Cobre skill

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.

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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

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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.

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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/.

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BIDS Preparation

Script: scripts/reorganize_cobre.py

Converts COBRE raw directory structure to BIDS-compliant layout.

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

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Phenotype Extraction

Script: scripts/extract_cobre_phenotype.py

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

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QC Integration

Script: scripts/cobre_qc_summary.py

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

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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)

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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.

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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.

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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.

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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.

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Complementary / Related Skills

• smri-skill
• fmri-skill
• bids-organizer
• fmriprep-tool
• freesurfer-tool
• brain_gnn
• neurostorm
• dependency-planner
• conda-env-manager
• claw-shell

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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