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pnc-skill

Orchestrates BIDS validation and multimodal processing of Philadelphia Neurodevelopmental Cohort neuroimaging data.

89|5|Updated Mar 25, 2026
Search Tags:#quality control#neuroimaging#fmri#phenotype extraction#bids validation#dmri#pnc
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill pnc-skill-cuhk-aim-group
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pnc-skill
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/pnc-skill
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill pnc-skill-cuhk-aim-group

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve? Processing the Philadelphia Neurodevelopmental Cohort (PNC) dataset requires coordinating BIDS validation, structural MRI, resting-state and task fMRI, diffusion MRI, phenotype extraction, and quality control across thousands of subjects, which is error-prone when done manually. ## Core Features & Use Cases - BIDS Validation: Scans PNC subject directories for T1w, rs-fMRI, task-fMRI, and dMRI completeness and generates a per-subject compliance report. - Multimodal Delegation: Routes sMRI, fMRI, and dMRI processing to dedicated modality skills through a confirmed, numbered execution plan. - Phenotype Extraction & QC: Merges Penn CNB cognitive, psychiatric, and demographic tables and produces pediatric-adjusted QC summaries with exclusion lists. - Use Case: A researcher downloads the PNC BIDS dataset and asks for an end-to-end run; the skill validates the structure, delegates each modality pipeline, merges phenotypes, and outputs a clean pnc_output/ directory with QC exclusions. ## Quick Start Ask the agent to run the full PNC multimodal pipeline on your local BIDS dataset, starting with validation and ending with phenotype and QC reports.

Frequently Asked Questions about pnc-skill

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

FAQPage Schema
How do I process PNC neuroimaging data end to end?▼

Request the PNC workflow and the skill generates a numbered plan covering BIDS validation, sMRI, rs-fMRI, task-fMRI, and dMRI processing. After you confirm with YES or proceed, each step is delegated to the corresponding modality skill and outputs are saved under pnc_output/.

How do I validate a PNC BIDS dataset?▼

Run scripts/validate_pnc.py with --input pointing to the BIDS root and --output for the report path. It checks each subject for T1w, resting-state, task fMRI runs, and dMRI presence, then writes a per-subject compliance CSV with summary counts.

What modalities and tasks does the PNC dataset include?▼

PNC includes T1w structural MRI, resting-state fMRI, task fMRI, and diffusion MRI collected on a 3T Siemens TIM Trio. Task paradigms cover Go/No-Go, emotion recognition, Penn Line Orientation, and Penn Word Memory.

Does PNC quality control account for pediatric motion?▼

Yes, the QC script uses a default framewise displacement threshold of 0.4mm, which is higher than adult standards, to accommodate developmental data. It reads fMRIPrep confounds files and outputs per-subject exclusion reasons.

Can I extract PNC cognitive and psychiatric phenotypes?▼

Yes, scripts/extract_pnc_phenotype.py merges Penn CNB cognitive scores, GOASSESS psychiatric diagnoses, and demographics from multiple CSV or TSV files. It can filter results to subjects present in your imaging dataset.

What are the limitations of the PNC orchestration workflow?▼

The skill is orchestration-only and contains no preprocessing implementation; all modality work is delegated to smri-skill, fmri-skill, and dwi-skill. Execution requires explicit plan confirmation and routing through claw-shell, and analyses should account for age effects in the 8-21 year cohort.

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