├── .blackignore ├── .codespellrc ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── help-me-curate-my-data.md └── workflows │ ├── codespell.yml │ ├── matlab.yaml │ ├── phantoms.yaml │ ├── python.yaml │ ├── readthedocs.yaml │ └── windows.yaml ├── .gitignore ├── .readthedocs.yaml ├── CITATION.cff ├── Dockerfile ├── JOSS_metadata ├── codemeta.json ├── generate.rb └── persons_info.txt ├── LICENSE ├── Makefile ├── README.md ├── code_of_conduct.md ├── contributing.md ├── contributors.md ├── docs ├── ImageReconstructionAlpgorithmsinPET.pdf ├── Makefile ├── about.rst ├── conf.py ├── index.rst ├── installation.rst ├── make.bat ├── matlab.rst ├── media │ ├── check_python_path_windows_install.png │ ├── image_example_bids_spreadsheet.png │ ├── image_example_excel_collecting_units.png │ ├── image_example_excel_miscalculation_InjectedMass.png │ ├── image_example_excel_mixing_columns.png │ ├── image_example_excel_user_error.png │ ├── pypet2bids_floow.drawio │ ├── pypet2bids_floow.drawio.png │ └── screen_shoot_of_custom_translation_script.png ├── modules.rst ├── pypet2bids.rst ├── spreadsheets.rst └── usage.rst ├── ecat_testing ├── ints │ ├── README.md │ ├── check_ecat_read.py │ ├── ints.m │ ├── ints.py │ ├── matlab_sample_bytes.bytes │ ├── nii_tool.m │ ├── python_sample_bytes.bytes │ └── template.variables.env ├── read_matlab_nii.py └── test_nii_vs_ecat.m ├── ecat_validation ├── ECAT7_multiframe.json ├── ECAT7_multiframe.v.gz ├── Readme.md ├── ecat_info │ ├── ECAT63_header_fields.pdf │ ├── ECAT71_headers.pdf │ └── ECAT72_headers.pdf ├── synthetic_ecat_integer_16x16x16x4.mat ├── synthetic_ecat_integer_16x16x16x4.v.gz ├── synthetic_ecat_integer_16x16x16x4.v.jpg └── synthetic_ecat_integer_16x16x16x4.v_error.avi ├── matlab ├── Readme.md ├── check_metaradioinputs.m ├── dcm2niix4pet.m ├── ecat2nii.m ├── first_middle_last_frames_to_text.m ├── first_middle_last_frames_to_text_cell.m ├── flattenstruct.m ├── get_pet_metadata.m ├── get_recon_method.m ├── jsonwrite.m ├── nii_tool.m ├── readECAT7.m ├── run_m2docgen_example.m ├── run_structure_example.m ├── telemetry.m ├── template_txt │ ├── GEAdvanceparameters.txt │ ├── PhillipsVereosparameters.txt │ ├── SiemensBiographparameters.txt │ └── SiemensHRRTparameters.txt ├── unit_tests │ ├── ECAT7_multiframe.v.jpg │ ├── ECAT7_multiframe.v_error.avi │ ├── Readme.md │ ├── check_metaradioinputs_test.m │ ├── ecat2nii_test.m │ ├── error.jpg │ ├── niftiwrite_test.m │ └── readECAT7_test.m └── updatejsonpetfile.m ├── metadata ├── PET_Radionuclide.mkd ├── PET_metadata.json ├── PET_reconstruction_filters.json ├── PET_reconstruction_methods.json ├── README ├── Readme.md ├── blood_metadata.json ├── definitions.json ├── dicom2bids.json └── schema.json ├── pypet2bids ├── README.md ├── pypet2bids │ ├── Pipfile │ ├── README.md │ ├── __init__.py │ ├── convert_pmod_to_blood.py │ ├── dcm2niix4pet.py │ ├── ecat.py │ ├── ecat2nii.py │ ├── ecat_cli.py │ ├── ecat_header_update.py │ ├── ecat_headers.json │ ├── golden_ecat.py │ ├── helper_functions.py │ ├── is_pet.py │ ├── metadata_spreadsheet_example_reader.py │ ├── multiple_spreadsheets.py │ ├── pet_metadata.py │ ├── read_ecat.py │ ├── sidecar.py │ ├── single_spreadsheet.py │ ├── telemetry.py │ ├── template.env │ ├── template_json.json │ ├── update_json_pet_file.py │ └── write_ecat.py ├── pyproject.toml ├── template.env ├── template_env │ ├── GEAdvanceparameters.env │ └── SiemensHRRTparameters.env ├── tests │ ├── __init__.py │ ├── metadata_excel_example_reader.py │ ├── scannerparams.txt │ ├── test_convert_pmod_to_blood.py │ ├── test_dcm2niix4pet.py │ ├── test_ecat.py │ ├── test_ecatread.py │ ├── test_helper_functions.py │ ├── test_library_command_line_interfaces.py │ ├── test_nifti_write.py │ ├── test_thisbytes.py │ └── test_write_ecat.py └── uv.lock ├── scripts ├── add_python_dependency ├── compare_jsons.py ├── installpackage ├── installuv ├── matlab_conversions.m ├── python_conversions.sh ├── schema_json_to_py ├── test_all_python_versions └── testphantoms └── spreadsheet_conversion ├── Readme.md ├── blood ├── blood_example.xlsx └── pmod │ ├── Ex_bld_manual_and_autosampled_mixed │ ├── S001_ParentFraction.bld │ ├── S001_Plasma Activity.bld │ ├── S001_Plasma-WholeBlood-Ratio.bld │ ├── S001_Whole Blood Activity.bld │ ├── converted_blood.json │ ├── converted_recording-autosampler_blood.tsv │ └── converted_recording-manual_blood.tsv │ ├── Ex_bld_wholeblood_and_plasma_only │ ├── converted__recording-manual_blood.json │ ├── converted__recording-manual_blood.tsv │ ├── plasma_parent.bld │ ├── test_recording-manual_blood.json │ ├── test_recording-manual_blood.tsv │ └── whole_blood.bld │ ├── Ex_txt_manual_and_autosampled_mixed │ ├── ParentFraction.txt │ ├── PlasmaWholeBloodRatio.txt │ ├── WholeBloodActivity.txt │ ├── converted_blood.json │ ├── converted_recording-autosampler_blood.tsv │ └── converted_recording-manual_blood.tsv │ ├── README.mkd │ ├── convert_pmod_to_blood.m │ └── convert_pmod_to_blood.py ├── many_subjects_sheet ├── 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