HCP-A Skill (Dataset-Orchestration Layer)

Overview

hcpa-skill is the NeuroClaw orchestration skill for the HCP Aging (HCP-A) dataset.

It strictly follows the NeuroClaw hierarchical design principles:

• This skill only describes WHAT needs to be done and which tool skill to delegate to.
• It contains no implementation code or concrete commands.
• All concrete execution is delegated to existing base/tool skills via claw-shell.
• Companion scripts in scripts/ provide reference implementations for data reorganization, phenotype extraction, and QC.

Core workflow (never bypassed):

1. Identify input HCP-A data and target modalities.
2. Generate a numbered execution plan clearly stating WHAT needs to be done and which tool skill will handle each step.
3. Present the full plan, estimated runtime, resource requirements, and risks to the user and wait for explicit confirmation ("YES" / "execute" / "proceed").
4. On confirmation, delegate every step to the appropriate skill via claw-shell.
5. After execution, save all outputs in a clean directory structure (hcpa_output/).

Research use only.

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Quick Reference

Task	What needs to be done	Delegate to	Expected output
Data download	Select HCP-A/AABC packages in ConnectomeDB powered by BALSA	claw-shell	Raw or preprocessed imaging packages
BIDS staging	Reorganize HCP-A native layout to BIDS	scripts/reorganize_hcpa.py	BIDS-compliant dataset
sMRI processing	Brain extraction, tissue segmentation, cortical reconstruction	smri-skill	smri_output/ derivatives
fMRI processing	Preprocessing, denoising, connectivity, task GLM	fmri-skill	fmri_output/ derivatives
dMRI processing	Eddy correction, tensor metrics, tractography	dwi-skill	dwi_output/ metrics
ASL processing	Perfusion preprocessing and CBF quantification	asl-skill	asl_output/ derivatives
Phenotype extraction	Cognitive, health, demographic data	scripts/extract_hcpa_phenotype.py	Merged phenotype CSV
QC summary	Per-subject quality control	scripts/hcpa_qc_summary.py	QC summary + exclusion list

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Download Stage (Mandatory First Step)

Source

Current HCP-A/AABC data is distributed through ConnectomeDB powered by BALSA:

• Release page: https://www.humanconnectome.org/study/hcp-lifespan-aging/data-releases
• Current release: AABC Release 2 (2026-01-28)
• Register for BALSA and accept the AABC Data Use Terms. An academic, nonprofit, or government email address is required.
• Imaging packages transfer through IBM Aspera Connect. Select a modality package or subject subset and calculate storage before transfer.

Dataset Characteristics

• AABC Release 2: 1,396 participants and 2,878 sessions; imaging is available for 1,390 participants across 2,789 sessions
• Modalities: T1w, T2w, high-resolution hippocampal T2, dMRI, rs-fMRI, task-fMRI, and ASL
• Focus: Normal aging, cognitive decline, brain structure-function changes across the lifespan
• Unique feature: Complements HCP-YA to cover the full adult lifespan (22-100 years)

Download Inputs to Confirm in Plan

• BALSA/ConnectomeDB account and accepted AABC terms
• Release (AABC Release 2 by default or legacy HCP-A Lifespan 2.0 for reproduction)
• Target modalities (structural, functional, diffusion, ASL, or non-imaging)
• Subject list scope (full or custom subset)
• Destination directory with capacity calculated from selected package sizes

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HCP-A Task Paradigms

Task	Description
VISMOTOR	Simultaneous visual and motor activation paradigm
CARIT	Conditioned Approach Response Inhibition Task
FACENAME	Face-name paired-associates memory task
REST	Resting-state functional MRI

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BIDS Preparation

Script: scripts/reorganize_hcpa.py

Converts HCP-A native directory structure to BIDS-compliant layout.

python skills/hcpa-skill/scripts/reorganize_hcpa.py \
  --input /path/to/HCPA/raw \
  --output /path/to/HCPA/bids \
  --participants /path/to/subject_list.txt

Features:

• Subject ID normalization: HCP format to BIDS sub- labels
• Session handling: multiple visits if applicable
• Modality routing: T1w, T2w, dMRI, rs-fMRI, task-fMRI
• Sidecar JSON generation from HCP metadata
• dataset_description.json and participants.tsv generation
• Dry-run mode: --dry-run to preview without copying

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Core Workflow (Never Bypassed)

1. Identify user target: full HCP-A processing, imaging subset, phenotype extraction, or BIDS staging only.
2. Generate a numbered plan with tools, outputs, runtime, storage, and risks.
3. Wait for explicit confirmation (YES / execute / proceed).
4. On confirmation, run download stage first (if needed).
5. After download success, run BIDS preparation using scripts/reorganize_hcpa.py.
6. Delegate to smri-skill for structural MRI processing.
7. Delegate to fmri-skill for functional MRI processing.
8. Delegate to dwi-skill for diffusion MRI processing.
9. Delegate to asl-skill when ASL data is selected.
10. If phenotype extraction is requested, run scripts/extract_hcpa_phenotype.py.
11. If QC summary is requested, run scripts/hcpa_qc_summary.py.
12. Save outputs into hcpa_output/.

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Modality Processing Delegation

Modality	Delegated skill	Typical tasks	Main outputs
sMRI (T1w/T2w)	smri-skill	brain extraction, tissue segmentation, cortical reconstruction, ROI morphometry	smri_output/ derivatives
fMRI (rs-fMRI/task-fMRI)	fmri-skill	preprocessing, denoising, ROI time series, connectivity, task GLM	fmri_output/ derivatives
dMRI (DWI)	dwi-skill	eddy correction, tensor metrics, tractography, connectome	dwi_output/ metrics
ASL	asl-skill	perfusion preprocessing and cerebral blood-flow quantification	asl_output/ derivatives

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Standard Output Layout

hcpa_output/
├── raw/                    # Downloaded original HCP-A files
├── bids/                   # BIDS-staged data
├── smri/                   # Structural MRI derivatives
├── fmri/                   # Functional MRI derivatives
├── dwi/                    # Diffusion MRI derivatives
├── asl/                    # ASL/perfusion derivatives
├── phenotype/              # Merged phenotype tables
├── qc/                     # QC summaries and exclusion lists
└── logs/                   # Download + orchestration logs

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Benchmark Adapter Guidance

For benchmark-style prompts, do not force the full orchestration when the task only asks for local HCP-A data staging.

• If the task starts from raw HCP-A data already present on disk and only asks for BIDS-style staging:
  • Skip the mandatory download stage
  • Default to the narrow path local raw HCP-A discovery -> BIDS-style staging -> minimal metadata -> validation/report
• In benchmark mode, do not require explicit confirmation before presenting the direct staging solution.

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Safety and Execution Policy

• No execution before explicit plan confirmation.
• All execution must be routed via claw-shell.
• Missing dependencies must be resolved by dependency-planner before running.

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Important Notes and Limitations

• HCP-A complements HCP-YA to cover the full adult lifespan (22-100 years).
• HCP-A processing is resource intensive; plan storage and compute accordingly.
• The HCP-A/AABC cohort is designed around typical aging; do not infer a clinical impairment cohort from age alone.
• Do not mix legacy Lifespan 2.0 packages with AABC Release 2 without documenting and harmonizing release-specific processing differences.
• For HCP-native preprocessing, optionally delegate to hcppipeline-tool.
• hcpa-skill is orchestration-only; detailed preprocessing logic remains in modality skills.

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When to Call This Skill

• User asks for end-to-end HCP Aging workflow.
• User asks to download HCP-A and run sMRI/fMRI/DTI processing.
• User needs BIDS staging for HCP-A data.
• User asks to extract HCP-A phenotype data (cognitive, health, demographic).

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Complementary / Related Skills

• smri-skill → structural MRI preprocessing
• fmri-skill → functional MRI preprocessing and analysis
• dwi-skill → diffusion MRI preprocessing and analysis
• hcppipeline-tool → HCP-native minimal preprocessing pipelines
• bids-organizer → BIDS validation and organization
• brain-visualization → visualization of derivatives
• dependency-planner → dependency resolution
• conda-env-manager → environment management
• claw-shell → command execution

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Reference

• HCP Aging: https://www.humanconnectome.org/study/hcp-lifespan-aging
• AABC Release 2: https://www.humanconnectome.org/study/hcp-lifespan-aging/data-releases
• HCP-A task protocols: https://www.humanconnectome.org/study/hcp-lifespan-aging/project-protocols
• Bookheimer et al. (2019): The Lifespan Human Connectome Project in Aging

Created At: 2026-05-06 13:02 HKT Last Updated At: 2026-08-11 HKT Author: chengwang96