meganorm package

Subpackages

• meganorm.src package
  • Submodules
  • meganorm.src.featureExtraction module
    • FOOOFDecomposer
      • FOOOFDecomposer.get_aperiodic_params()
      • FOOOFDecomposer.get_peak_params()
      • FOOOFDecomposer.get_periodic_spectrum()
      • FOOOFDecomposer.get_r_squared()
    • PYRASADecomposer
      • PYRASADecomposer.get_aperiodic_params()
      • PYRASADecomposer.get_peak_params()
      • PYRASADecomposer.get_periodic_spectrum()
      • PYRASADecomposer.get_r_squared()
    • SpectralDecomposer
      • SpectralDecomposer.get_aperiodic_params()
      • SpectralDecomposer.get_peak_params()
      • SpectralDecomposer.get_periodic_spectrum()
      • SpectralDecomposer.get_r_squared()
    • abs_canonical_power()
    • abs_individual_power()
    • add_feature()
    • band_power_ratio()
    • compute_hemispheric_asymmetry()
    • create_feature_container()
    • feature_extract()
    • rel_canonical_power()
    • rel_individual_power()
    • summarizeFeatures()
  • meganorm.src.mainParallel module
    • main()
    • main_argparser()
    • set_logger()
  • meganorm.src.preprocess module
    • AutoIca_with_IcaLabel()
    • annotate_noisy_raw()
    • apply_auto_ica_pipeline()
    • apply_chpi()
    • apply_gradient_comp()
    • apply_tsss()
    • auto_ica_with_corr()
    • auto_ica_with_mean()
    • auto_reject_segmentation()
    • drop_mag_or_grad()
    • drop_noisy_meg_channels()
    • drop_noisy_segments()
    • extract_rs_blocks()
    • find_ica_component()
    • find_ref_meg_artifact()
    • gedai_preprocess()
    • head_motion_correction()
    • pca_elbow_locator()
    • prepare_eeg_data()
    • preprocess()
    • remove_environmental_noise()
    • segment_epoch()
  • meganorm.src.psdParameterize module
    • computePsd()
    • fooof()
    • irasa_epochs()
    • parameterize_psds()
    • sqc_parameterize_psds()
  • Module contents
• meganorm.utils package
  • Submodules
  • meganorm.utils.EEGlab module
    • RawEEGLAB
    • read_raw_eeglab()
  • meganorm.utils.IO module
    • BandRatio
      • BandRatio.denominator
      • BandRatio.model_config
      • BandRatio.numerator
    • Config
      • Config.save()
      • Config.load()
      • Config.Head_movement_limit_from_mean
      • Config.SL_conductivity
      • Config.SL_conductivity_mv()
      • Config.SL_inverse_operator
      • Config.SL_source_space
      • Config.aperiodic_mode
      • Config.apply_Head_movement_correction
      • Config.apply_chpi_filter
      • Config.apply_empty_room_recording
      • Config.apply_environmental_noise_correction
      • Config.apply_environmental_noise_ica_with_ref_meg
      • Config.apply_environmental_noise_ssp_with_eroom
      • Config.apply_gedai
      • Config.apply_ica
      • Config.apply_ica_elbow_detection
      • Config.apply_morphing
      • Config.apply_mri_QC
      • Config.apply_mri_template
      • Config.apply_oversampled_temporal_projection
      • Config.apply_source_localization
      • Config.auto_ica_corr_thr
      • Config.autoreject_consensus_percs
      • Config.autoreject_cv
      • Config.autoreject_n_interpolates
      • Config.autoreject_thresh_method
      • Config.bad_segment_removal_method
      • Config.beamforme_depth
      • Config.beamformer_arg_check()
      • Config.beamformer_pick_ori
      • Config.beamformer_weight_norm
      • Config.center_head_bias_scale_check()
      • Config.coregisteration_final_n_iterations
      • Config.coregisteration_final_nasion_weight
      • Config.coregisteration_scale_mode
      • Config.covariance_method
      • Config.ctf_gradient_comp_level
      • Config.cutoffFreqHigh
      • Config.cutoffFreqLow
      • Config.digital_filter
      • Config.drop_noisy_flat_channel
      • Config.eeg_flat_threshold
      • Config.eeg_var_threshold
      • Config.either_template_mri_or_mri_qc()
      • Config.env_noise_removal_same()
      • Config.environmental_noise_ica_with_ref_meg_measure
      • Config.environmental_noise_ica_with_ref_meg_method
      • Config.environmental_noise_ica_with_ref_meg_thr
      • Config.feature_categories
      • Config.fooof_freq_range_high
      • Config.fooof_freq_range_low
      • Config.fooof_min_peak_height
      • Config.fooof_peak_threshold
      • Config.fooof_peak_width_limits
      • Config.fooof_res_save_path
      • Config.freesurfer_home
      • Config.freesurfer_license
      • Config.freesurfer_template_path
      • Config.freq_bands
      • Config.gcaatlas
      • Config.gedai_duration
      • Config.gedai_epoch_size_in_cycles
      • Config.gedai_highpass_cutoff
      • Config.gedai_method
      • Config.gedai_noise_multiplier
      • Config.gedai_overlap
      • Config.gedai_params_check()
      • Config.gedai_preliminary_broadband_noise_multiplier
      • Config.gedai_wavelet_level
      • Config.gedai_wavelet_low_cutoff
      • Config.gedai_wavelet_type
      • Config.grad_flat_threshold
      • Config.grad_var_threshold
      • Config.ica_e_noise_removal()
      • Config.ica_if_reject_by_annotation
      • Config.ica_max_iter
      • Config.ica_method
      • Config.ica_n_component
      • Config.individualized_band_ranges
      • Config.inverse_regularization_value
      • Config.irasa_hset
      • Config.load()
      • Config.mag_flat_threshold
      • Config.mag_var_threshold
      • Config.make_new_watershed_bem
      • Config.min_r_squared
      • Config.model_config
      • Config.mri_template_check()
      • Config.muscle_activity_filter_freq
      • Config.muscle_activity_filter_freq_fv()
      • Config.muscle_activity_min_length_good
      • Config.muscle_activity_thr
      • Config.muscle_activity_thr_fv()
      • Config.notch_filter
      • Config.pacellation_checker()
      • Config.parametrization_method
      • Config.parcellation_annot_fname
      • Config.parcellation_parc
      • Config.power_band_ratios_list
      • Config.psd_method
      • Config.psd_n_fft
      • Config.psd_n_overlap
      • Config.psd_n_per_seg
      • Config.random_state
      • Config.rereference_method
      • Config.resampling_rate
      • Config.same_environmental_noise_removal
      • Config.save()
      • Config.save_psds
      • Config.save_source_localized_epochs
      • Config.segments_length
      • Config.segments_overlap
      • Config.segments_tmax
      • Config.segments_tmin
      • Config.sensai_method
      • Config.source_space_res()
      • Config.source_space_spacing
      • Config.source_space_spacing_number
      • Config.which_layout
      • Config.which_meg_session
      • Config.which_sensor
      • Config.zscore_std_thresh
    • clean_nan_columns()
    • find_failed_meg_subjects()
    • find_other_meg_session()
    • find_other_mri_session()
    • make_demo_file_bids()
    • merge_datasets_with_glob()
    • merge_fidp_demo()
    • separate_eyes_open_close_eeglab()
    • set_path()
  • meganorm.utils.freesurfer module
    • check_log_for_success()
    • classify_subject_status()
    • create_slurm_script()
    • discover_subjects()
    • find_bids_t1w_files()
    • freesurfer_QC()
    • get_freesurfer_home()
    • is_success()
    • log_tail_lines()
    • prepare_mri_data()
    • retrieve_freesurfer_eulernum()
    • run_parallel_reconall()
  • meganorm.utils.nm module
    • cal_stats_for_INOCs()
    • calculate_PNOCs()
    • estimate_centiles()
    • evaluate_mace()
    • haddbr_data_split()
    • prepare_prediction_data()
    • shapiro_stat()
    • wilcoxon_rank_test()
  • meganorm.utils.parallel module
    • auto_parallel_feature_extraction()
    • check_jobs_status()
    • check_user_jobs()
    • collect_results()
    • progress_bar()
    • sbatch_feature_extraction_runner()
    • sbatchfile()
    • submit_jobs()
  • Module contents
• meganorm.plots package
  • Submodules
  • meganorm.plots.plots module
  • Module contents
• meganorm.layouts package
  • Submodules
  • meganorm.layouts.layouts module
    • add_specific_layout()
    • create_layouts()
    • get_relative_path()
    • load_specific_layout()
    • save_sensor_layouts()
  • Module contents

Module contents