Index

_

_add_domain (msqms.qc.metrics_factory.MetricsFactory attribute)

_registry (msqms.qc.metrics_factory.MetricsFactory attribute)

B

bad_before_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) bad_chan_index (msqms.qc.metrics.Metrics attribute)

bad_chan_mask (msqms.qc.metrics.Metrics attribute) bad_chan_names (msqms.qc.metrics.Metrics attribute) bad_seg_mask (msqms.qc.metrics.Metrics attribute)

C

calculate_category_score() (msqms.qc.msqm.MSQM method) calculate_quality_metrics() (in module msqms.quality_reference.quality_reference) check_if_directory() (in module msqms.utils.utils) compute_1d_arv() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_1d_factors() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_baseline_offset() (msqms.qc.statistic_metrics.StatsDomainMetric method) compute_energy_entropy() (msqms.qc.entropy_metrics.EntropyDomainMetric method) compute_entropies() (msqms.qc.entropy_metrics.EntropyDomainMetric method) compute_fractal_dimension() (msqms.qc.fractal_metrics.FractalDomainMetric method) compute_kurtosis() (msqms.qc.statistic_metrics.StatsDomainMetric method) compute_mag_field_change() (msqms.qc.statistic_metrics.StatsDomainMetric method) compute_max_field_change() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_max_min_range() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_metrics() (msqms.qc.entropy_metrics.EntropyDomainMetric method) (msqms.qc.fractal_metrics.FractalDomainMetric method) (msqms.qc.freq_domain_metrics.FreqDomainMetric method) (msqms.qc.metrics.Metrics method) (msqms.qc.statistic_metrics.StatsDomainMetric method) (msqms.qc.time_domain_metrics.TimeDomainMetric method)

compute_msqm_score() (msqms.qc.msqm.MSQM method) compute_ptp() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_rms() (msqms.qc.time_domain_metrics.TimeDomainMetric method) compute_single_metric() (msqms.qc.msqm.MSQM method) compute_skewness() (msqms.qc.statistic_metrics.StatsDomainMetric method) config_default (msqms.qc.metrics.Metrics attribute) convert_to_yaml() (in module msqms.quality_reference.quality_reference) create_metric() (msqms.qc.metrics_factory.MetricsFactory class method) (msqms.qc.metrics_factory.MetricsFactory method)

D

data_type (msqms.qc.metrics.Metrics attribute) data_type_specific_config (msqms.qc.metrics.Metrics attribute) detect_artefacts() (in module msqms.libs.osl.osl_wrappers)

detect_badchannels() (in module msqms.libs.osl.osl_wrappers) detect_badsegments() (in module msqms.libs.osl.osl_wrappers) detect_maxfilt_zeros() (in module msqms.libs.osl.osl_wrappers) drop_bad_epochs() (in module msqms.libs.osl.osl_wrappers)

E

EEG_before_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute)

EntropyDomainMetric (class in msqms.qc.entropy_metrics)

F

fill_zeros_with_nearest_value() (in module msqms.utils.utils) filter() (in module msqms.utils.utils) find_all_bads() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_correlation() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_deviation() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_hfnoise() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_nan_flat() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_ransac() (in module msqms.libs.pyprep.ransac) (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_by_SNR() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method) find_bad_channels_by_osl() (msqms.qc.statistic_metrics.StatsDomainMetric method)

find_bad_channels_by_prep() (msqms.qc.statistic_metrics.StatsDomainMetric method) find_bad_channels_by_psd() (msqms.qc.statistic_metrics.StatsDomainMetric method) find_bad_segments_by_osl() (msqms.qc.statistic_metrics.StatsDomainMetric method) find_flat() (msqms.qc.statistic_metrics.StatsDomainMetric method) find_NaN_values() (msqms.qc.statistic_metrics.StatsDomainMetric method) find_zero_values() (msqms.qc.statistic_metrics.StatsDomainMetric method) fit() (msqms.libs.pyprep.prep_pipeline.PrepPipeline method) flat_mask (msqms.qc.metrics.Metrics attribute) format_timedelta() (in module msqms.utils.utils) FractalDomainMetric (class in msqms.qc.fractal_metrics) FreqDomainMetric (class in msqms.qc.freq_domain_metrics)

G

gen_base_template() (msqms.reports.report.HtmlReport method) gen_body_html() (msqms.reports.report.HtmlReport method) gen_html_report() (msqms.reports.report.HtmlReport method) gen_nav_html() (msqms.reports.report.HtmlReport method) gen_quality_report() (in module msqms.reports.report) gen_summary_quality_report() (in module msqms.reports.report) gesd() (in module msqms.libs.osl.osl_wrappers) get_bads() (msqms.libs.pyprep.find_noisy_channels.NoisyChannels method)

get_configure() (in module msqms.utils.utils) (msqms.qc.metrics.Metrics method) (msqms.qc.msqm.MSQM method) get_header_info() (in module msqms.qc.basic_info) get_info_from_bids() (in module msqms.io.bids_dataset) get_quality_references() (msqms.qc.msqm.MSQM method) get_subjects_from_bids() (in module msqms.io.bids_dataset) get_template() (msqms.reports.report.HtmlReport method) (msqms.reports.report.SummaryHtmlReport method)

H

HtmlReport (class in msqms.reports.report)

I

identify_bad_channels() (msqms.qc.statistic_metrics.StatsDomainMetric method)

interpolated_channels (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) is_bids_dataset() (in module msqms.quality_reference.quality_reference)

L

list_existing_quality_references() (in module msqms.quality_reference.quality_reference)

M

meg_data (msqms.qc.metrics.Metrics attribute) meg_names (msqms.qc.metrics.Metrics attribute) meg_type (msqms.qc.metrics.Metrics attribute) Metrics (class in msqms.qc.metrics) MetricsFactory (class in msqms.qc.metrics_factory) module msqms msqms.cli msqms.cli.workflow msqms.constants msqms.io msqms.io.bids_dataset msqms.io.raw_dataset msqms.libs msqms.libs.osl msqms.libs.osl.osl_wrappers msqms.libs.pyprep msqms.libs.pyprep.find_noisy_channels msqms.libs.pyprep.prep_pipeline msqms.libs.pyprep.ransac msqms.libs.pyprep.reference msqms.libs.pyprep.removeTrend msqms.libs.pyprep.utils msqms.qc msqms.qc.basic_info msqms.qc.entropy_metrics msqms.qc.fractal_metrics msqms.qc.freq_domain_metrics msqms.qc.metrics msqms.qc.metrics_factory msqms.qc.msqm msqms.qc.statistic_metrics msqms.qc.time_domain_metrics msqms.qc.visual_inspection msqms.quality_reference msqms.quality_reference.format_yaml msqms.quality_reference.quality_reference msqms.reports msqms.reports.report msqms.tests msqms.tests.test_data_path msqms.utils msqms.utils.logging msqms.utils.natural_sort msqms.utils.utils msqms.workflows msqms.workflows.opmqc_reference MSQM (class in msqms.qc.msqm) msqms module msqms.cli module msqms.cli.workflow module msqms.constants module msqms.io module msqms.io.bids_dataset module msqms.io.raw_dataset module msqms.libs module msqms.libs.osl module

msqms.libs.osl.osl_wrappers module msqms.libs.pyprep module msqms.libs.pyprep.find_noisy_channels module msqms.libs.pyprep.prep_pipeline module msqms.libs.pyprep.ransac module msqms.libs.pyprep.reference module msqms.libs.pyprep.removeTrend module msqms.libs.pyprep.utils module msqms.qc module msqms.qc.basic_info module msqms.qc.entropy_metrics module msqms.qc.fractal_metrics module msqms.qc.freq_domain_metrics module msqms.qc.metrics module msqms.qc.metrics_factory module msqms.qc.msqm module msqms.qc.statistic_metrics module msqms.qc.time_domain_metrics module msqms.qc.visual_inspection module msqms.quality_reference module msqms.quality_reference.format_yaml module msqms.quality_reference.quality_reference module msqms.reports module msqms.reports.report module msqms.tests module msqms.tests.test_data_path module msqms.utils module msqms.utils.logging module msqms.utils.natural_sort module msqms.utils.utils module msqms.workflows module msqms.workflows.opmqc_reference module

N

n_jobs (msqms.qc.metrics.Metrics attribute) nan_mask (msqms.qc.metrics.Metrics attribute) natural_sort_key() (in module msqms.utils.natural_sort) noisy_channels_after_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute)

noisy_channels_before_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) noisy_channels_original (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) NoisyChannels (class in msqms.libs.pyprep.find_noisy_channels) normative_score() (in module msqms.utils.utils)

O

obtain_quality_ranges() (in module msqms.quality_reference.quality_reference) (in module msqms.workflows.opmqc_reference)

origin_raw (msqms.qc.metrics.Metrics attribute)

P

perform_reference() (msqms.libs.pyprep.reference.Reference method) plot_average_freq() (msqms.qc.visual_inspection.VisualInspection method) plot_average_psd() (msqms.qc.visual_inspection.VisualInspection method) plot_bad_channel_dist() (msqms.qc.visual_inspection.VisualInspection method) plot_bad_channel_topo() (msqms.qc.visual_inspection.VisualInspection method) plot_bad_segment_dist() (msqms.qc.visual_inspection.VisualInspection method)

plot_chan_variance_ts() (msqms.qc.visual_inspection.VisualInspection method) plot_constant_dist() (msqms.qc.visual_inspection.VisualInspection method) plot_multivariate_time_series() (msqms.qc.visual_inspection.VisualInspection method) plot_power_on_ts() (msqms.qc.visual_inspection.VisualInspection method) PrepPipeline (class in msqms.libs.pyprep.prep_pipeline) process_meg_quality() (in module msqms.quality_reference.quality_reference)

Q

QualityReport (class in msqms.reports.report)

R

raw (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) (msqms.libs.pyprep.prep_pipeline.PrepPipeline property) (msqms.qc.metrics.Metrics attribute) raw_eeg (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) raw_non_eeg (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) read_raw_bids_dataset() (in module msqms.io.bids_dataset) read_raw_dataset() (in module msqms.io.raw_dataset) read_yaml() (in module msqms.utils.utils) Reference (class in msqms.libs.pyprep.reference) reference_after_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute)

reference_before_interpolation (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) register_custom_metric() (msqms.qc.metrics_factory.MetricsFactory class method) (msqms.qc.metrics_factory.MetricsFactory method) register_metric() (msqms.qc.metrics_factory.MetricsFactory class method) (msqms.qc.metrics_factory.MetricsFactory method) remove_reference() (msqms.libs.pyprep.reference.Reference static method) removeTrend() (in module msqms.libs.pyprep.removeTrend) render_html() (msqms.reports.report.HtmlReport method) (msqms.reports.report.SummaryHtmlReport method) robust_reference() (msqms.libs.pyprep.reference.Reference method) runline() (in module msqms.libs.pyprep.removeTrend)

S

samp_freq (msqms.qc.metrics.Metrics attribute) save_quality_reference_to_yaml() (in module msqms.quality_reference.quality_reference) save_yaml() (in module msqms.utils.utils) segment_raw_data() (in module msqms.utils.utils) slog() (in module msqms.utils.logging)

stats_summary() (msqms.qc.time_domain_metrics.TimeDomainMetric method) StatsDomainMetric (class in msqms.qc.statistic_metrics) still_noisy_channels (msqms.libs.pyprep.prep_pipeline.PrepPipeline attribute) SummaryHtmlReport (class in msqms.reports.report) SummaryQualityReport (class in msqms.reports.report)

T

TimeDomainMetric (class in msqms.qc.time_domain_metrics) to_html() (msqms.reports.report.QualityReport method) (msqms.reports.report.SummaryQualityReport method)

to_json() (msqms.reports.report.QualityReport method) (msqms.reports.report.SummaryQualityReport method)

U

update_quality_reference_file() (in module msqms.quality_reference.quality_reference)

V

verbose (msqms.qc.metrics.Metrics attribute) visual_bad_channel_topomap() (msqms.qc.visual_inspection.VisualInspection method) visual_bad_channels_distribution() (msqms.qc.visual_inspection.VisualInspection method) visual_heatmap_grid() (msqms.qc.visual_inspection.VisualInspection method) visual_psd() (msqms.qc.visual_inspection.VisualInspection method)

VisualInspection (class in msqms.qc.visual_inspection) visualize_bad_segments() (msqms.qc.visual_inspection.VisualInspection method) visualize_heatmap() (msqms.qc.visual_inspection.VisualInspection method) visualize_nan_values() (msqms.qc.visual_inspection.VisualInspection method) visualize_zero_values() (msqms.qc.visual_inspection.VisualInspection method)

Z

zero_mask (msqms.qc.metrics.Metrics attribute)