MEG_QC API documentation

Contents:

• Tutorial
• Installation
• API documentation
  • Pipeline Settings
    • Default settings [DEFAULT]
    • Filtering [Filtering]
    • Epoching [Epoching]
    • Standard deviation [STD]
    • Power spectral density [PSD]
    • Peak-to-peak amplitude manual [PTP_manual]
    • Peak-to-peak amplitude auto (based on MNE annotatons) [PTP_auto]
    • Heart beat artifacts [ECG]
    • Eye movement artifacts [EOG]
    • Head_movement artifacts [Head_movement]
    • Muscle artifacts [Muscle]
  • Internal Pipeline Settings
    • [ECG]
    • [EOG]
    • [PSD]
  • QC_derivative, MEG_channel classes
    • MEG_channel
    • QC_channel
    • QC_derivative
  • Calculation pipeline
  • Initial processing
    • Epoch_meg()
    • add_3d_ch_locations()
    • add_EEG_lobes()
    • apply_eeg_montage()
    • apply_eeg_reference()
    • assign_channels_properties()
    • change_ch_type_CTF()
    • check_chosen_ch_types()
    • choose_channels()
    • chs_dict_to_csv()
    • delete_temp_folder()
    • get_all_config_params()
    • get_internal_config_params()
    • initial_processing()
    • load_data()
    • remove_fif_and_splits()
    • save_meg_with_suffix()
    • sort_channels_by_lobe()
    • stim_data_to_df()
  • Standard deviation
    • STD_meg_qc()
    • get_big_small_std_ptp_all_data()
    • get_noisy_flat_std_ptp_epochs()
    • get_std_all_data()
    • get_std_epochs()
    • make_dict_global_std_ptp()
    • make_dict_local_std_ptp()
    • make_simple_metric_std()
  • Frequency spectrum
    • PSD_meg_qc()
    • add_log_buttons()
    • assign_psds_to_channels()
    • cut_the_noise_from_psd()
    • find_noisy_freq_bands_complex()
    • find_noisy_freq_bands_simple()
    • find_number_and_ampl_of_noise_freqs()
    • get_ampl_of_brain_waves()
    • get_ampl_of_noisy_freqs()
    • get_bands_amplitude_per_ch()
    • get_nfft_nperseg()
    • make_dict_global_psd()
    • make_dict_local_psd()
    • make_simple_metric_psd()
    • plot_one_psd()
    • split_blended_freqs_at_the_lowest_point()
  • Peak to peak amplitude manual
    • PP_manual_meg_qc()
    • get_ptp_all_data()
    • get_ptp_epochs()
    • make_simple_metric_ptp_manual()
    • neighbour_peak_amplitude()
  • Peak to peak amplitude auto: based on MNE annotations
  • ECG and EOG
    • Avg_artif
    • ECG_meg_qc()
    • EOG_meg_qc()
    • align_artif_data()
    • align_mean_rwave()
    • assign_lobe_to_artifacts()
    • calculate_artifacts_on_channels()
    • check_3_conditions()
    • check_mean_wave()
    • detect_channels_above_norm()
    • detect_noisy_ecg()
    • estimate_t0()
    • find_affected_by_amplitude_ratio()
    • find_affected_by_correlation()
    • find_affected_by_similarity_score()
    • find_affected_over_mean()
    • find_epoch_peaks()
    • find_mean_rwave_blink()
    • find_t0_channels()
    • find_t0_highest()
    • find_t0_mean()
    • flip_channels()
    • get_ECG_data_choose_method()
    • get_EOG_data()
    • make_dict_global_ECG_EOG()
    • make_simple_metric_ECG_EOG()
    • minmax_amplitude()
    • reconstruct_ecg_and_check()
    • rms_amplitude()
    • shift_mean_wave()
    • split_correlated_artifacts_into_3_groups()
  • High frequency (muscle) disturbancies
    • MUSCLE_meg_qc()
    • attach_dummy_data()
    • calculate_muscle_NO_threshold()
    • filter_noise_before_muscle_detection()
    • find_powerline_noise_short()
    • make_simple_metric_muscle()
    • save_muscle_to_csv()
  • Head movement artifacts
    • HEAD_movement_meg_qc()
    • compute_head_pos_std_and_max_rotation_movement()
    • get_head_positions()
    • head_pos_to_csv()
    • make_simple_metric_head()
  • Plots and reports pipeline
  • Plotting functions
    • Plot_psd_csv()
    • add_log_buttons()
    • assign_epoched_std_ptp_to_channels()
    • boxplot_all_time_csv()
    • boxplot_epoched_xaxis_channels_csv()
    • boxplot_epoched_xaxis_epochs_csv()
    • boxplot_epochs()
    • build_metric_derivatives_from_tsv()
    • edit_legend_pie_SNR()
    • figure_x_axis()
    • get_meg_system()
    • get_tit_and_unit()
    • keep_unique_locs()
    • make_3d_sensors_trace()
    • make_head_annots_plot()
    • make_head_pos_plot_mne()
    • plot_3d_topomap_ecg_eog_csv()
    • plot_3d_topomap_psd_csv()
    • plot_3d_topomap_std_ptp_csv()
    • plot_ECG_EOG_channel_csv()
    • plot_affected_channels_csv()
    • plot_artif_per_ch_3_groups()
    • plot_ch_df_as_lines_by_lobe_csv()
    • plot_correlation_csv()
    • plot_ecg_eog_mne()
    • plot_event_count_bar()
    • plot_event_timeline()
    • plot_head_pos_csv()
    • plot_mean_rwave_csv()
    • plot_mean_rwave_shifted()
    • plot_muscle_annotations_mne()
    • plot_muscle_csv()
    • plot_pie_chart_freq_csv()
    • plot_sensors_3d_csv()
    • plot_stim_csv()
    • plot_stim_csv_colored_leveled()
    • plot_stim_csv_simple()
    • plot_stim_events_comparison_table()
    • plot_topomap_std_ptp_csv()
    • split_affected_into_3_groups_csv()
    • switch_names_on_off()
  • Report functions
    • combine_howto_sensors_and_metric()
    • keep_fig_derivs()
    • make_howto_use_plots_section()
    • make_joined_report()
    • make_joined_report_mne()
    • make_metric_section()
    • make_sensor_figs_section()
    • make_summary_qc_report()
    • simple_metric_basic()

Indices and tables

• Index

• Module Index

• Search Page