--- name: cobre-skill description: "Use this skill whenever the user wants an end-to-end workflow for the COBRE dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data for schizophrenia research. Triggers include: 'COBRE', 'process COBRE', 'COBRE schizophrenia', 'COBRE fMRI', or any request to run the COBRE pipeline. This is the NeuroClaw dataset-orchestration layer for COBRE." license: MIT License (NeuroClaw custom skill - freely modifiable within the project) layer: subagent skill_type: dataset dependencies: - smri-skill - fmri-skill - bids-organizer - claw-shell --- # COBRE Skill (Dataset-Orchestration Layer) ## Overview `cobre-skill` is the NeuroClaw orchestration skill for the **COBRE (Center for Biomedical Research Excellence)** dataset. COBRE contains 147 participants: 72 schizophrenia patients and 75 healthy controls, with T1w structural and rs-fMRI data. It is commonly used as a benchmark for brain disorder classification. It coordinates a fixed three-phase workflow: 1. Download COBRE data from the FCP/INDI repository. 2. Prepare and validate BIDS-style data organization for downstream processing. 3. Delegate modality pipelines to `smri-skill` and `fmri-skill`. It also provides **phenotype extraction** and **QC integration** paths: - Extract COBRE phenotype data (diagnosis, demographics, handedness). - Generate per-subject QC summaries with exclusion lists. This skill follows NeuroClaw hierarchy: - Defines **WHAT to do**, not low-level implementation details. - Does **not** execute direct shell commands itself. - Delegates all execution via `claw-shell` to base/tool skills. **Research use only.** --- ## Download Stage (Mandatory First Step) ### Source COBRE data is distributed through the **FCP/INDI** repository: - Website: https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html ### Supported COBRE Data Packages - **Imaging data**: T1w, rs-fMRI (NIfTI format) - **Phenotype data**: CSV files with diagnosis, demographics, handedness - **Participants**: 147 total (72 schizophrenia, 75 healthy controls) ### Delegation Rules for Download - Environment/setup checks: `dependency-planner` + `conda-env-manager` - Download tool installation and execution: `claw-shell` - Optional raw-data organization to BIDS-style staging: `bids-organizer` ### Download Inputs to Confirm in Plan - Subject list scope (full or custom subset) - Whether to download raw data or preprocessed derivatives - Destination directory with sufficient disk space --- ## Narrow Path: COBRE Raw NIfTI -> BIDS Staging Use this path when the task only asks to reorganize raw COBRE NIfTI files into a BIDS-style dataset and does not require preprocessing or downstream analysis. ### Expected narrow-path behavior 1. Detect COBRE-style subject IDs (numeric) and normalize to BIDS labels such as `sub-NNNNN`. 2. Route modalities: - T1w -> `anat/*_T1w` - rs-fMRI/BOLD -> `func/*_task-rest_bold` 3. Preserve or rename matching JSON sidecars when available. 4. Emit dataset-level outputs such as `dataset_description.json`, `participants.tsv`. --- ## Core Workflow (Never Bypassed) 1. Identify user target: full COBRE download, imaging subset, phenotype extraction, or BIDS staging only. 2. Generate a numbered plan with tools, outputs, runtime, storage, and risks. 3. Wait for explicit confirmation (`YES` / `execute` / `proceed`). 4. On confirmation, run download stage first (if needed). 5. After download success, run BIDS preparation using `scripts/reorganize_cobre.py`. 6. Delegate to modality skills: - `smri-skill` for structural MRI (T1w) - `fmri-skill` for resting-state fMRI (rs-fMRI) 7. If phenotype extraction is requested, run `scripts/extract_cobre_phenotype.py`. 8. If QC summary is requested, run `scripts/cobre_qc_summary.py`. 9. Save outputs into a COBRE-centered structure under `cobre_output/`. --- ## BIDS Preparation ### Script: `scripts/reorganize_cobre.py` Converts COBRE raw directory structure to BIDS-compliant layout. ```bash python skills/cobre-skill/scripts/reorganize_cobre.py \ --input /path/to/cobre_raw \ --output /path/to/cobre_bids \ --phenotype /path/to/cobre_raw/phenotype/cobre_phenotypic.csv ``` --- ## Phenotype Extraction ### Script: `scripts/extract_cobre_phenotype.py` ```bash python skills/cobre-skill/scripts/extract_cobre_phenotype.py \ --phenotype-dir /path/to/cobre_raw/phenotype \ --output /path/to/cobre_output/phenotype/merged_phenotype.csv \ --imaging-ids /path/to/cobre_output/bids/participants.tsv ``` --- ## QC Integration ### Script: `scripts/cobre_qc_summary.py` ```bash python skills/cobre-skill/scripts/cobre_qc_summary.py \ --fmriprep-dir /path/to/cobre_output/fmriprep \ --output /path/to/cobre_output/qc/qc_summary.csv \ --exclude-output /path/to/cobre_output/qc/exclude_list.csv \ --fd-threshold 0.3 ``` --- ## Recommended Output Layout All assets should be organized under `./cobre_output/`: - `cobre_output/raw/` (downloaded original COBRE files) - `cobre_output/bids/` (staged BIDS data) - `cobre_output/smri/` (links or copies from `smri_output/`) - `cobre_output/fmri/` (links or copies from `fmri_output/`) - `cobre_output/phenotype/` (merged phenotype tables) - `cobre_output/qc/` (QC summaries and exclusion lists) - `cobre_output/logs/` (download + orchestration logs) --- ## Benchmark Adapter Guidance For benchmark-style prompts, do not force the full `download -> staging -> multimodal processing` orchestration when the task is only asking for local COBRE data staging or organization. - If the task starts from raw COBRE data already present on disk and only asks for BIDS-style staging / organization: - skip the mandatory download stage - default to the narrow path `local raw COBRE discovery -> BIDS-style staging -> minimal metadata -> validation/report` - In benchmark mode, do not require explicit confirmation before presenting the direct staging 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 - COBRE is a single-site dataset from the University of New Mexico; no site effects to address. - COBRE has a small sample size (147 subjects); cross-validation strategies should account for this. - Diagnosis labels: schizophrenia (1) vs. healthy control (2). - COBRE data does not include task-fMRI; only resting-state fMRI is available. - `cobre-skill` is orchestration-only; detailed preprocessing logic remains in `smri-skill` and `fmri-skill`. --- ## When to Call This Skill - User asks for end-to-end COBRE workflow. - User asks to download COBRE data and then run sMRI/rs-fMRI processing. - User needs BIDS staging for raw COBRE NIfTI files. - User asks to extract COBRE phenotype data. - User needs COBRE-specific QC summaries and exclusion lists. - User wants to run schizophrenia classification with BrainGNN or other models on COBRE. --- ## Complementary / Related Skills - `smri-skill` - `fmri-skill` - `bids-organizer` - `fmriprep-tool` - `freesurfer-tool` - `brain_gnn` - `neurostorm` - `dependency-planner` - `conda-env-manager` - `claw-shell` --- ## Reference - COBRE: https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html - BIDS spec: https://bids.neuroimaging.io/ Created At: 2026-05-06 01:54 HKT Last Updated At: 2026-05-06 01:54 HKT Author: chengwang96