| name | rest-mneta-mdd-skill |
| description | Use this skill whenever the user wants an end-to-end workflow for the REST-meta-MDD (Resting-State Meta-Major Depressive Disorder) dataset, including BIDS validation, processing of rs-fMRI, phenotype extraction, and QC integration. Triggers include: 'REST-meta-MDD', 'MDD', 'Major Depressive Disorder', 'depression resting-state', 'process REST-meta-MDD', or any request to run the REST-meta-MDD pipeline. |
| license | MIT License (NeuroClaw custom skill - freely modifiable within the project) |
| layer | subagent |
| skill_type | dataset |
| dependencies | ["fmri-skill","bids-organizer","claw-shell"] |
| complementary_skills | ["smri-skill","brain-visualization"] |
REST-meta-MDD Skill (Dataset-Orchestration Layer)
Overview
rest-mneta-mdd-skill is the NeuroClaw orchestration skill for the REST-meta-MDD (Resting-State Meta-Major Depressive Disorder) dataset, a large-scale multi-site consortium project pooling resting-state fMRI data from 17 research sites across China.
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 BIDS validation, phenotype extraction, and QC.
Core workflow (never bypassed):
- Identify input REST-meta-MDD data and target modalities.
- Generate a numbered execution plan clearly stating WHAT needs to be done and which tool skill will handle each step.
- Present the full plan, estimated runtime, resource requirements, and risks to the user and wait for explicit confirmation ("YES" / "execute" / "proceed").
- On confirmation, delegate every step to the appropriate skill via
claw-shell.
- After execution, save all outputs in a clean directory structure (
rest_mdd_output/).
Research use only.
Quick Reference
| Task | What needs to be done | Delegate to | Expected output |
|---|
| BIDS validation | Validate REST-meta-MDD BIDS structure | scripts/validate_rest_mdd.py | Validation report |
| rs-fMRI processing | Preprocessing, denoising, connectivity | fmri-skill | fmri_output/ connectivity |
| Phenotype extraction | Diagnosis, clinical measures, site info | scripts/extract_rest_mdd_phenotype.py | Merged phenotype CSV |
| Site harmonization | Multi-site effect correction | scripts/harmonize_sites.py | Harmonized data |
| QC summary | Per-subject quality control | scripts/rest_mdd_qc_summary.py | QC summary + exclusion list |
Dataset Characteristics
- Cohort: ~3,600+ participants
- MDD patients: ~1,837 Major Depressive Disorder patients
- Healthy controls: ~1,779 age/sex-matched controls
- Sites: 17 research sites across China
- Scanner: Multi-site (various 3T scanners)
- Modalities: rs-fMRI (primary), T1w sMRI (some sites)
- Clinical: Diagnosis (SCID), HAMD, HAMA, medication status
- Access: Chinese Data Sharing Platform, REST-meta-MDD consortium
- Format: NIfTI (community BIDS conversion available)
- Reference: Yan et al. (2019), Science Bulletin
Supported Modalities
| Modality | Description | Details |
|---|
| rs-fMRI | Resting-state functional MRI | Eyes closed, 5-10 min |
| T1w | Structural MRI (some sites) | 1mm isotropic |
REST-meta-MDD Clinical Measures
| Measure | Description | Domain |
|---|
| Diagnosis | MDD vs. Healthy Control (SCID-based) | Clinical status |
| HAMD | Hamilton Depression Rating Scale | Depression severity |
| HAMA | Hamilton Anxiety Rating Scale | Anxiety severity |
| Medication | Medication status (medicated vs. drug-naive) | Treatment |
| Site | Data collection site (1-17) | Multi-site |
| Age | Age at scan | Demographics |
| Sex | Biological sex | Demographics |
| Education | Years of education | Demographics |
BIDS Preparation
Script: scripts/validate_rest_mdd.py
Validates REST-meta-MDD BIDS structure and generates a compliance report.
python skills/rest-mneta-mdd-skill/scripts/validate_rest_mdd.py \
--input /path/to/REST-meta-MDD/bids \
--output /path/to/rest_mdd_output/qc/bids_validation.csv
Features:
- BIDS directory structure validation
- Site identification and completeness check
- Diagnostic group labeling (MDD vs. control)
- Modality completeness (rs-fMRI required, T1w optional)
Core Workflow (Never Bypassed)
- Identify user target: full REST-meta-MDD processing, rs-fMRI only, phenotype extraction, or BIDS validation only.
- Generate a numbered plan with tools, outputs, runtime, storage, and risks.
- Wait for explicit confirmation (
YES / execute / proceed).
- On confirmation, run BIDS validation using
scripts/validate_rest_mdd.py.
- Delegate to
fmri-skill for rs-fMRI processing.
- If T1w data available, delegate to
smri-skill.
- If phenotype extraction is requested, run
scripts/extract_rest_mdd_phenotype.py.
- If site harmonization is requested, run
scripts/harmonize_sites.py.
- If QC summary is requested, run
scripts/rest_mdd_qc_summary.py.
- Save outputs into
rest_mdd_output/.
Modality Processing Delegation
| Modality | Delegated skill | Typical tasks | Main outputs |
|---|
| rs-fMRI | fmri-skill | preprocessing, denoising, connectivity | fmri_output/ connectivity |
| sMRI (T1w) | smri-skill | brain extraction, tissue segmentation | smri_output/ derivatives |
Standard Output Layout
rest_mdd_output/
āāā bids/ # BIDS-staged data (or validation report)
āāā fmri/ # Functional MRI derivatives (rs-fMRI connectivity)
āāā smri/ # Structural MRI derivatives (if available)
āāā phenotype/ # Merged phenotype tables (diagnosis, clinical, site)
āāā harmonized/ # Site-harmonized data (ComBat or similar)
āāā qc/ # QC summaries and exclusion lists
āāā logs/ # Processing logs
Multi-Site Harmonization
REST-meta-MDD is a multi-site dataset (17 sites). Site effects are a major confound:
- ComBat: Commonly used batch effect correction for neuroimaging data
- Site-wise z-scoring: Normalize metrics within site before pooling
- Mixed-effects models: Include site as random effect in statistical analyses
- The
scripts/harmonize_sites.py script provides reference implementations
Benchmark Adapter Guidance
For benchmark-style prompts, do not force the full orchestration when the task only asks for local REST-meta-MDD data validation.
- If the task starts from REST-meta-MDD data already present on disk and only asks for BIDS validation:
- Skip the download stage
- Default to the narrow path
local REST-meta-MDD discovery -> BIDS validation -> report
- In benchmark mode, do not require explicit confirmation before presenting the validation solution.
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.
Important Notes and Limitations
- Multi-site data (17 sites) requires careful site effect handling.
- Scanner heterogeneity across sites introduces variability.
- rs-fMRI is the primary modality; structural data is limited.
- MDD diagnosis is SCID-based across all sites.
- Large sample size (~3,600) provides good statistical power for case-control analyses.
- Medication status is an important confound; subgroup analyses (medicated vs. drug-naive) are recommended.
rest-mneta-mdd-skill is orchestration-only; detailed preprocessing logic remains in modality skills.
When to Call This Skill
- User asks for end-to-end REST-meta-MDD workflow.
- User asks to process REST-meta-MDD resting-state fMRI data.
- User needs BIDS validation for REST-meta-MDD data.
- User asks to extract REST-meta-MDD phenotype data (diagnosis, HAMD, site).
- User asks for depression neuroimaging analysis or multi-site harmonization.
Complementary / Related Skills
fmri-skill ā functional MRI preprocessing and analysis
smri-skill ā structural MRI preprocessing (if available)
bids-organizer ā BIDS validation and organization
brain-visualization ā visualization of derivatives
dependency-planner ā dependency resolution
conda-env-manager ā environment management
claw-shell ā command execution
Reference
- REST-meta-MDD: Chinese Data Sharing Platform
- Yan et al. (2019): Reduced default mode network functional connectivity in patients with recurrent major depressive disorder. Science Bulletin.
- REST-meta-MDD consortium
Created At: 2026-05-06 13:55 HKT
Last Updated At: 2026-05-06 13:55 HKT
Author: chengwang96