Index

A

ad_hoc_checks() (in module pypet2bids.helper_functions)

ask_recording_type() (pypet2bids.convert_pmod_to_blood.PmodToBlood method)

B

bold_red (pypet2bids.helper_functions.CustomFormatter attribute)

C

check_for_dcm2niix() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) check_for_interpolated_data() (pypet2bids.convert_pmod_to_blood.PmodToBlood method) check_fraction_is_fraction() (pypet2bids.convert_pmod_to_blood.PmodToBlood method) check_json() (in module pypet2bids.update_json_pet_file) check_meta_radio_inputs() (in module pypet2bids.update_json_pet_file) check_metaradioinputs() (in module matlab) check_pet2bids_config() (in module pypet2bids.helper_functions) check_posix() (pypet2bids.dcm2niix4pet.Dcm2niix4PET static method) check_time_info() (pypet2bids.convert_pmod_to_blood.PmodToBlood method) check_units() (in module pypet2bids.helper_functions) cli() (in module pypet2bids.convert_pmod_to_blood) (in module pypet2bids.dcm2niix4pet) (in module pypet2bids.ecat_cli) (in module pypet2bids.multiple_spreadsheets)

collect_bids_part() (in module pypet2bids.helper_functions) collect_date_time_from_file_name() (in module pypet2bids.dcm2niix4pet) collect_specific_bytes() (in module pypet2bids.read_ecat) collect_spreadsheets() (in module pypet2bids.helper_functions) compress() (in module pypet2bids.helper_functions) convert() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) (pypet2bids.ecat.Ecat method) CustomFormatter (class in pypet2bids.helper_functions)

D

Dcm2niix4PET (class in pypet2bids.dcm2niix4pet) dcm2niix4pet() (in module matlab)

decompress() (in module pypet2bids.helper_functions) dicom_datetime_to_dcm2niix_time() (in module pypet2bids.dcm2niix4pet) drop_row() (in module pypet2bids.helper_functions)

E

Ecat (class in pypet2bids.ecat) ecat2nii() (in module matlab) (in module pypet2bids.ecat2nii)

expand_path() (in module pypet2bids.helper_functions) extract_affine() (pypet2bids.ecat.Ecat method) extract_dicom_headers() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) extract_metadata() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method)

F

filter_bytes() (in module pypet2bids.read_ecat) flatten_series() (in module pypet2bids.helper_functions)

flattenstruct() (in module matlab) format() (pypet2bids.helper_functions.CustomFormatter method) FORMATS (pypet2bids.helper_functions.CustomFormatter attribute)

G

get_buffer_size() (in module pypet2bids.read_ecat) get_coordinates_containing() (in module pypet2bids.helper_functions) get_directory_data() (in module pypet2bids.read_ecat) get_ecat_bytes() (in module pypet2bids.read_ecat) get_header_data() (in module pypet2bids.read_ecat) get_metadata_from_spreadsheet() (in module pypet2bids.update_json_pet_file)

get_pet_metadata() (in module matlab) get_radionuclide() (in module pypet2bids.update_json_pet_file) get_recon_method() (in module matlab) (in module pypet2bids.helper_functions) get_version() (in module pypet2bids.helper_functions) grey (pypet2bids.helper_functions.CustomFormatter attribute)

H

hash_fields() (in module pypet2bids.helper_functions)

I

import_and_write_out_module() (in module pypet2bids.helper_functions)

is_numeric() (in module pypet2bids.helper_functions)

J

json_out() (pypet2bids.ecat.Ecat method)

jsonwrite() (in module matlab)

L

load_pet_bids_requirements_json() (in module pypet2bids.helper_functions) load_pmod_file() (pypet2bids.convert_pmod_to_blood.PmodToBlood static method)

load_spread_sheet_data() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) load_vars_from_config() (in module pypet2bids.helper_functions) logger() (in module pypet2bids.helper_functions)

M

main() (in module pypet2bids.convert_pmod_to_blood) (in module pypet2bids.dcm2niix4pet) (in module pypet2bids.ecat_cli) make_nifti() (pypet2bids.ecat.Ecat method) match_dicom_header_to_file() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) matlab (module) modify_config_file() (in module pypet2bids.helper_functions) module pypet2bids pypet2bids.convert_pmod_to_blood pypet2bids.dcm2niix4pet pypet2bids.ecat pypet2bids.ecat2nii pypet2bids.ecat_cli pypet2bids.helper_functions pypet2bids.multiple_spreadsheets pypet2bids.read_ecat pypet2bids.sidecar pypet2bids.update_json_pet_file

O

open_meta_data() (in module pypet2bids.helper_functions) (pypet2bids.dcm2niix4pet.Dcm2niix4PET method)

P

parse_this_date() (in module pypet2bids.ecat) ParseKwargs (class in pypet2bids.helper_functions) PmodToBlood (class in pypet2bids.convert_pmod_to_blood) populate_sidecar() (pypet2bids.ecat.Ecat method) post_dcm2niix() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method) prune_sidecar() (pypet2bids.ecat.Ecat method) pypet2bids module pypet2bids.convert_pmod_to_blood module pypet2bids.dcm2niix4pet module pypet2bids.ecat module

pypet2bids.ecat2nii module pypet2bids.ecat_cli module pypet2bids.helper_functions module pypet2bids.multiple_spreadsheets module pypet2bids.read_ecat module pypet2bids.sidecar module pypet2bids.update_json_pet_file module

R

read_bytes() (in module pypet2bids.read_ecat) read_ecat() (in module pypet2bids.read_ecat) read_multi_subject_spreadsheets() (in module pypet2bids.multiple_spreadsheets) readECAT7() (in module matlab)

red (pypet2bids.helper_functions.CustomFormatter attribute) replace_nones() (in module pypet2bids.helper_functions) reset (pypet2bids.helper_functions.CustomFormatter attribute) run_dcm2niix() (pypet2bids.dcm2niix4pet.Dcm2niix4PET method)

S

sanitize_bad_path() (in module pypet2bids.helper_functions) scale_time_rename_columns() (pypet2bids.convert_pmod_to_blood.PmodToBlood method) show_affine() (pypet2bids.ecat.Ecat method) show_directory_table() (pypet2bids.ecat.Ecat method)

show_header() (pypet2bids.ecat.Ecat method) show_sidecar() (pypet2bids.ecat.Ecat method) show_subheaders() (pypet2bids.ecat.Ecat method) single_spreadsheet_reader() (in module pypet2bids.helper_functions)

T

transform_row_to_dict() (in module pypet2bids.helper_functions)

translate_metadata() (in module pypet2bids.helper_functions) type_cast_cli_input() (in module pypet2bids.convert_pmod_to_blood)

U

update_json_cli() (in module pypet2bids.update_json_pet_file) update_json_with_dicom_value() (in module pypet2bids.update_json_pet_file) update_json_with_dicom_value_cli() (in module pypet2bids.update_json_pet_file)

update_json_with_ecat_value_cli() (in module pypet2bids.ecat_cli) update_pet_json() (pypet2bids.ecat.Ecat method) updatejsonpetfile() (in module matlab)

V

very_tolerant_literal_eval() (in module pypet2bids.helper_functions)

W

write_multi_subject_spreadsheets() (in module pypet2bids.multiple_spreadsheets) write_out_blood_files() (pypet2bids.ecat.Ecat method)

write_out_jsons() (pypet2bids.convert_pmod_to_blood.PmodToBlood method) write_out_module() (in module pypet2bids.helper_functions) write_out_tsvs() (pypet2bids.convert_pmod_to_blood.PmodToBlood method)

Y

yellow (pypet2bids.helper_functions.CustomFormatter attribute)