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name: dicom-and-formats description: "Handle TotalSegmentator NIfTI and DICOM inputs, DICOM outputs, modality checks, and crop-to-body preprocessing." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

DICOM and Formats

Use this sub-skill when an agent needs to decide whether a TotalSegmentator input is NIfTI, a DICOM directory, or a DICOM zip; when it needs DICOM SEG or RTSTRUCT output; or when it needs crop-to-body preprocessing to reduce volume size.

Start Here

1. Classify the input with scripts/validate_input_layout.py before building a long-running segmentation command.
2. Use .nii or .nii.gz inputs for ordinary NIfTI workflows; use a DICOM folder or zip when DICOM SEG/RTSTRUCT output is required.
3. For DICOM SEG/RTSTRUCT, pass DICOM input and set --output_type dicom_seg or --output_type dicom_rtstruct; do not request DICOM output from NIfTI input.
4. For memory reduction before a NIfTI segmentation, build a crop_to_body command with scripts/crop_to_body_command.py and review it before running.
5. If the task/classes/device/model execution choices are the main question, route to ../segmentation-workflows/SKILL.md after the format decision is settled.

Local References

• references/dicom-and-nifti.md covers accepted input layouts, DICOM conversion behavior, DICOM output rules, modality auto-correction, and crop-to-body usage.
• references/troubleshooting.md maps common format, DICOM dependency, orientation, zip, and crop-to-body failures to fixes.
• scripts/validate_input_layout.py inspects a candidate input path and optional output settings without loading model weights or running segmentation.
• scripts/crop_to_body_command.py prints a shell-quoted crop_to_body command; it does not execute the command.

Route Elsewhere

• Use ../capability-discovery/SKILL.md to discover valid tasks and class names with totalseg_info or the registry API.
• Use ../segmentation-workflows/SKILL.md to run TotalSegmentator or python_api.totalsegmentator(...) after format choices are known.
• Use ../outputs-and-statistics/SKILL.md for run reports, statistics, multilabel NIfTI consumption, probability outputs, and mask combination.
• Use ../runtime-configuration/SKILL.md for installing optional DICOM libraries, model weights, licenses, offline config, devices, or backend setup.
• Use ../auxiliary-analysis/SKILL.md for explicit NIfTI modality/phase/body-stats helper CLIs.

Safe Defaults

• Validate NIfTI input: python scripts/validate_input_layout.py ct.nii.gz --output-type nifti.
• Validate DICOM SEG preflight: python scripts/validate_input_layout.py series.zip --output-type dicom_seg --task total --strict.
• Build DICOM SEG run only after preflight: TotalSegmentator -i series.zip -o seg.dcm -ta total -ot dicom_seg --report run_report.json --quiet.
• Build crop command only: python scripts/crop_to_body_command.py -i ct.nii.gz -o ct_cropped.nii.gz --device cpu --quiet.