Index

A

ABCDPHAMetrics (class in datman.metrics) add_repeat_num() (datman.exporters.BidsExporter method) add_scan() (in module datman.dashboard) add_session() (in module datman.dashboard) add_subject() (in module datman.dashboard)

add_tech_notes() (datman.exporters.DBExporter method) AnatMetrics (class in datman.metrics) AnatPHAMetrics (class in datman.metrics) assign_scan_names() (datman.xnat.XNATExperiment method) auth (datman.xnat.xnat attribute)

B

belongs_to_session() (datman.exporters.NiiLinkExporter method)

BidsExporter (class in datman.exporters) BIDSFile (class in datman.scanid)

C

caption (datman.metrics.QCOutput attribute) cd (class in datman.utils) check_bvals() (in module datman.header_checks) check_dependency_configured() (in module datman.utils) check_diff() (in module datman.fs_log_scraper) check_returncode() (in module datman.utils) choose_standard_sub() (in module datman.fs_log_scraper)

clear_errors() (datman.exporters.NiiLinkExporter method) command_succeeded() (datman.metrics.Metric method) compare_headers() (in module datman.header_checks) config (class in datman.config) ConfigException construct_diffs() (in module datman.header_checks) create_resource_folder() (datman.xnat.xnat method)

D

dashboard_required() (in module datman.dashboard) DashboardException datman module datman.config module datman.dashboard module datman.exceptions module datman.exporters module datman.fs_log_scraper module datman.header_checks module datman.metrics module datman.scan module

datman.scan_list module datman.scanid module datman.utils module datman.xnat module DatmanIdentifier (class in datman.scanid) DatmanNamed (class in datman.scan) DBExporter (class in datman.exporters) DcmExporter (class in datman.exporters) define_folder() (in module datman.utils) delete_resource() (datman.xnat.xnat method) dismiss_autorun() (datman.xnat.xnat method) download() (datman.xnat.XNATExperiment method) (datman.xnat.XNATScan method) DTIMetrics (class in datman.metrics) DTIPHAMetrics (class in datman.metrics)

E

errors_outdated() (datman.exporters.DBExporter method) exists() (datman.metrics.IgnoreMetrics method) (datman.metrics.Metric method) export() (datman.exporters.BidsExporter method) (datman.exporters.DBExporter method) (datman.exporters.DcmExporter method) (datman.exporters.Exporter method) (datman.exporters.NiiExporter method) (datman.exporters.NiiLinkExporter method) (datman.exporters.SharedExporter method)

Exporter (class in datman.exporters) ExporterException ExportException ext (datman.exporters.DcmExporter attribute) (datman.exporters.NiiExporter attribute) (datman.exporters.NiiLinkExporter attribute) (datman.exporters.SeriesExporter attribute) (datman.exporters.SharedExporter attribute)

F

filename_required() (in module datman.dashboard) filter_niftis() (in module datman.utils) find_bids_files() (datman.exporters.SharedExporter method) find_bvals() (in module datman.header_checks) find_dm_files() (datman.exporters.SharedExporter method) find_files() (datman.scan.Scan method) find_project() (datman.xnat.xnat method)

find_resource_files() (datman.exporters.SharedExporter method) find_source_session() (datman.exporters.SharedExporter method) find_subject() (datman.xnat.xnat method) find_tech_notes() (in module datman.utils) FMRIMetrics (class in datman.metrics) FMRIPHAMetrics (class in datman.metrics) FSLog (class in datman.fs_log_scraper)

G

generate() (datman.metrics.ABCDPHAMetrics method) (datman.metrics.AnatMetrics method) (datman.metrics.AnatPHAMetrics method) (datman.metrics.DTIMetrics method) (datman.metrics.DTIPHAMetrics method) (datman.metrics.FMRIMetrics method) (datman.metrics.FMRIPHAMetrics method) (datman.metrics.IgnoreMetrics method) (datman.metrics.Metric method) (datman.metrics.QAPHAMetrics method) generate_scan_list() (in module datman.scan_list) get() (datman.config.TagInfo method) get_all_headers_in_folder() (in module datman.utils) get_archive_headers() (in module datman.utils) get_args() (datman.fs_log_scraper.FSLog static method) get_auth() (in module datman.xnat) get_autorun_ids() (datman.xnat.XNATExperiment method) get_bids_name() (datman.exporters.DBExporter method) (datman.scanid.Identifier method) get_bids_niftis() (datman.exporters.NiiLinkExporter method) get_bids_scan() (in module datman.dashboard) get_bids_subject() (in module datman.dashboard) get_connection() (in module datman.xnat) get_date() (datman.fs_log_scraper.FSLog method) get_default_user() (in module datman.dashboard) get_dicom() (datman.xnat.xnat method) get_dm_names() (datman.exporters.NiiLinkExporter method) get_error_file() (datman.exporters.NiiLinkExporter method) get_experiment() (datman.xnat.xnat method) get_experiment_ids() (datman.xnat.xnat method) get_exporter() (in module datman.exporters) get_extension() (in module datman.utils) get_field() (in module datman.scanid) get_files_with_tag() (in module datman.utils) get_folder_headers() (in module datman.utils) get_full_subjectid() (datman.scanid.Identifier method) get_full_subjectid_with_timepoint() (datman.scanid.Identifier method) get_full_subjectid_with_timepoint_session() (datman.scanid.Identifier method) get_handlers() (in module datman.metrics) get_kcni_identifier() (in module datman.scanid) get_kernel() (datman.fs_log_scraper.FSLog method) get_key() (datman.config.config method) get_loaded_modules() (in module datman.utils) get_niftis() (datman.fs_log_scraper.FSLog static method) get_output_dir() (datman.exporters.DBExporter class method) (datman.exporters.Exporter class method) (datman.exporters.NiiLinkExporter class method) (datman.exporters.SharedExporter class method)

get_path() (datman.config.config method) get_port_str() (in module datman.xnat) get_project() (in module datman.dashboard) get_projects() (datman.xnat.xnat method) get_relative_source() (in module datman.utils) get_requirements() (datman.metrics.Metric class method) get_resource() (datman.xnat.xnat method) get_resource_archive() (datman.xnat.xnat method) get_resource_dir() (datman.scan.Scan method) get_resource_ids() (datman.xnat.xnat method) get_resource_list() (datman.xnat.xnat method) get_resources() (datman.xnat.XNATExperiment method) (in module datman.utils) get_scan() (datman.xnat.xnat method) (in module datman.dashboard) get_scan_ids() (datman.xnat.xnat method) get_scan_list_contents() (in module datman.scan_list) get_series_num() (datman.exporters.NiiLinkExporter method) get_server() (in module datman.xnat) get_session() (in module datman.dashboard) get_session_num() (in module datman.scanid) get_sidecars() (datman.exporters.BidsExporter method) get_sites() (datman.config.config method) get_study_base() (datman.config.config method) get_study_subjects() (in module datman.dashboard) get_study_tags() (datman.config.config method) get_subid() (in module datman.scanid) get_subject() (datman.fs_log_scraper.FSLog method) (datman.xnat.xnat method) (in module datman.dashboard) get_subject_ids() (datman.xnat.xnat method) get_subject_metadata() (in module datman.utils) get_tagged_nii() (datman.scan.Scan method) get_tags() (datman.config.config method) get_tarfile_headers() (in module datman.utils) get_target_name() (datman.scan_list.ScanEntryABC method) get_xnat_credentials() (in module datman.utils) get_xnat_experiment_id() (datman.scanid.DatmanIdentifier method) (datman.scanid.Identifier method) (datman.scanid.KCNIIdentifier method) get_xnat_projects() (datman.config.config method) get_xnat_subject_id() (datman.scanid.DatmanIdentifier method) (datman.scanid.Identifier method) (datman.scanid.KCNIIdentifier method) get_zipfile_headers() (in module datman.utils)

H

handle_diff() (in module datman.header_checks)

has_permissions() (in module datman.utils) headers (datman.xnat.xnat attribute)

I

Identifier (class in datman.scanid) IgnoreMetrics (class in datman.metrics) InputException install_config (datman.config.config attribute) is_derived() (datman.xnat.XNATScan method) is_dicom() (in module datman.utils) is_multiecho() (datman.xnat.XNATScan method)

is_named_like_a_dicom() (in module datman.utils) is_phantom() (in module datman.scanid) is_runnable() (datman.metrics.Metric class method) is_scanid() (in module datman.scanid) is_scanid_with_session() (in module datman.scanid) is_shared() (datman.xnat.XNATExperiment method) is_usable() (datman.xnat.XNATScan method)

K

KCNIIdentifier (class in datman.scanid)

keys() (datman.config.TagInfo method)

L

load_yaml() (datman.config.config method)

locate_metadata() (in module datman.utils)

M

make_datman_name() (datman.exporters.NiiLinkExporter method) make_experiment() (datman.xnat.xnat method) make_filename() (in module datman.scanid) make_image() (datman.metrics.Metric method) make_link() (datman.exporters.NiiLinkExporter method) make_manifest() (datman.metrics.Metric method) make_montage() (datman.metrics.Metric method) make_name_map() (datman.exporters.SharedExporter method) make_new_entries() (in module datman.scan_list) make_output_dir() (datman.exporters.Exporter method) make_scan() (datman.exporters.DBExporter method) make_session() (datman.exporters.DBExporter method) make_standards() (in module datman.fs_log_scraper) make_subject() (datman.xnat.xnat method) make_temp_directory() (in module datman.utils) make_zip() (in module datman.utils) makedirs() (in module datman.utils) manifest_path (datman.metrics.Metric property) map_xnat_archive_to_project() (datman.config.config method) match() (datman.scanid.Identifier method)

match_dm_to_bids() (datman.exporters.NiiLinkExporter method) message (datman.exceptions.XnatException attribute) MetadataException Metric (class in datman.metrics) MetricDTI (class in datman.metrics) module datman datman.config datman.dashboard datman.exceptions datman.exporters datman.fs_log_scraper datman.header_checks datman.metrics datman.scan datman.scan_list datman.scanid datman.utils datman.xnat move_file() (datman.exporters.NiiExporter method)

N

names (datman.exporters.DBExporter property) needs_raw_data() (datman.exporters.BidsExporter method) (datman.exporters.DBExporter method) (datman.exporters.Exporter method) (datman.exporters.NiiLinkExporter method) (datman.exporters.SeriesExporter method) (datman.exporters.SharedExporter method)

nifti_basename() (in module datman.utils) niftis (datman.scan.Scan property) NiiExporter (class in datman.exporters) NiiLinkExporter (class in datman.exporters)

O

open_session() (datman.xnat.xnat method) order (datman.metrics.QCOutput attribute) outputs (datman.metrics.ABCDPHAMetrics attribute) (datman.metrics.AnatMetrics attribute) (datman.metrics.AnatPHAMetrics attribute) (datman.metrics.DTIMetrics attribute) (datman.metrics.DTIPHAMetrics attribute) (datman.metrics.FMRIMetrics attribute) (datman.metrics.FMRIPHAMetrics attribute) (datman.metrics.IgnoreMetrics attribute) (datman.metrics.QAPHAMetrics attribute)

outputs() (datman.metrics.Metric method) outputs_exist() (datman.exporters.BidsExporter method) (datman.exporters.DBExporter method) (datman.exporters.Exporter method) (datman.exporters.NiiLinkExporter method) (datman.exporters.SeriesExporter method) (datman.exporters.SharedExporter method)

P

parse() (in module datman.scanid) parse_bids_filename() (in module datman.scanid) parse_file() (in module datman.header_checks) parse_filename() (in module datman.scanid) parse_recon_done() (datman.fs_log_scraper.FSLog method) ParseException

pha_pattern (datman.scanid.DatmanIdentifier attribute) (datman.scanid.KCNIIdentifier attribute) pha_re (datman.scanid.DatmanIdentifier attribute) (datman.scanid.KCNIIdentifier attribute) put_dicoms() (datman.xnat.xnat method) put_resource() (datman.xnat.xnat method)

Q

QAPHAMetrics (class in datman.metrics)

QCException QCOutput (class in datman.metrics)

R

raw_dicoms_exist() (datman.xnat.XNATScan method) read_blacklist() (in module datman.utils) read_checklist() (in module datman.utils) read_credentials() (in module datman.utils) read_json() (in module datman.header_checks) (in module datman.utils) read_log() (datman.fs_log_scraper.FSLog method) read_manifest() (datman.metrics.Metric method) release_db() (in module datman.dashboard)

remove_empty_files() (in module datman.utils) remove_fields() (in module datman.header_checks) rename_experiment() (datman.xnat.xnat method) rename_subject() (datman.xnat.xnat method) report_errors() (datman.exporters.NiiLinkExporter method) report_issues() (datman.exporters.NiiExporter method) requires (datman.metrics.Metric attribute) run() (datman.metrics.Metric method) (in module datman.utils) run_dummy_q() (in module datman.utils)

S

Scan (class in datman.scan) scan_pattern (datman.scanid.DatmanIdentifier attribute) (datman.scanid.KCNIIdentifier attribute) scan_re (datman.scanid.DatmanIdentifier attribute) (datman.scanid.KCNIIdentifier attribute) ScanEntryABC (class in datman.scan_list) scanid_required() (in module datman.dashboard) scrape_logs() (in module datman.fs_log_scraper) Series (class in datman.scan) series_map (datman.config.TagInfo property) SeriesExporter (class in datman.exporters) server (datman.xnat.xnat attribute) session (datman.exceptions.XnatException attribute) (datman.scanid.DatmanIdentifier property) (datman.xnat.xnat attribute) SessionExporter (class in datman.exporters) set_datman_name() (datman.xnat.XNATScan method)

set_outputs() (datman.metrics.Metric method) set_study() (datman.config.config method) set_study_status() (in module datman.dashboard) set_tag() (datman.xnat.XNATScan method) share_experiment() (datman.xnat.xnat method) share_subject() (datman.xnat.xnat method) SharedExporter (class in datman.exporters) split_path() (in module datman.utils) splitext() (in module datman.utils) start_new_scan_list() (in module datman.scan_list) study (datman.exceptions.XnatException attribute) study_config (datman.config.config attribute) study_config_file (datman.config.config attribute) study_name (datman.config.config attribute) study_required() (in module datman.config) submit_job() (in module datman.utils) system_config (datman.config.config attribute)

T

TagInfo (class in datman.config) title (datman.metrics.QCOutput attribute) type (datman.exporters.BidsExporter attribute) (datman.exporters.DBExporter attribute) (datman.exporters.DcmExporter attribute) (datman.exporters.Exporter attribute) (datman.exporters.NiiExporter attribute) (datman.exporters.NiiLinkExporter attribute) (datman.exporters.SharedExporter attribute)

U

UndefinedSetting update_blacklist() (in module datman.utils)

update_checklist() (in module datman.utils) update_expected_outputs() (datman.metrics.QAPHAMetrics method) update_scans_csv() (in module datman.scan_list)

V

validate_subject_id() (in module datman.utils)

verify_standards() (in module datman.fs_log_scraper)

W

write_diff_log() (in module datman.header_checks) write_json() (in module datman.utils)

write_manifest() (datman.metrics.IgnoreMetrics method) (datman.metrics.Metric method) write_metadata() (in module datman.utils)

X

xnat (class in datman.xnat) XNATConnection (class in datman.utils) XnatException

XNATExperiment (class in datman.xnat) XNATObject (class in datman.xnat) XNATScan (class in datman.xnat) XNATSubject (class in datman.xnat)