Dicom Metadata Extract
NVIDIAOfficialCreated by NVIDIA MedTech Team
- Skill
- Tool integration
- Science and research
- Apache-2.0
- Medium risk
- Has scripts
AutoGineer summary
Written by AutoGineer from the skill’s own files, not by the author
The dicom-metadata-extract skill provides a programmatic interface for reading DICOM files to retrieve core metadata and identify the presence of Protected Health Information (PHI) based on a subset of standard tags. It is designed for technical evaluation and data processing workflows rather than clinical or regulatory use. The skill outputs structured JSON containing modality, transfer syntax, and grouped study information, while explicitly warning against its use for anonymization or clinical decision-making.
What it does
- Extracts study, series, and image metadata from a single DICOM file.
- Flags the presence of PHI based on standard DICOM tags.
- Outputs metadata in a structured JSON format.
- Provides a command-line interface for integration into automated pipelines.
- Supports validation of output quality through dedicated verification tools.
When to use it
- When you need to inspect DICOM file headers for technical metadata.
- When performing initial data screening to identify standard PHI tags.
- When building automated data processing pipelines for medical imaging research.
- When verifying the structure of DICOM files during development or testing.
Advantages
- Provides a lightweight and standardized way to access DICOM metadata.
- Includes built-in PHI flagging for common standard tags.
- Integrates easily with existing Python-based medical imaging workflows.
- Supports trusted execution patterns for evidence-based review.
Usage examples
- “Extract metadata from the file scan_01.dcm and save it to output.json.”
- The agent runs the extraction script on the specified file and generates a JSON file containing the extracted metadata and PHI flags.
- “Check if the DICOM file at /data/ct_scan.dcm contains any standard PHI tags.”
- The agent processes the file and returns a report indicating whether PHI was detected and which specific tags were identified.
Install
Download the skill as a ZIP:
https://mp-staging.autogineer.com/agent-skills/nvidia/dicom-metadata-extract/downloadUnzip it into the cross-client skills folder of your project:
mkdir -p .agents/skills && unzip dicom-metadata-extract.zip -d .agents/skills
Documentation by NVIDIA MedTech Team
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 aremetadata_json.
Instructions
Read
skill_manifest.yamlbefore changing arguments, side effects, or validation gates.Run
scripts/extract_metadata.pythrough the documented command below; keep outputs under a caller-provided run directory.If a host agent exposes
run_script, userun_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_v1on 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.jsonOutput 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_trustedFiles
- AGENTS.md508 B
- ATTRIBUTION.mdAdded by AutoGineer937 B
- BENCHMARK.md7.0 KiB
- LICENSELicence file added by AutoGineer11.2 KiB
- SKILL.md3.2 KiB
- evals/baseline.yaml2.2 KiB
- evals/evals.json1.8 KiB
- fixtures/generate_sample.pyScript3.0 KiB
- scripts/extract_metadata.pyScript5.3 KiB
- skill-card.md4.5 KiB
- skill.oms.sig6.1 KiB
- skill_manifest.yaml5.0 KiB
- tests/test_basic.pyScript2.5 KiB
- validators/output_schema.json2.3 KiB
LICENSE
Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright [yyyy] [name of copyright owner]
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Requirements and compatibility
Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta
“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.
Needs: Declares allowed tools, Needs Python
Security
What our scanner noticed· Medium risk
- Large base64-encoded blobs
- Scripts that your agent may run
This skill includes scripts that your agent may run. Read them before you use it.
A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.
Attribution and licence
- Created by
- NVIDIA MedTech Team
- Publisher
- NVIDIA (Official)
- Source
- NVIDIA/skills · skills/dicom-metadata-extract · commit fce3cca
- Licence
- Apache License 2.0 (redistribution allowed)
- LICENSE (added by AutoGineer from LICENSE-APACHE)
- ATTRIBUTION.md (written by AutoGineer)
- Synced
AutoGineer is not affiliated with or endorsed by NVIDIA MedTech Team or NVIDIA.
Download ZIP
The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download dicom-metadata-extract.zip