cobre-skill
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cobre-skill --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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_
- Overview
- Download Stage (Mandatory First Step)
- Source
- Supported COBRE Data Packages
- Delegation Rules for Download
- Download Inputs to Confirm in Plan
- Narrow Path: COBRE Raw NIfTI -> BIDS Staging
- Expected narrow-path behavior
- Core Workflow (Never Bypassed)
- BIDS Preparation
- Script: scripts/reorganizecobre.py
- Phenotype Extraction
- Script: scripts/extractcobrephenotype.py
- QC Integration
python skills/cobre-skill/scripts/reorganize_cobre.py \ python skills/cobre-skill/scripts/extract_cobre_phenotype.py \ python skills/cobre-skill/scripts/cobre_qc_summary.py \
What does the cobre-skill skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cobre-skill --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.