO.Config attribute) FOOOFDecomposer (class in meganorm.src.featureExtraction) freesurfer_home (meganorm.utils.IO.Config attribute) freesurfer_license (meganorm.utils.IO.Config attribute) freesurfer_QC() (in module meganorm.utils.freesurfer) freesurfer_template_path (meganorm.utils.IO.Config attribute) freq_bands (meganorm.utils.IO.Config attribute)

G

gcaatlas (meganorm.utils.IO.Config attribute) gedai_duration (meganorm.utils.IO.Config attribute) gedai_epoch_size_in_cycles (meganorm.utils.IO.Config attribute) gedai_highpass_cutoff (meganorm.utils.IO.Config attribute) gedai_method (meganorm.utils.IO.Config attribute) gedai_noise_multiplier (meganorm.utils.IO.Config attribute) gedai_overlap (meganorm.utils.IO.Config attribute) gedai_params_check() (meganorm.utils.IO.Config method) gedai_preliminary_broadband_noise_multiplier (meganorm.utils.IO.Config attribute) gedai_preprocess() (in module meganorm.src.preprocess) gedai_wavelet_level (meganorm.utils.IO.Config attribute) gedai_wavelet_low_cutoff (meganorm.utils.IO.Config attribute) gedai_wavelet_type (meganorm.utils.IO.Config attribute) get_aperiodic_params() (meganorm.src.featureExtraction.FOOOFDecomposer method) (meganorm.src.featureExtraction.PYRASADecomposer method) (meganorm.src.featureExtraction.SpectralDecomposer method)

get_freesurfer_home() (in module meganorm.utils.freesurfer) get_peak_params() (meganorm.src.featureExtraction.FOOOFDecomposer method) (meganorm.src.featureExtraction.PYRASADecomposer method) (meganorm.src.featureExtraction.SpectralDecomposer method) get_periodic_spectrum() (meganorm.src.featureExtraction.FOOOFDecomposer method) (meganorm.src.featureExtraction.PYRASADecomposer method) (meganorm.src.featureExtraction.SpectralDecomposer method) get_r_squared() (meganorm.src.featureExtraction.FOOOFDecomposer method) (meganorm.src.featureExtraction.PYRASADecomposer method) (meganorm.src.featureExtraction.SpectralDecomposer method) get_relative_path() (in module meganorm.layouts.layouts) grad_flat_threshold (meganorm.utils.IO.Config attribute) grad_var_threshold (meganorm.utils.IO.Config attribute)

H

haddbr_data_split() (in module meganorm.utils.nm)

head_motion_correction() (in module meganorm.src.preprocess) Head_movement_limit_from_mean (meganorm.utils.IO.Config attribute)

I

ica_e_noise_removal() (meganorm.utils.IO.Config method) ica_if_reject_by_annotation (meganorm.utils.IO.Config attribute) ica_max_iter (meganorm.utils.IO.Config attribute) ica_method (meganorm.utils.IO.Config attribute) ica_n_component (meganorm.utils.IO.Config attribute)

individualized_band_ranges (meganorm.utils.IO.Config attribute) inverse_regularization_value (meganorm.utils.IO.Config attribute) irasa_epochs() (in module meganorm.src.psdParameterize) irasa_hset (meganorm.utils.IO.Config attribute) is_success() (in module meganorm.utils.freesurfer)

L

load() (meganorm.utils.IO.Config class method) (meganorm.utils.IO.Config method)

load_specific_layout() (in module meganorm.layouts.layouts) log_tail_lines() (in module meganorm.utils.freesurfer)

M

mag_flat_threshold (meganorm.utils.IO.Config attribute) mag_var_threshold (meganorm.utils.IO.Config attribute) main() (in module meganorm.src.mainParallel) main_argparser() (in module meganorm.src.mainParallel) make_demo_file_bids() (in module meganorm.utils.IO) make_new_watershed_bem (meganorm.utils.IO.Config attribute) meganorm module meganorm.layouts module meganorm.layouts.layouts module meganorm.src module meganorm.src.featureExtraction module meganorm.src.mainParallel module meganorm.src.preprocess module meganorm.src.psdParameterize module meganorm.utils module meganorm.utils.EEGlab module meganorm.utils.freesurfer module meganorm.utils.IO module

meganorm.utils.nm module meganorm.utils.parallel module merge_datasets_with_glob() (in module meganorm.utils.IO) merge_fidp_demo() (in module meganorm.utils.IO) min_r_squared (meganorm.utils.IO.Config attribute) model_config (meganorm.utils.IO.BandRatio attribute) (meganorm.utils.IO.Config attribute) module meganorm meganorm.layouts meganorm.layouts.layouts meganorm.src meganorm.src.featureExtraction meganorm.src.mainParallel meganorm.src.preprocess meganorm.src.psdParameterize meganorm.utils meganorm.utils.EEGlab meganorm.utils.freesurfer meganorm.utils.IO meganorm.utils.nm meganorm.utils.parallel mri_template_check() (meganorm.utils.IO.Config method) muscle_activity_filter_freq (meganorm.utils.IO.Config attribute) muscle_activity_filter_freq_fv() (meganorm.utils.IO.Config class method) muscle_activity_min_length_good (meganorm.utils.IO.Config attribute) muscle_activity_thr (meganorm.utils.IO.Config attribute) muscle_activity_thr_fv() (meganorm.utils.IO.Config class method)

N

notch_filter (meganorm.utils.IO.Config attribute)

numerator (meganorm.utils.IO.BandRatio attribute)

P

pacellation_checker() (meganorm.utils.IO.Config method) parameterize_psds() (in module meganorm.src.psdParameterize) parametrization_method (meganorm.utils.IO.Config attribute) parcellation_annot_fname (meganorm.utils.IO.Config attribute) parcellation_parc (meganorm.utils.IO.Config attribute) pca_elbow_locator() (in module meganorm.src.preprocess) power_band_ratios_list (meganorm.utils.IO.Config attribute) prepare_eeg_data() (in module meganorm.src.preprocess)

prepare_mri_data() (in module meganorm.utils.freesurfer) prepare_prediction_data() (in module meganorm.utils.nm) preprocess() (in module meganorm.src.preprocess) progress_bar() (in module meganorm.utils.parallel) psd_method (meganorm.utils.IO.Config attribute) psd_n_fft (meganorm.utils.IO.Config attribute) psd_n_overlap (meganorm.utils.IO.Config attribute) psd_n_per_seg (meganorm.utils.IO.Config attribute) PYRASADecomposer (class in meganorm.src.featureExtraction)

R

random_state (meganorm.utils.IO.Config attribute) RawEEGLAB (class in meganorm.utils.EEGlab) read_raw_eeglab() (in module meganorm.utils.EEGlab) rel_canonical_power() (in module meganorm.src.featureExtraction) rel_individual_power() (in module meganorm.src.featureExtraction)

remove_environmental_noise() (in module meganorm.src.preprocess) rereference_method (meganorm.utils.IO.Config attribute) resampling_rate (meganorm.utils.IO.Config attribute) retrieve_freesurfer_eulernum() (in module meganorm.utils.freesurfer) run_parallel_reconall() (in module meganorm.utils.freesurfer)

S

same_environmental_noise_removal (meganorm.utils.IO.Config attribute) save() (meganorm.utils.IO.Config method), [1] save_psds (meganorm.utils.IO.Config attribute) save_sensor_layouts() (in module meganorm.layouts.layouts) save_source_localized_epochs (meganorm.utils.IO.Config attribute) sbatch_feature_extraction_runner() (in module meganorm.utils.parallel) sbatchfile() (in module meganorm.utils.parallel) segment_epoch() (in module meganorm.src.preprocess) segments_length (meganorm.utils.IO.Config attribute) segments_overlap (meganorm.utils.IO.Config attribute) segments_tmax (meganorm.utils.IO.Config attribute) segments_tmin (meganorm.utils.IO.Config attribute) sensai_method (meganorm.utils.IO.Config attribute) separate_eyes_open_close_eeglab() (in module meganorm.utils.IO)

set_logger() (in module meganorm.src.mainParallel) set_path() (in module meganorm.utils.IO) shapiro_stat() (in module meganorm.utils.nm) SL_conductivity (meganorm.utils.IO.Config attribute) SL_conductivity_mv() (meganorm.utils.IO.Config method) SL_inverse_operator (meganorm.utils.IO.Config attribute) SL_source_space (meganorm.utils.IO.Config attribute) source_space_res() (meganorm.utils.IO.Config method) source_space_spacing (meganorm.utils.IO.Config attribute) source_space_spacing_number (meganorm.utils.IO.Config attribute) SpectralDecomposer (class in meganorm.src.featureExtraction) sqc_parameterize_psds() (in module meganorm.src.psdParameterize) submit_jobs() (in module meganorm.utils.parallel) summarizeFeatures() (in module meganorm.src.featureExtraction)

W

which_layout (meganorm.utils.IO.Config attribute) which_meg_session (meganorm.utils.IO.Config attribute)

which_sensor (meganorm.utils.IO.Config attribute) wilcoxon_rank_test() (in module meganorm.utils.nm)

Z

zscore_std_thresh (meganorm.utils.IO.Config attribute)