SCAN Skill (Dataset-Orchestration Layer)

Overview

Use this skill to turn an approved SCAN export into an auditable multimodal workflow. Keep access control, identifier handling, staging, phenotype linkage, and modality processing explicit.

SCAN means Standardized Centralized Alzheimer's and Related Dementias Neuroimaging. It combines standardized MRI and PET from Alzheimer's Disease Research Centers with longitudinal NACC clinical and cognitive data.

Research use only.

Access gate

• Request SCAN data through the NACC Quick Access File system.
• Access is free but is not anonymous: NACC records a project proposal and approves the request.
• Defaced images, QC fields, imaging summaries, and analysis variables are available through the request system. Availability varies because images must complete defacing and QC before release.
• Do not automate account creation, approval, or authenticated scraping. Begin execution only after the user has placed an approved export on local storage.
• Never ask the user to paste credentials into commands, logs, chat, or repository files.

Intake contract

Before processing, identify:

• approved request or release identifier
• export root and whether images are DICOM, NIfTI, or already BIDS-like
• requested modalities and subject/session subset
• NACC clinical/UDS tables supplied with the export
• available stable identifiers and visit/date fields
• local storage, compute, and DUA restrictions

Do not assume every participant has every optional sequence. Build modality availability from the files and QC tables, not from cohort-level descriptions.

Quick reference

Task	Delegate to	Output
Inventory approved export	claw-shell	immutable file and checksum manifest
Convert approved DICOM	dcm2nii	NIfTI, JSON, bval, and bvec files
Stage or validate BIDS	bids-organizer	BIDS dataset plus validation report
T1w, T2w, or FLAIR processing	smri-skill	structural derivatives and QC
Resting/task fMRI processing	fmri-skill	functional derivatives and QC
dMRI processing	dwi-skill	diffusion derivatives and QC
ASL/perfusion processing	asl-skill	perfusion derivatives and QC
Amyloid, tau, or FDG PET processing	pet-skill	PET derivatives, SUVRs, and QC
Join NACC phenotype tables	claw-shell with structured tabular tools	keyed analysis table and join audit

Core workflow

1. Inspect the approved local export without modifying source files.
2. Create a manifest containing relative path, size, checksum, inferred modality, and source package identifier.
3. Identify the subject and visit keys in both imaging and NACC tables. Preserve the source keys in a restricted crosswalk and generate separate BIDS-safe labels.
4. Convert DICOM only when needed through dcm2nii; otherwise retain NIfTI and sidecars as received.
5. Stage and validate the requested subset through bids-organizer. Record missing sidecars or acquisition metadata instead of inventing them.
6. Join phenotype and imaging records using documented keys. Report unmatched, duplicated, and many-to-many records before analysis.
7. Delegate only modalities actually present and approved for the project.
8. Save QC, provenance, exclusions, and the exact cohort query beside the derivatives.

For a request that only asks whether SCAN is obtainable, stop after explaining the NACC access gate and do not claim that data were downloaded.

Identifier and privacy rules

• Treat NACCID, PTID, visit dates, and crosswalks as controlled data even when images are defaced.
• Keep source identifiers out of public filenames, reports, model artifacts, and example data.
• Never attempt re-identification or facial reconstruction.
• Do not redistribute source images, subject-level tables, or restricted derivatives.
• Preserve the required SCAN/NACC acknowledgements and publication terms with the project provenance.

Expected output layout

scan_output/
|-- source_manifest/
|-- bids/
|-- phenotype/
|-- smri/
|-- fmri/
|-- dwi/
|-- perf/
|-- pet/
|-- qc/
`-- logs/

Completion criteria

• The approved export and governing request are identified.
• Checksums and modality inventory are saved.
• Imaging-to-phenotype joins have explicit keys and an exception report.
• BIDS validation and modality QC results are retained.
• No restricted credentials, crosswalks, or source data are committed to Git.

References

• SCAN: https://scan.naccdata.org/
• NACC data access: https://www.naccdata.org/about-nacc-data
• Repository access matrix: docs/DATASET_ACCESS.md

Created At: 2026-08-11 HKT Last Updated At: 2026-08-11 HKT