# dicom-metadata-extract

Runs a pydicom script on a single DICOM file to extract metadata and detect standard PHI tags. Useful for quick agent inspections of medical imaging files.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · 1900 installs · ★ 3735
- Author: NVIDIA MedTech Team
- License: Apache-2.0 · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/NVIDIA/skills/tree/HEAD/skills/dicom-metadata-extract/SKILL.md
- Updated: 2026-10-23
- HTML: https://affpapa.org/en/nevibecode/skills/dicom-metadata-extract

## What it does

Created by NVIDIA MedTech Team, this skill acts as an entrypoint for parsing single DICOM files. It invokes `scripts/extract_metadata.py` with an input `dicom_path` and prints JSON to stdout or writes it via `--output`. The resulting schema contains `transfer_syntax`, `modality`, study, series, and image structures, along with a `phi_present` flag and `phi_tags_found`.

The host agent can call the wrapper using `run_script` or execute it directly in Bash. Output verification relies on `medagent.verifiers.dicom_metadata_quality_v1`. You can also generate trusted runs using `eval_engine.run_trusted` against sample fixtures. Required Python dependencies are listed in `skill_manifest.yaml`.

Do not deploy this wrapper for clinical tasks or regulatory de-identification. Its inspection logic covers only a narrow subset of PS3.15 standard tags. Private tags and burnt-in pixel text remain unchecked.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add NVIDIA/skills --skill dicom-metadata-extract -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/dicom-metadata-extract/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/dicom-metadata-extract/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add NVIDIA/skills --skill dicom-metadata-extract -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/dicom-metadata-extract/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add NVIDIA/skills --skill dicom-metadata-extract -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/dicom-metadata-extract/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install NVIDIA/skills dicom-metadata-extract
```

2. **Manually: put the files in place**
- File: `.github/skills/dicom-metadata-extract/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add NVIDIA/skills --skill dicom-metadata-extract -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/NVIDIA/skills --path skills/dicom-metadata-extract
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/dicom-metadata-extract/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add NVIDIA/skills --skill dicom-metadata-extract -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/NVIDIA/skills/tree/HEAD/skills/dicom-metadata-extract/SKILL.md

## When to use it
- extract metadata from a single DICOM file into JSON
- inspect transfer syntax and modality attributes
- flag standard PHI tags from a PS3.15 subset
- verify run output with medagent.verifiers.dicom_metadata_quality_v1

## Example prompts
- Run `scripts/extract_metadata.py` on `sample_ct.dcm` and write the output to `result.json`.
- Inspect `study.dcm` for PHI tags and show the extracted metadata JSON.
- Execute `python -m eval_engine.run_trusted` on skills/dicom-metadata-extract with the CT fixture.

## Source text · SKILL.md · Apache-2.0

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: 24886da9c1a8f660.

BEGIN THIRD-PARTY FILE 24886da9c1a8f660
````text
---
name: dicom-metadata-extract
description: Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.
license: Apache-2.0
allowed-tools: Bash
permissions: [file_read, file_write, shell]
metadata:
  author: 'NVIDIA MedTech Team'
  tags:
    - MedTech
    - DICOM
    - metadata
---

# 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.

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