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S10: QC Aggregation & Release

Step Code: S10_qc_aggregation_and_release Depends on: S1–S9 (all finished per-run QC and outputs) Required by: — (final step)

Purpose

S10 turns the per-run results of the whole pipeline into a release: a set of cross-dataset quality-control views, a reproducibility receipt, ready-to-paste methods text, and a BIDS-Derivatives compliant manifest. It runs no image processing; it walks the QC files every earlier step wrote and assembles them into human- and machine-readable deliverables.

Deliverables

Aggregation core

  • Per-subject HTML report linking each step's key reportlet thumbnail (cord-mask montage, functional localization, motion tSNR comparison, crop box, BOLD-on-anatomy overlay, PAM50 overlay, confound columns, tSNR map).
  • Group dashboard in the MRIQC style: one boxplot per metric (mean FD, cord Dice, native and template registration Dice, post-smoothing tSNR), with one dot per subject coloured by dataset.
  • Metrics index and run inventory tables across all datasets.

Cord-specific cohort views

  • Coverage matrix — which vertebral levels each subject covers.
  • tSNR heatmap — per-spinal-level tSNR (from S9's per-level table), one box per level across the cohort.

Publication and reproducibility

  • Reproducibility receipt capturing tool and package versions (the policy SHA and git SHA make any run re-creatable).
  • Methods manifest — auto-generated methods boilerplate in Markdown, LaTeX and HTML.
  • References bibliography of every method the chain used.
  • Citation file (CITATION.cff) and dataset_description.json (BIDS-Derivatives manifest, DatasetType = derivative with GeneratedBy).
  • participants.tsv summarising per-subject counts, mean FD, median in-cord tSNR, and an inclusion recommendation (flagging mean FD > 0.5 mm or tSNR < 5).
  • A top-level release_report.html index tying the above together.

Step Metric and QC

S10's checks are about completeness of the release, not image quality.

Metric PASS WARN
fraction of subjects with a report ≥ 0.80 ≥ 0.50
fraction of missing per-step QC ≤ 0.05 —

Outputs

derivatives/spineprep/{dataset}/
├── release_report.html              # top-level index
├── group_dashboard.html
├── dataset_description.json          # BIDS-Derivatives manifest
├── participants.tsv
├── CITATION.cff
├── references.bib
├── methods.{md,tex,html}             # methods boilerplate
└── reproducibility_receipt.json      # tool/package versions, policy + git SHA

derivatives/spineprep/{dataset}/sub-{id}/
└── sub-{id}_report.html              # per-subject aggregated report

References

  1. Group QC dashboard convention: Esteban et al. (MRIQC). PLOS ONE 12(9):e0184661 (2017). DOI
  2. BIDS Derivatives: Markiewicz et al. eLife 10:e71774 (2021). DOI

Last updated: June 2026