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Dicom Series Preflight

NVIDIAOfficialCreated by NVIDIA MedTech Team

  • Skill
  • Review and audit
  • Science and research
  • Apache-2.0
  • Medium risk
  • Has scripts

From the author

Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.
— the description by NVIDIA MedTech Team

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

The DICOM Series Preflight skill provides a mechanism to inspect DICOM series directories by analyzing headers without decoding pixel data. It generates a structured JSON output containing an inventory of the series, orientation axcodes, potential PHI flags, and a verdict of pass, warn, or fail. This tool is intended for pre-processing validation to ensure data quality before conversion or inference tasks, and it is explicitly not designed for clinical clearance, de-identification, or production ingestion.

What it does

  • Scans a single DICOM series directory for header-based validation.
  • Generates a JSON report including inventory, orientation, and findings.
  • Assigns a preflight verdict of pass, warn, or fail.
  • Identifies potential PHI flags within the headers.
  • Provides integration with trusted verifier workflows.

When to use it

  • Before running inference or conversion on DICOM data.
  • When you need to verify series orientation and header integrity.
  • To perform rapid quality checks on medical imaging datasets.
  • As a gatekeeper in automated medical imaging pipelines.

Advantages

  • Fast execution due to header-only analysis without pixel decoding.
  • Standardized output format for downstream automated processing.
  • Helps identify potential issues early in the data pipeline.
  • Integrates with existing workflow automation tools.

Usage examples

“Run a preflight check on the DICOM series located in /data/dicom/series_01.”
The agent executes the preflight script on the specified directory and returns a JSON report containing the series inventory, orientation axcodes, and a pass/warn/fail verdict.
“Validate the DICOM series in /data/scan_01 using the trusted preflight verifier.”
The agent runs the preflight script and pipes the output through the trusted verifier to confirm the data meets the required engineering invariants.

Install

  1. Download the skill as a ZIP:

    https://mp-staging.autogineer.com/agent-skills/nvidia/dicom-series-preflight/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip dicom-series-preflight.zip -d .agents/skills

Documentation by NVIDIA MedTech Team

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

ScriptPurposeArguments
scripts/preflight_series.pyPrimary 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

ErrorCauseFix
Missing dependency or import errorRuntime package drift from skill_manifest.yaml.Install the packages declared in the manifest or use the documented setup command.
Empty or schema-invalid outputWrong input path, unsupported modality, or upstream failure.Re-run with a known fixture and inspect the wrapper JSON plus stderr.
Validation gate failureOutput 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.

Files

BENCHMARK.md

Skill Benchmark: dicom-series-preflight

✅ Overall verdict: PASS — Recommended for publication

Publication Recommendation

Recommended for publication based on the completed evaluation evidence in this report.

Evaluation Metadata

  • Skill: dicom-series-preflight

  • Evaluation date: 2026-09-14

  • Evaluator version: 1.5.6

  • Agents: Claude Code (aws/anthropic/bedrock-claude-opus-4-8), Codex (openai/openai/gpt-5.5)

  • Tasks: 3 evaluation tasks (3 positive)

  • Dataset digest: sha256:62a39511ef1fe2d4954937d2a8a22b8e447484afd22c4b0ef6cf8e2f26b337ff (skill-evaluator-dataset-snapshot/1)

  • Attempts per task: 3

  • Environment: k8s-sandbox

  • Tier 2 evidence: required for publication

  • Tier 3 evidence: required for publication

Each task attempt ran in its own isolated sandbox pod.

What This Report Answers

The three-tier evaluation checks whether the skill:

  • is safe to use;

  • produces correct answers;

  • is discovered and activated when needed;

  • helps the agent complete the user's goal and expected workflow; and

  • avoids wasted skill and tool usage.

Results at a Glance

MeasureClaude Code (Baseline → Skill Uplift)Codex (Baseline → Skill Uplift)
Overall75.3% — baseline ran, but no comparable score was available; uplift unavailable71.6% — baseline ran, but no comparable score was available; uplift unavailable
Security100.0% → 66.7% (-33.3 points)100.0% → 66.7% (-33.3 points)
Correctness2.9% → 80.0% (+77.1 points)2.5% → 80.0% (+77.5 points)
Discoverability88.3% — baseline ran, but no comparable score was available; uplift unavailable81.7% — baseline ran, but no comparable score was available; uplift unavailable
Effectiveness13.6% → 56.1% (+42.5 points)17.5% → 49.7% (+32.2 points)
Efficiency85.2% — baseline ran, but no comparable score was available; uplift unavailable79.8% — baseline ran, but no comparable score was available; uplift unavailable

How to read this table: baseline is the same task attempted without the target skill. Scores are rounded to one decimal; threshold-adjacent values use additional precision so their displayed band matches the verdict. Uplift is derived from those displayed scores and shown in percentage points.

Example: 47.0% → 92.0% (+45.0 points) means the skill-assisted run scored 92.0%, 45.0 percentage points above its 47.0% no-skill baseline.

Token Usage

Actual Tier 3 execution usage is reported for every observed agent/case pair and both conditions.

AgentDataset caseWith skillWithout skillDeltaChangeCoverage
claude-codeAll cases1,398,0581,184,793N/AN/Askill 3/3; base 7/7
claude-codepreflight-clean-axial-flags-phi634,914510,580N/AN/Askill 1/1; base 3/3
claude-codepreflight-clean-no-phi-greenlights458,381483,512N/AN/Askill 1/1; base 3/3
claude-codepreflight-flipped-lr-blocks-segmentation304,763190,701+114,062+59.81%skill 1/1; base 1/1
codexAll cases1,156,112813,778N/AN/Askill 3/3; base 8/8
codexpreflight-clean-axial-flags-phi389,303264,463N/AN/Askill 1/1; base 3/3
codexpreflight-clean-no-phi-greenlights319,585341,802N/AN/Askill 1/1; base 3/3
codexpreflight-flipped-lr-blocks-segmentation447,224207,513N/AN/Askill 1/1; base 2/2
ALL AGENTSDataset aggregate2,554,1701,998,571N/AN/Askill 6/6; base 15/15

Prompt tokens include cached reads, so total tokens are prompt + completion (cached is not added twice). The Efficiency score uses (prompt - cached) + completion. N/A means the relevant trajectory counters were not available; coverage is never estimated.

Tier Status

TierPurposeStatusEvidence
Tier 1Static validationPASSED WITH OBSERVATIONS11 validator(s); 12 finding(s)
Tier 2Semantic deduplicationPASSED2 validator(s); 0 finding(s)
Tier 3Live agent evaluationPASS2 agent(s); 3 task(s)

Findings and Observations

<details> <summary>Show detailed findings and successful checks</summary>

  • MEDIUM SCHEMA/body_recommended_section: Missing recommended section: '## Examples' (skills/dicom-series-preflight/SKILL.md)

  • MEDIUM SECURITY/subprocess module call (AST4): Dangerous Code Execution: subprocess.run( [sys.executable, str(FIXTURES / "generate_fixtures.py")], check=True, cwd=REPO, ) (tests/test_preflight_series.py:37)

  • LOW QUALITY/quality_reliability: Inputs are used but no dedicated Inputs section is documented (skills/dicom-series-preflight/SKILL.md)

  • LOW QUALITY/quality_reliability: Structured output is used but no dedicated Output Format section is documented (skills/dicom-series-preflight/SKILL.md)

  • LOW SCHEMA/unexpected_file: Unexpected 'fixtures' in skill root (skills/dicom-series-preflight/fixtures)

  • 7 additional finding(s) are available in the full evaluation artifacts.

</details>

Scoring Methodology

<details> <summary>Show dimension definitions, source signals, and thresholds</summary>

DimensionQuestionScored signals
SecurityIs it safe to use?security (100%)
CorrectnessIs the answer correct?accuracy (100%)
DiscoverabilityWas the right skill loaded when needed?skill_execution (100%)
EffectivenessDid the skill help complete the task?goal_accuracy (50%) + behavior_check (50%)
EfficiencyDid it avoid wasted tool calls and token usage?skill_efficiency (50%) + token_efficiency (50%)
  • Dimension bands: PASS at 50% or above; NEUTRAL from 40% to below 50%; FAIL below 40%.

  • Overall Tier 3 lift: PASS at +5 points or more; FAIL at -10 points or less; values between those bands are NEUTRAL.

  • Overall verdict: PASS only when every configured dimension passes for at least one supported agent. Lift is reported as diagnostic evidence and does not override this gate.

  • The 50% attempt pass threshold is a separate per-task gate; it is not the dimension pass threshold.

  • Effectiveness is the equal-weight mean of goal completion (goal_accuracy) and expected workflow adherence (behavior_check).

  • Efficiency is 50% tool-call productivity (the backward-compatible skill_efficiency wire id) and 50% token_efficiency. Positive-case skill routing is scored under Discoverability, not Efficiency; a negative case without a routing target is N/A. N/A sources are omitted, remaining weights are renormalized, and the dimension is marked partial.

Signals present in this run:

  • security (Security): unsafe operations, secret leakage, and unauthorized access.

  • skill_execution (Skill Execution): whether the expected skill was selected, decoys were avoided, and the workflow executed.

  • skill_efficiency (Tool Productivity): tool-call productivity (legacy wire id; routing is scored under Discoverability).

  • accuracy (Accuracy): final-answer correctness against the reference answer.

  • goal_accuracy (Goal Accuracy): whether the user's goal was achieved.

  • behavior_check (Behavior Check): whether the expected workflow behavior was followed.

  • token_efficiency (Token Efficiency): actual uncached prompt plus completion usage (50% of Efficiency).

</details>

Freshness

Regenerate this benchmark when the skill, evaluation dataset, target agent/model, evaluator version, environment, or scoring policy changes.

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-series-preflight · 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-series-preflight.zip