camcan-skill

Orchestrates end-to-end Cam-CAN dataset processing across sMRI, fMRI, MEG, and dMRI modalities.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve? Processing the Cam-CAN neuroimaging dataset requires coordinating BIDS validation, multimodal MRI and MEG pipelines, phenotype extraction, and quality control, which is error-prone when done manually across separate tools. ## Core Features & Use Cases - BIDS Validation: Checks Cam-CAN directory structure, modality completeness, sidecar JSON presence, and participant ID consistency, producing a compliance CSV report. - Multimodal Delegation: Routes structural MRI, resting-state and movie-watching fMRI, MEG, and diffusion MRI processing to dedicated modality skills with a confirmed execution plan. - Phenotype and QC Integration: Merges cognitive, sensory, and health phenotype tables and generates per-subject QC summaries with exclusion recommendations based on framewise displacement thresholds. - Use Case: A researcher downloads Cam-CAN from OpenNeuro ds003097 and asks for a full lifespan aging analysis; the skill validates the BIDS layout, plans the pipeline, delegates each modality, and outputs organized derivatives under camcan_output/. ## Quick Start Ask the agent to validate and process your local Cam-CAN BIDS dataset, including fMRI, MEG, and phenotype extraction, and wait for the numbered execution plan before confirming.

Frequently Asked Questions about camcan-skill

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

FAQPage Schema
How do I process the Cam-CAN dataset end to end?

Provide the path to your Cam-CAN BIDS directory and request full processing. The skill generates a numbered plan covering BIDS validation, sMRI, fMRI, MEG, and phenotype extraction, then delegates each step to modality skills after you confirm.

How do I validate Cam-CAN BIDS structure?

Run scripts/validate_camcan.py with --input pointing to the BIDS root and --output for the report CSV. It checks anat, func, meg, and dwi completeness, sidecar JSON files, and summarizes how many subjects have complete modalities.

What modalities does the Cam-CAN dataset include?

Cam-CAN includes T1w structural MRI, multi-echo resting-state and movie-watching fMRI, CTF 275-channel MEG with rest, auditory, and visual tasks, and diffusion-weighted imaging across roughly 700 participants aged 18 to 88.

Can I run only BIDS validation without full processing?

Yes. If the task only asks for validation of local Cam-CAN data, the skill takes the narrow path of discovery, BIDS validation, and reporting, skipping downloads and full orchestration, and in benchmark mode does not require confirmation.

How are subjects excluded in Cam-CAN quality control?

The camcan_qc_summary.py script computes mean framewise displacement from fMRIPrep confounds and flags subjects whose mean FD exceeds a configurable threshold, defaulting to 0.3 mm, writing an exclusion list CSV with reasons.

What are the limitations of this Cam-CAN workflow?

The skill is orchestration-only and contains no preprocessing implementation; all execution is delegated to modality skills like smri-skill, fmri-skill, and meg-skill. Movie-watching fMRI may not suit standard GLM analysis, and MEG requires CTF system-specific handling.