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dicom-series-preflight

Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.

Published by NVIDIA ↗NVIDIA/skills

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Use dicom-series-preflight to perform a header-only preflight of the DICOM series in [dicom folder] and save the JSON evidence pack under [run directory]; do not treat it as de-identification or clinical clearance.

Required inputs

[dicom folder]
[run directory]

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SKILL.md

name: dicom-series-preflightdescription: Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.license: Apache-2.0allowed-tools: Bashmetadata:   author: 'NVIDIA MedTech Team'  tags:     - MedTech    - DICOM    - preflight

DICOM Series Preflight

Purpose

Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.
Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
Manifest I/O: inputs are dicom_dir; outputs are preflight_json.

Instructions

Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
Run scripts/preflight_series.py through the documented command below; keep outputs under a caller-provided run directory.
If a host agent exposes run_script, use run_script("scripts/preflight_series.py", args=[...]); otherwise run the Bash/Python command shown below.
Check the emitted JSON and paired verifier guidance before treating the run as evidence.

Available Scripts

Script	Purpose	Arguments
`scripts/preflight_series.py`	Primary entrypoint declared by skill_manifest.yaml.	`PATH_TO_DICOM_DIR`

Prerequisites

Runtime requirements: Python packages listed in runtime.side_effects.pip_packages.
NiBabel 5.4 or newer is required so extreme-oblique axes remain labeled consistently across reorientation.
Run commands from the repository root unless an existing section below says otherwise.

Limitations

Header-only; does not decode pixel data or detect burnt-in PHI.
Canonical orientation gate assumes LPS-derived CT axcodes L,P,S.
Compressed transfer syntax and multi-frame instances are warned, not decoded.
Single-directory scan; does not reconcile multiple studies in one tree.
Not for clinical deployment, regulatory de-identification, autonomous diagnosis, production ingestion without a vetted converter.

Troubleshooting

Error	Cause	Fix
Missing dependency or import error	Runtime package drift from `skill_manifest.yaml`.	Install the packages declared in the manifest or use the documented setup command.
Empty or schema-invalid output	Wrong input path, unsupported modality, or upstream failure.	Re-run with a known fixture and inspect the wrapper JSON plus stderr.
Validation gate failure	Output violated a declared engineering invariant.	Keep the failed evidence pack and use the gate message to repair inputs or wrapper code.

Scans a DICOM directory (one series per folder) without decoding pixels. Emits JSON with inventory, orientation axcodes, PHI flags, findings, and a preflight.verdict of pass, warn, or fail.

python scripts/preflight_series.py PATH_TO_DICOM_DIR

Pair with verifiers/dicom_preflight_quality_v1 for a trusted preflight pack:

make run-trusted SKILL=dicom_series_preflight \
  FIXTURE=skills/dicom-series-preflight/fixtures/clean_no_phi \
  OUT=runs/dicom_preflight_demo

Flagship workflow:

make run-workflow \
  WORKFLOW=examples/workflows/dicom_preflight_gate.yaml \
  WORKFLOW_INPUT=skills/dicom-series-preflight/fixtures/clean_no_phi \
  WORKFLOW_OUT=runs/dicom_preflight_gate

Not for de-identification, private-tag review, or clinical clearance.