dicom-series-preflight

bởi nvidia

Được sử dụng để kiểm tra trước chỉ với header của một thư mục chuỗi DICOM trước khi chuyển đổi hoặc suy luận. Không dùng cho việc khử nhận dạng hoặc thông quan lâm sàng.

npx skills add https://github.com/nvidia/skills --skill dicom-series-preflight

Tải ZIP GitHub

3.6k

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.