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/dicom-metadata-extract

@2cd3507
by NVIDIA Corporationnvidia/skills3.5k stars
424

Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.

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Use this Skill: https://skilld.dev/gh/nvidia/skills/dicom-metadata-extract

This session only. Nothing lands on disk.

SKILL.md

≈40 tokens always: the name and description. ≈730 when used: this file. ≈6k more on demand in 7 files.

DICOM Metadata Extract

Purpose

  • Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.
  • Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
  • Manifest I/O: inputs are dicom_path; outputs are metadata_json.

Instructions

  • Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
  • Run scripts/extract_metadata.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/extract_metadata.py", args=[...]); otherwise run the Bash/Python command shown below.
  • Check the emitted JSON and run medagent.verifiers.dicom_metadata_quality_v1 on evidence packs before treating the run as reviewed evidence.

Available Scripts

Script Purpose Arguments
scripts/extract_metadata.py Primary entrypoint declared by skill_manifest.yaml. PATH_TO_DICOM [--output OUT.json]

Prerequisites

  • Runtime requirements: Python packages listed in runtime.side_effects.pip_packages.
  • Run commands from the repository root unless an existing section below says otherwise.

Limitations

  • Small PS3.15-inspired standard-tag subset only; not a complete Basic Application Confidentiality Profile implementation.
  • Private tags not checked
  • Burnt-in pixel PHI not detected
  • Multi-frame handling minimal
  • Not for clinical deployment, regulatory de-identification, autonomous diagnosis, patient-facing use.

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.

Reads one DICOM file with pydicom and emits JSON on stdout.

python scripts/extract_metadata.py PATH_TO_DICOM
python scripts/extract_metadata.py PATH_TO_DICOM --output result.json

Output includes transfer_syntax, modality, grouped study/series/image metadata, phi_present, and phi_tags_found.

Use this as the smallest end-to-end example of a Medical AI Skills skill. Do not use it for anonymization, private-tag review, pixel PHI detection, or clinical interpretation.

For second-pass evidence review, generate a trusted run:

python -m eval_engine.run_trusted skills/dicom-metadata-extract \
  --fixture skills/dicom-metadata-extract/fixtures/sample_ct.dcm \
  --out runs/dicom_metadata_trusted

Source: SKILL.md on GitHub

Third-party checks

No alerts16d3 checks · Risk SAFE
  • Gen Agent Trust Hub16d

    The skill is a metadata extraction tool for DICOM medical imaging files. It allows agents to read headers and check for standard Private Health Information (PHI) tags. No malicious behavior, obfuscation, or unauthorized data exfiltration was detected. The skill includes appropriate disclaimers regarding the scope of its PHI detection capabilities.

  • Socket16d

    No alerts

  • Snyk16d

    Risk: LOW · No issues

Provenance

Signed by skilld at 2cd3507. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub yesterday.

Activeupdated 2 weeks ago

Capability

What it can do
Runs commands
permissions
[
  "file_read",
  "file_write",
  "shell"
]
All 1 allowed tools
Bash
Other metadata
metadata
{
  "author": "NVIDIA MedTech Team",
  "tags": [
    "MedTech",
    "DICOM",
    "metadata"
  ]
}

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