dcm-checker

name	dcm-checker
description	Inspect DICOM (X-ray) header labels — verify presence/missingness of 21 clinically important header tags and compute a curation score (0-100). Use for LYDUS data quality assessment of DICOM imaging metadata before large-scale analysis.
tier	community
category	lydus
parameters	{"dcm_path":{"description":"Path to a single DICOM file (.dcm).","type":"string"},"threshold":{"description":"Curation score below which the DICOM file is flagged as risky for research.","default":90,"type":"integer"}}

LYDUS DICOM Checker

Inspects the header-label quality of DICOM (X-ray) imaging data: parses the DICOM header, checks which of 21 clinically important tags are present vs missing, and assigns a curation score (0-100). A low score means many missing labels that may cause trouble in large-scale analysis.

When to Use This Skill

• Evaluating DICOM imaging metadata completeness before a large-scale imaging study
• Standardizing missing-header handling across a DICOM dataset (LYDUS Smart Curation)
• Quick per-file curation scoring of a DICOM header

Checked Tags (21)

21 of ~250 DICOM headers, selected for clinical/technical X-ray use and confirmed by clinicians/radiologists:

Group,Element	Name		Group,Element	Name
0008,002A	Acquisition DateTime		0018,1147	Field of View Shape
0008,0060	Modality		0018,1149	Field of View Dimensions
0008,0070	Manufacturer		0018,1164	Imager Pixel Spacing
0008,1030	Study Description		0018,5101	View Position
0008,103E	Series Description		0020,0060	Laterality
0010,0020	Patient ID		0028,0004	Photometric Interpretation
0010,0040	Patient's Sex		0028,0010	Rows
0010,1010	Patient's Age		0028,0011	Columns
0018,0015	Body Part Examined		0028,0030	Pixel Spacing
0018,1000	Device Serial Number		0028,0106	Smallest Image Pixel Value
			0028,0107	Largest Image Pixel Value

Scoring

curation_score = int( present / 21 * 100 )   # 0-100

A tag is present if it exists in the header and its value is non-empty; otherwise missing.

Auto-fill (described but not implemented)

The abstract describes auto-filling missing labels that can be derived from other fields (e.g., Patient's Age from Birth Date + Study Date). This is not implemented in the original code (v1.0.6) — the shipped tool only checks presence/missingness — so this skill does not implement it either, staying faithful to the source. It is noted here only so the gap between the abstract and the code is explicit.

SQL Support

Not applicable. Operates on raw DICOM files, not a QUIQ table.

How to Run

scripts/dcm_checker.py is a headless reimplementation of the original PyQt5 GUI, preserving the same 21-tag set and score formula, using pydicom for portability. (The original GUI is not vendored — see PROVENANCE.yaml for the source repo.)

from scripts.dcm_checker import get_curation_score, format_report

result = get_curation_score("/path/to/image.dcm")
print(format_report(result, threshold=90))
# result["curation_score"], result["missing"], result["present"]

Or as a CLI:

python scripts/dcm_checker.py --dcm_path /path/to/image.dcm --threshold 90

Critical Notes

1. Faithful to the original — no auto-fill. The abstract describes auto-filling derivable labels, but the shipped program.py (v1.0.6) only checks presence/missingness. This skill keeps that behavior; dcm_checker.py is a headless refactor of the same logic. This slimmed skill ships only dcm_checker.py (the original PyQt5 GUI is not vendored).

2. Library choice. The original GUI reads DICOM via SimpleITK (metadata keys like 0010|1010). The headless version uses pydicom (tags like (0x0010,0x1010)) — more standard and testable. The 21-tag set and int(present/21*100) formula are identical, so scores match.

3. Presence only for range/type. The reference says "data type and data range will be considered," but v1.0.6 checks presence/missingness only. Range/type validation is not implemented.

4. Single file per run. v1.0.6 scores one DICOM file at a time. Multi-file batch analysis and integrated visualization are planned but not yet implemented.

5. Threshold. The reference flags files scoring below 90 (the default here).

6. Pixel data / image rendering. load_dicom reads headers only (stop_before_pixels=True) for speed. The original GUI also renders the image (SimpleITK + Qt); that display step is intentionally omitted from the headless checker.

References

• LYDUS-DCM-Checker: https://github.com/Impku/LYDUS-DCM-Checker
• Cho SW, Han S, Hong N. "DCM-Checker" v1.0.6, Bonecentriq (Yonsei University), 2022.
• DICOM PS3.6 data dictionary (tag definitions).