Index

A

accession2hash() (in module scanometrics.utils.dicom2bids) add_brain_snapshot() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) add_default_metrics() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) add_items() (scanometrics.GUI.DropDownMenu.SelectPKLFile.SelectPKLFile method)

add_layout_separators() (scanometrics.GUI.MainWindow.MainWindow method) add_line() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) add_plot() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) add_ses_row() (scanometrics.core.ScanOMetrics_project method) add_session_files() (in module scanometrics.utils.bids_util)

B

Brain3D (class in scanometrics.GUI.Brain3D.Brain3D)

browse_path() (scanometrics.GUI.PathSelector.PathSelector.PathSelector method)

C

calc_area_gauscurv() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) camera_updated (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere attribute) capture_and_emit_screenshot() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) check_bids_format() (scanometrics.GUI.PathSelector.PathSelector.PathSelector static method) check_tsv_folder_congruency() (in module scanometrics.utils.bids_util) CheckBox (class in scanometrics.GUI.CheckBox.CheckBox)

clear_layout() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method) click() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) closeEvent() (scanometrics.GUI.MainWindow.MainWindow method) ColorBar (class in scanometrics.GUI.Brain3D.Brain3D) compute_uncertainty() (scanometrics.normative_models.normative_model_template method) create_pdf_report() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) create_spiderplot() (in module scanometrics.GUI.Figures.SpiderPlot) CS_to_session() (in module scanometrics.utils.bids_util)

D

decode_model_filename() (in module scanometrics.utils.zenodo_api) del_all_widgets() (scanometrics.GUI.MainWindow.MainWindow method)

download_file() (in module scanometrics.utils.zenodo_api) DropDownMenu (class in scanometrics.GUI.DropDownMenu.DropDownMenu)

E

emit_fig_data() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method) emit_signal() (scanometrics.GUI.CheckBox.CheckBox.CheckBox method) enterEvent() (scanometrics.GUI.Icon.Icon.Icon method) error (scanometrics.GUI.Thread.EvaluationThread.EvaluationThread attribute)

ERROR() (in module scanometrics.utils.logging) evaluate_singleSubject_allSes() (scanometrics.core.ScanOMetrics_project method) evaluate_subject() (scanometrics.GUI.MainWindow.MainWindow method) EvaluationThread (class in scanometrics.GUI.Thread.EvaluationThread)

F

fdr() (in module scanometrics.utils.stats) FigureWindow (class in scanometrics.GUI.Figures.FigureWindow) fill_layout() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) (scanometrics.GUI.CheckBox.MetricCheckBox.MetricCheckBox method) (scanometrics.GUI.MainWindow.MainWindow method)

finished (scanometrics.GUI.Thread.EvaluationThread.EvaluationThread attribute) fit() (scanometrics.normative_models.Polynomial method) flag_outliers() (scanometrics.normative_models.normative_model_template method) fsl_pve_vols() (in module scanometrics.processing.fsl)

G

generate_location_plots() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) generate_report() (scanometrics.GUI.MainWindow.MainWindow method) get_atlas() (scanometrics.processing.dldirect.proc_pipeline method) get_cloud_points() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method) get_documents_path() (scanometrics.GUI.ReportGenerator.ReportGenerator.ReportGenerator method) get_items() (scanometrics.GUI.DropDownMenu.SelectAcqlab.SelectAcqLab method) (scanometrics.GUI.DropDownMenu.SelectROI.SelectROI method) (scanometrics.GUI.DropDownMenu.SelectSes.SelectSes method) (scanometrics.GUI.DropDownMenu.SelectSub.SelectSub method) get_lobe_roi() (scanometrics.processing.dldirect.proc_pipeline method) get_logps_vals() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) get_scannrad_records() (in module scanometrics.utils.zenodo_api) get_selected_value() (scanometrics.GUI.CheckBox.MetricCheckBox.MetricCheckBox method) get_spiderplot() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method)

get_subj_rows() (scanometrics.core.ScanOMetrics_project method) get_subjSesAcq_array() (scanometrics.core.ScanOMetrics_project method) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) get_subjSesAcq_id() (scanometrics.core.ScanOMetrics_project method) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) get_subjSesAcq_row() (scanometrics.core.ScanOMetrics_project method) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) get_subjSesAcq_T1s() (scanometrics.core.ScanOMetrics_project method) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) get_value() (scanometrics.GUI.MainWindow.MainWindow method) get_values() (in module scanometrics.GUI.Figures.SpiderPlot) get_verbose() (in module scanometrics.utils.logging)

H

handle_sgn() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) (scanometrics.GUI.CheckBox.MetricCheckBox.MetricCheckBox method) (scanometrics.GUI.MainWindow.MainWindow method)

Hemisphere (class in scanometrics.GUI.Brain3D.Hemisphere)

I

Icon (class in scanometrics.GUI.Icon.Icon) initialize_interactor() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) initialize_som_project() (scanometrics.GUI.MainWindow.MainWindow method) initUI() (scanometrics.GUI.DropDownMenu.DropDownMenu.DropDownMenu method) (scanometrics.GUI.DropDownMenu.SelectAcqlab.SelectAcqLab method) (scanometrics.GUI.DropDownMenu.SelectPKLFile.SelectPKLFile method) (scanometrics.GUI.DropDownMenu.SelectROI.SelectROI method) (scanometrics.GUI.DropDownMenu.SelectSes.SelectSes method) (scanometrics.GUI.DropDownMenu.SelectSub.SelectSub method) (scanometrics.GUI.MainWindow.MainWindow method) (scanometrics.GUI.PathSelector.PathSelector.PathSelector method)

is_checked() (scanometrics.GUI.CheckBox.CheckBox.CheckBox method)

L

list_normative_models() (in module scanometrics.utils.zenodo_api) load_annot_file() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) load_brain_model() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) load_model_parameters() (scanometrics.normative_models.Polynomial method) load_normative_model() (scanometrics.core.ScanOMetrics_project method) load_participants() (in module scanometrics.utils.bids_util) load_proc_metrics() (scanometrics.core.ScanOMetrics_project method) load_project() (in module scanometrics.utils.io)

load_subject_metrics_from_ID() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) load_subject_metrics_from_stats2tableFolder() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) load_subjects() (scanometrics.core.ScanOMetrics_project method) load_X() (scanometrics.normative_models.Polynomial method) LOG() (in module scanometrics.utils.logging) logpval_to_color() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere static method)

M

main() (in module scanometrics.GUI.MainWindow) (in module scanometrics.scripts.scanometrics) (in module scanometrics.scripts.scanometrics_gui) (in module scanometrics.utils.dicom2bids) MainWindow (class in scanometrics.GUI.MainWindow) MetricCheckBox (class in scanometrics.GUI.CheckBox.MetricCheckBox) module scanometrics scanometrics.core scanometrics.GUI scanometrics.GUI.Brain3D scanometrics.GUI.Brain3D.Brain3D scanometrics.GUI.Brain3D.Hemisphere scanometrics.GUI.CheckBox scanometrics.GUI.CheckBox.CheckBox scanometrics.GUI.CheckBox.MetricCheckBox scanometrics.GUI.DropDownMenu scanometrics.GUI.DropDownMenu.DropDownMenu scanometrics.GUI.DropDownMenu.SelectAcqlab scanometrics.GUI.DropDownMenu.SelectPKLFile scanometrics.GUI.DropDownMenu.SelectROI scanometrics.GUI.DropDownMenu.SelectSes scanometrics.GUI.DropDownMenu.SelectSub scanometrics.GUI.Figures scanometrics.GUI.Figures.FigureWindow scanometrics.GUI.Figures.SpiderPlot scanometrics.GUI.Icon scanometrics.GUI.Icon.Icon scanometrics.GUI.MainWindow scanometrics.GUI.PathSelector scanometrics.GUI.PathSelector.PathSelector scanometrics.GUI.PushButton scanometrics.GUI.PushButton.PushButton scanometrics.GUI.ReportGenerator scanometrics.GUI.ReportGenerator.ReportGenerator scanometrics.GUI.styles scanometrics.GUI.Thread scanometrics.GUI.Thread.EvaluationThread scanometrics.normative_models scanometrics.processing scanometrics.processing.dldirect scanometrics.processing.freesurfer scanometrics.processing.fsl scanometrics.processing.pipeline_template scanometrics.processing.quantifyBrainStructures scanometrics.scripts scanometrics.scripts.scanometrics scanometrics.scripts.scanometrics_gui scanometrics.utils scanometrics.utils.bids_util scanometrics.utils.dicom2bids scanometrics.utils.io scanometrics.utils.logging scanometrics.utils.misc scanometrics.utils.stats scanometrics.utils.zenodo_api

N

normative_model_template (class in scanometrics.normative_models)

NOTE() (in module scanometrics.utils.logging)

O

on_camera_update() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method)

on_click() (scanometrics.GUI.PushButton.PushButton.PushButton method) on_evaluation_finished() (scanometrics.GUI.MainWindow.MainWindow method)

P

paintEvent() (scanometrics.GUI.Brain3D.Brain3D.ColorBar method) PathSelector (class in scanometrics.GUI.PathSelector.PathSelector) pial2outer() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) plot_single_metric() (scanometrics.core.ScanOMetrics_project method) Polynomial (class in scanometrics.normative_models) predict_values() (scanometrics.normative_models.Polynomial method) PRINT() (in module scanometrics.utils.logging) proc2metric() (in module scanometrics.processing.pipeline_template) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method)

proc2table() (scanometrics.core.ScanOMetrics_project method) (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) proc_pipeline (class in scanometrics.processing.dldirect) (class in scanometrics.processing.freesurfer) progress (scanometrics.GUI.Thread.EvaluationThread.EvaluationThread attribute) PushButton (class in scanometrics.GUI.PushButton.PushButton)

Q

quantifybrainstem() (in module scanometrics.processing.quantifyBrainStructures)

quantifyhippocampalsubfields() (in module scanometrics.processing.quantifyBrainStructures)

R

ReportGenerator (class in scanometrics.GUI.ReportGenerator.ReportGenerator) reset_cam() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) reset_camera_position() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) reset_checkboxes() (scanometrics.GUI.CheckBox.MetricCheckBox.MetricCheckBox method) reset_variables() (scanometrics.GUI.MainWindow.MainWindow method) run() (scanometrics.GUI.Thread.EvaluationThread.EvaluationThread method)

run_pipeline() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) run_proc2table() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method) run_proc_pipeline() (scanometrics.core.ScanOMetrics_project method) run_recon_all() (scanometrics.processing.freesurfer.proc_pipeline method)

S

save_model_parameters() (scanometrics.normative_models.Polynomial method) save_normative_model() (scanometrics.core.ScanOMetrics_project method) save_project() (in module scanometrics.utils.io) save_screenshot() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) save_X() (scanometrics.normative_models.Polynomial method) scannercode() (in module scanometrics.utils.dicom2bids) scanometrics module scanometrics.core module scanometrics.GUI module scanometrics.GUI.Brain3D module scanometrics.GUI.Brain3D.Brain3D module scanometrics.GUI.Brain3D.Hemisphere module scanometrics.GUI.CheckBox module scanometrics.GUI.CheckBox.CheckBox module scanometrics.GUI.CheckBox.MetricCheckBox module scanometrics.GUI.DropDownMenu module scanometrics.GUI.DropDownMenu.DropDownMenu module scanometrics.GUI.DropDownMenu.SelectAcqlab module scanometrics.GUI.DropDownMenu.SelectPKLFile module scanometrics.GUI.DropDownMenu.SelectROI module scanometrics.GUI.DropDownMenu.SelectSes module scanometrics.GUI.DropDownMenu.SelectSub module scanometrics.GUI.Figures module scanometrics.GUI.Figures.FigureWindow module scanometrics.GUI.Figures.SpiderPlot module scanometrics.GUI.Icon module scanometrics.GUI.Icon.Icon module scanometrics.GUI.MainWindow module scanometrics.GUI.PathSelector module scanometrics.GUI.PathSelector.PathSelector module scanometrics.GUI.PushButton module scanometrics.GUI.PushButton.PushButton module scanometrics.GUI.ReportGenerator module scanometrics.GUI.ReportGenerator.ReportGenerator module scanometrics.GUI.styles module scanometrics.GUI.Thread module scanometrics.GUI.Thread.EvaluationThread module scanometrics.normative_models module

scanometrics.processing module scanometrics.processing.dldirect module scanometrics.processing.freesurfer module scanometrics.processing.fsl module scanometrics.processing.pipeline_template module scanometrics.processing.quantifyBrainStructures module scanometrics.scripts module scanometrics.scripts.scanometrics module scanometrics.scripts.scanometrics_gui module scanometrics.utils module scanometrics.utils.bids_util module scanometrics.utils.dicom2bids module scanometrics.utils.io module scanometrics.utils.logging module scanometrics.utils.misc module scanometrics.utils.stats module scanometrics.utils.zenodo_api module ScanOMetrics_project (class in scanometrics.core) select_option() (scanometrics.GUI.DropDownMenu.DropDownMenu.DropDownMenu method) SelectAcqLab (class in scanometrics.GUI.DropDownMenu.SelectAcqlab) SelectPKLFile (class in scanometrics.GUI.DropDownMenu.SelectPKLFile) SelectROI (class in scanometrics.GUI.DropDownMenu.SelectROI) SelectSes (class in scanometrics.GUI.DropDownMenu.SelectSes) SelectSub (class in scanometrics.GUI.DropDownMenu.SelectSub) set() (scanometrics.processing.dldirect.proc_pipeline method) set_checked() (scanometrics.GUI.CheckBox.CheckBox.CheckBox method) set_default_message() (scanometrics.GUI.DropDownMenu.DropDownMenu.DropDownMenu method) set_eval_page() (scanometrics.GUI.MainWindow.MainWindow method) set_figures() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method) set_header() (scanometrics.GUI.MainWindow.MainWindow method) set_home_page() (scanometrics.GUI.MainWindow.MainWindow method) set_info_page() (scanometrics.GUI.MainWindow.MainWindow method) set_normative_model() (scanometrics.core.ScanOMetrics_project method) set_proc_pipeline() (scanometrics.core.ScanOMetrics_project method) set_settings() (scanometrics.processing.freesurfer.proc_pipeline method) set_title() (scanometrics.GUI.MainWindow.MainWindow method) set_verbose() (in module scanometrics.utils.logging) setup_ui() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) setup_vtk() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) sgn (scanometrics.GUI.Brain3D.Brain3D.Brain3D attribute) (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere attribute) (scanometrics.GUI.CheckBox.CheckBox.CheckBox attribute) (scanometrics.GUI.CheckBox.MetricCheckBox.MetricCheckBox attribute) (scanometrics.GUI.DropDownMenu.DropDownMenu.DropDownMenu attribute) (scanometrics.GUI.Figures.FigureWindow.FigureWindow attribute) (scanometrics.GUI.PathSelector.PathSelector.PathSelector attribute) (scanometrics.GUI.PushButton.PushButton.PushButton attribute) show_error() (scanometrics.GUI.MainWindow.MainWindow method) show_missing_values() (scanometrics.GUI.MainWindow.MainWindow method) switch_page() (scanometrics.GUI.MainWindow.MainWindow method) sync_cam() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method)

T

test_group_differences() (scanometrics.core.ScanOMetrics_project method)

tivproxy_rois() (scanometrics.processing.dldirect.proc_pipeline method)

U

uniform_subsample_scheme() (in module scanometrics.normative_models) uniform_subsample_scheme_old() (in module scanometrics.normative_models) update_camera() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) update_display() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method)

update_polydata_with_annot() (scanometrics.GUI.Brain3D.Hemisphere.Hemisphere method) update_region_label() (scanometrics.GUI.Brain3D.Brain3D.Brain3D method) update_version() (scanometrics.processing.dldirect.proc_pipeline method) (scanometrics.processing.freesurfer.proc_pipeline method)

W

WARNING() (in module scanometrics.utils.logging)

window_builder() (scanometrics.GUI.Figures.FigureWindow.FigureWindow method)