hcpa-skill

Orchestrates HCP Aging dataset download, BIDS staging, and multimodal MRI processing workflows.

89|5|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hcpa-skill-cuhk-aim-group
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: hcpa-skill
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/hcpa-skill
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hcpa-skill-cuhk-aim-group

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, and includes scripts (resource) components.

What problem does it solve? Working with the HCP Aging (HCP-A) dataset requires coordinating many steps: downloading packages from ConnectomeDB/BALSA, converting the native HCP directory layout to BIDS, running sMRI/fMRI/dMRI/ASL processing pipelines, and merging phenotype data. This Skill orchestrates that entire end-to-end workflow so researchers do not have to manually chain tools together. ## Core Features & Use Cases - Dataset Download Guidance: Walks through BALSA/ConnectomeDB registration, AABC Release 2 package selection, and Aspera transfer planning with storage estimation. - BIDS Staging: Converts HCP-A native directory layouts into BIDS-compliant datasets with subject ID normalization, task mapping, and dataset_description.json generation via scripts/reorganize_hcpa.py. - Multimodal Processing Delegation: Routes structural, functional, diffusion, and ASL MRI processing to dedicated modality skills, plus phenotype extraction and per-subject QC summaries with exclusion lists. - Use Case: A researcher wants to study cognitive decline across the adult lifespan. They ask for the full HCP-A pipeline, receive a numbered execution plan with runtime and storage estimates, confirm it, and get BIDS-staged data, processed derivatives, merged phenotype tables, and QC reports in a clean hcpa_output/ directory. ## Quick Start Ask the agent to download the HCP Aging dataset and run the full multimodal processing pipeline for sMRI, fMRI, and dMRI data.

Frequently Asked Questions about hcpa-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download and process the HCP Aging dataset?

Register on BALSA/ConnectomeDB, accept the AABC Data Use Terms, and select imaging packages for transfer via IBM Aspera Connect. The skill then generates a numbered execution plan covering BIDS staging and modality processing, which runs after your explicit confirmation.

How to convert HCP-A native directory structure to BIDS format?

Run the reorganize_hcpa.py script with --input pointing to the raw HCP-A directory and --output for the BIDS target. It normalizes subject IDs, routes T1w, T2w, fMRI, and diffusion files into anat/func/dwi folders, and generates dataset_description.json. Use --dry-run to preview first.

What modalities does the HCP Aging dataset include?

AABC Release 2 includes T1w, T2w, high-resolution hippocampal T2, dMRI, resting-state fMRI, task fMRI (VISMOTOR, CARIT, FACENAME), and ASL perfusion imaging. It covers 1,390 imaged participants aged 22-100 across 2,789 sessions.

Can I process only local HCP-A data without downloading?

Yes. If raw HCP-A data already exists on disk, the skill skips the download stage and runs a narrow path of local data discovery, BIDS-style staging, minimal metadata generation, and validation reporting.

How is quality control handled for HCP-A fMRI processing?

The hcpa_qc_summary.py script computes per-subject metrics including mean and max framewise displacement from fMRIPrep confounds and FreeSurfer eTIV. Subjects exceeding the FD threshold (default 0.3mm) are flagged in an exclusion list with reasons.

What are the limitations of HCP Aging data for clinical research?

The HCP-A cohort is designed around typical aging, so clinical impairment cannot be inferred from age alone. Legacy Lifespan 2.0 and AABC Release 2 packages should not be mixed without documenting release-specific processing differences.