hcppipeline-tool
Use this skill whenever the user wants to perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion) using the official HCP Pipelines. Triggers include: 'HCP pipeline', 'HCP preprocessing', 'hcp-fmri', 'hcp-dwi', 'hcp-structural', 'MSMAll', 'ICA-FIX', 'bedpostx', 'probtrackx', or any request to run the Human Connectome Project preprocessing pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill hcppipeline-tool --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.
# HCP Pipeline Tool ## Overview The HCP Pipelines are the official, highly optimized preprocessing pipelines developed by the Human Connectome Project. They provide state-of-the-art processing for structural (T1w/T2w), functional (task/resting-state fMRI with ICA-FIX), and diffusion MRI (topup + eddy + bedpostx + probtrackx + MSMAll surface alignment). This skill serves as the **NeuroClaw interface-layer wrapper** for the HCP Pipelines and strictly follows the hierarchical design: 1. Check whether HCP Pipelines and dependencies are installed. 2. If missing → invoke `dependency-planner` to generate a safe installation plan. 3. Detect input data (preferably BIDS or HCP-style organized) and confirm processing stages. 4. Generate a clear, numbered execution plan with exact commands, flags, estimated runtime, and risks. 5. Present the plan and wait for explicit user confirmation (“YES” / “execute” / “proceed”). 6. On confirmation → delegate all pipeline stages to `claw-shell`. 7. After completion, summarize outputs and suggest next steps (e.g., connectivity analysis via `fmri-skill` or `fsl-tool`). **Research use only.** ## Quick Reference | Task | Recommended Pipeline Stage | Typical R
- Overview
- Quick Reference
- Common Shell Command Examples
- Installation (Handled by dependency-planner)
- NeuroClaw recommended wrapper script
- Important Notes & Limitations
- When to Call This Skill
- Complementary / Related Skills
- Reference
- Post-Execution Verification (Harness Integration)
Structural pipeline (benchmark-safe baseline: BIDS-aware discovery + validation first)
if [[ -n "${SESSION}" ]]; then
else
fi
Functional pipeline with ICA-FIX
Diffusion pipeline
echo $HCPPIPEDIRWhat does the hcppipeline-tool skill do?
Use this skill whenever the user wants to perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion) using the official HCP Pipelines. Triggers include: 'HCP pipeline', 'HCP preprocessing', 'hcp-fmri', 'hcp-dwi', 'hcp-structural', 'MSMAll', 'ICA-FIX', 'bedpostx', 'probtrackx', or any request to run the Human Connectome Project preprocessing pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill hcppipeline-tool --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.