├── .coveragerc ├── .flake8 ├── .github └── workflows │ ├── cff_validation.yml │ ├── codespell.yml │ ├── coverage.yml │ ├── make_binaries.yml │ ├── publish.yml │ ├── publish_doc.yaml │ └── tests.yml ├── .gitignore ├── .mailmap ├── .pylintrc ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── dcm2bids ├── __init__.py ├── acquisition.py ├── cli │ ├── __init__.py │ ├── dcm2bids.py │ ├── dcm2bids_helper.py │ └── dcm2bids_scaffold.py ├── dcm2bids_gen.py ├── dcm2niix_gen.py ├── participant.py ├── sidecar.py ├── utils │ ├── __init__.py │ ├── args.py │ ├── io.py │ ├── logger.py │ ├── scaffold.py │ ├── tools.py │ └── utils.py └── version.py ├── docs ├── LICENSE.txt ├── assets │ ├── extra.css │ └── img │ │ ├── dcm_qa_nih_repo-dark.png │ │ ├── dcm_qa_nih_repo-light.png │ │ ├── github-issue-dark.png │ │ ├── github-issue-light.png │ │ ├── neurostars-1-dark.png │ │ ├── neurostars-1-light.png │ │ ├── neurostars-2-dark.png │ │ ├── neurostars-2-light.png │ │ ├── neurostars-3-dark.png │ │ ├── neurostars-3-light.png │ │ ├── neurostars-4-dark.png │ │ └── neurostars-4-light.png ├── changelog │ └── index.md ├── code_of_conduct.md ├── get-started │ ├── index.md │ └── install.md ├── how-to │ ├── container.md │ ├── contributing.md │ ├── create-config-file.md │ ├── get-help.md │ ├── index.md │ ├── use-advanced-commands.md │ └── use-main-commands.md ├── index.md ├── tutorial │ ├── first-steps.md │ ├── index.md │ └── parallel.md └── upgrade.md ├── docs_helper ├── README.md └── templates │ └── main.html ├── environment.yml ├── example └── config.json ├── mkdocs.yml ├── pyproject.toml ├── requirements-doc.txt ├── requirements-test.txt ├── setup.py ├── tests ├── __init__.py ├── data │ ├── config_test.json │ ├── config_test_auto_extract.json │ ├── config_test_complex.json │ ├── config_test_dup.json │ ├── config_test_float.json │ ├── config_test_key_absent.json │ ├── config_test_multiple_intendedfor.json │ ├── config_test_multiple_intendedfor_uri_relative.json │ ├── config_test_no_reorder.json │ ├── config_test_not_case_sensitive_option.json │ ├── config_test_sidecar.json │ └── sidecars │ │ ├── 001_localizer_20100603125600_i00001.json │ │ ├── 001_localizer_20100603125600_i00001.nii │ │ ├── 001_localizer_20100603125600_i00002.json │ │ ├── 001_localizer_20100603125600_i00002.nii │ │ ├── 001_localizer_20100603125600_i00003.json │ │ ├── 001_localizer_20100603125600_i00003.nii │ │ ├── 002_ep2d_bold_20100603125600.json │ │ ├── 003_MPRAGE_20100603125600.json │ │ ├── 003_MPRAGE_20100603125600.nii │ │ ├── 004_DTI_20100603125600.json │ │ ├── 004_DTI_20100603125600.nii.gz │ │ ├── 005_DTI_20100603125600.json │ │ ├── 006_DTI_20100603125600.json │ │ ├── 007_DTI_20100603125600.json │ │ ├── 010_gre_field_mapping_20100603125600_e1.json │ │ ├── 010_gre_field_mapping_20100603125600_e2.json │ │ └── 011_gre_field_mapping_20100603125600_e2_ph.json ├── test_dcm2bids.py 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