.dockerignore
.gitignore
.pre-commit-config.yaml
CHANGELOG.md
CONTRIBUTING.md
Dockerfile
LICENSE
README.md
pyproject.toml
setup.py
.github/dependabot.yml
.github/workflows/codespell.yml
.github/workflows/lint.yml
.github/workflows/run_tests.yml
.github/workflows/run_tests_os.yml
.github/workflows/run_tests_subtasks.yml
TotalSegmentator.egg-info/PKG-INFO
TotalSegmentator.egg-info/SOURCES.txt
TotalSegmentator.egg-info/dependency_links.txt
TotalSegmentator.egg-info/entry_points.txt
TotalSegmentator.egg-info/not-zip-safe
TotalSegmentator.egg-info/requires.txt
TotalSegmentator.egg-info/top_level.txt
resources/contrast_phase_classifiers.pkl
resources/convert_dataset_to_nnunet.py
resources/evaluate.py
resources/evaluate_results.txt
resources/improvements_in_v2.md
resources/package_management.md
resources/release.sh
resources/results_all_classes_mr.json
resources/results_all_classes_v1.json
resources/server_setup.md
resources/totalsegmentator_server.service
resources/totalsegmentator_snomed_mapping.csv
resources/train_nnunet.md
resources/train_nnunet.sh
resources/imgs/overview_classes_mr.png
resources/imgs/overview_classes_v2.png
resources/imgs/overview_subclasses_2.png
resources/imgs/runtime_table.png
tests/test_end_to_end.py
tests/test_locally.py
tests/tests.sh
tests/tests_REMOVE.py
tests/tests_os.py
tests/tests_subtasks.sh
tests/update_test_files.sh
tests/helpers/combine_mask_to_multilabel.py
tests/helpers/test_img_split.py
tests/reference_files/example_ct.nii.gz
tests/reference_files/example_ct_sm.nii.gz
tests/reference_files/example_mr_sm.nii.gz
tests/reference_files/example_seg.nii.gz
tests/reference_files/example_seg_dicom.nii.gz
tests/reference_files/example_seg_fast.nii.gz
tests/reference_files/example_seg_fast_body_seg.nii.gz
tests/reference_files/example_seg_fast_force_split.nii.gz
tests/reference_files/example_seg_mr.nii.gz
tests/reference_files/example_seg_roi_subset.nii.gz
tests/reference_files/example_seg_roi_subset_mr.nii.gz
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tests/reference_files/example_ct_dicom/CT.1.3.12.2.1107.5.1.4.60064.30000022120808113428000016574
tests/reference_files/example_ct_dicom/CT.1.3.12.2.1107.5.1.4.60064.30000022120808113428000016575
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tests/reference_files/example_seg_appendicular_bones/metatarsal.nii.gz
tests/reference_files/example_seg_appendicular_bones/patella.nii.gz
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tests/reference_files/example_seg_appendicular_bones/tarsal.nii.gz
tests/reference_files/example_seg_appendicular_bones/tibia.nii.gz
tests/reference_files/example_seg_appendicular_bones/ulna.nii.gz
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tests/reference_files/example_seg_fast/aorta.nii.gz
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tests/reference_files/example_seg_fast/duodenum.nii.gz
tests/reference_files/example_seg_fast/esophagus.nii.gz
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tests/reference_files/example_seg_fast/inferior_vena_cava.nii.gz
tests/reference_files/example_seg_fast/kidney_cyst_left.nii.gz
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tests/reference_files/example_seg_fast/pancreas.nii.gz
tests/reference_files/example_seg_fast/portal_vein_and_splenic_vein.nii.gz
tests/reference_files/example_seg_fast/preview_total.png
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tests/reference_files/example_seg_fast/pulmonary_vein.nii.gz
tests/reference_files/example_seg_fast/rib_left_1.nii.gz
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tests/reference_files/example_seg_fast/spinal_cord.nii.gz
tests/reference_files/example_seg_fast/spleen.nii.gz
tests/reference_files/example_seg_fast/statistics.json
tests/reference_files/example_seg_fast/sternum.nii.gz
tests/reference_files/example_seg_fast/stomach.nii.gz
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tests/reference_files/example_seg_fast/thyroid_gland.nii.gz
tests/reference_files/example_seg_fast/trachea.nii.gz
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tests/reference_files/example_seg_fast/vertebrae_T7.nii.gz
tests/reference_files/example_seg_fast/vertebrae_T8.nii.gz
tests/reference_files/example_seg_fast/vertebrae_T9.nii.gz
tests/reference_files/example_seg_lung_vessels/lung_trachea_bronchia.nii.gz
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tests/reference_files/example_seg_tissue_types/skeletal_muscle.nii.gz
tests/reference_files/example_seg_tissue_types/subcutaneous_fat.nii.gz
tests/reference_files/example_seg_tissue_types/torso_fat.nii.gz
totalsegmentator/__init__.py
totalsegmentator/alignment.py
totalsegmentator/config.py
totalsegmentator/cropping.py
totalsegmentator/dicom_io.py
totalsegmentator/download_pretrained_weights.py
totalsegmentator/excel.py
totalsegmentator/libs.py
totalsegmentator/map_to_binary.py
totalsegmentator/map_to_total.py
totalsegmentator/nifti_ext_header.py
totalsegmentator/nnunet.py
totalsegmentator/postprocessing.py
totalsegmentator/preview.py
totalsegmentator/python_api.py
totalsegmentator/resampling.py
totalsegmentator/statistics.py
totalsegmentator/vtk_utils.py
totalsegmentator/bin/TotalSegmentator.py
totalsegmentator/bin/__init__.py
totalsegmentator/bin/crop_to_body.py
totalsegmentator/bin/totalseg_combine_masks.py
totalsegmentator/bin/totalseg_download_weights.py
totalsegmentator/bin/totalseg_get_phase.py
totalsegmentator/bin/totalseg_import_weights.py
totalsegmentator/bin/totalseg_set_license.py
totalsegmentator/bin/totalseg_setup_manually.py