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hcpya-skill

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

89|5|Updated Mar 25, 2026
Search Tags:#hcp#neuroimaging#fmri#bids#phenotype extraction#dmri#dataset orchestration
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hcpya-skill-cuhk-aim-group
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hcpya-skill
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/hcpya-skill
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hcpya-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 Young Adult (HCP1200) dataset requires navigating ConnectomeDB/BALSA downloads, converting the HCP-native directory layout to BIDS, and coordinating separate sMRI, fMRI, and dMRI processing pipelines. This Skill orchestrates that entire end-to-end workflow so researchers do not have to manually wire each stage together. ## Core Features & Use Cases - Dataset Download Guidance: Walks through BALSA/ConnectomeDB registration, release selection (2025 release vs legacy S1200), and package scoping before transfer. - BIDS Staging: Converts HCP-YA native layout (e.g., 100307/T1w/) into BIDS-compliant structure with dataset_description.json and participants metadata via scripts/reorganize_hcpya.py. - Multimodal Delegation: Routes structural, functional, and diffusion MRI processing to dedicated modality skills, plus phenotype extraction and QC summary generation. - Use Case: A researcher downloads 50 HCP-YA subjects and asks for resting-state fMRI connectivity analysis. The Skill produces a numbered execution plan, stages the data to BIDS, delegates fMRI processing, and outputs QC summaries with an exclusion list based on framewise displacement thresholds. ## Quick Start Ask the agent to download the HCP Young Adult 2025 release for a subject list, stage it to BIDS, and run the full sMRI, fMRI, and dMRI processing pipeline into an hcpya_output directory.

Frequently Asked Questions about hcpya-skill

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

FAQPage Schema
How do I convert HCP Young Adult data to BIDS format?▼

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

How do I download the HCP Young Adult dataset?▼

HCP-YA is distributed through ConnectomeDB powered by BALSA at balsa.wustl.edu. You must register, accept the HCP data-use terms, and select modality-specific packages from the 2025 release or the legacy S1200 release. Restricted non-imaging variables require separate restricted-data approval.

What tasks and modalities are included in HCP1200?▼

HCP-YA includes T1w/T2w structural MRI, diffusion MRI, four resting-state runs of about 15 minutes each, and seven task fMRI paradigms: Motor, Emotion, Gambling, Language, Relational, Social, and Working Memory. Participants are aged 22 to 35.

How is fMRI motion QC performed for HCP data?▼

The hcpya_qc_summary.py script reads fMRIPrep confounds files and computes mean and max framewise displacement per subject. Subjects exceeding the default 0.3 mm mean FD threshold are flagged with exclusion reasons in a separate CSV, alongside FreeSurfer eTIV metrics when available.

Can I process only local HCP data without downloading?▼

Yes. When raw HCP-YA data already exists on disk, the Skill skips the download stage and runs a narrow path of local discovery, BIDS staging, metadata generation, and validation. Full download-to-multimodal orchestration only triggers when explicitly requested.

What are the limitations of HCP-YA processing workflows?▼

Processing is resource intensive in CPU, RAM, and storage, and releases span many large packages, so storage must be estimated from selected BALSA packages before transfer. The 2025 release has processed data for 1,071 subjects, and 2025 packages should not be mixed with legacy S1200 processed data in one analysis.

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