fmriprep-tool
Use this skill whenever the user wants to perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep. Triggers include: 'fmriprep', 'fMRIPrep', 'fMRI preprocessing', 'BIDS fMRI', 'run fmriprep', 'preprocess bold', 'BOLD preprocessing', 'anatomical preprocessing', or any request involving BIDS-organized fMRI datasets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill fmriprep-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.
# fMRIPrep Tool ## Overview fMRIPrep is a robust, standardized preprocessing pipeline for BIDS-compliant functional and anatomical MRI data. It performs best-practice steps including anatomical segmentation, functional motion correction, susceptibility distortion correction, coregistration, normalization to standard space, and generates comprehensive QC reports. This skill serves as the **NeuroClaw interface-layer wrapper** for fMRIPrep and strictly follows the hierarchical design: 1. Check whether fMRIPrep and its dependencies (Docker or Singularity) are installed. 2. If missing → invoke `dependency-planner` to generate a safe installation plan. 3. Detect input BIDS dataset structure and confirm output directory. 4. Generate a clear, numbered execution plan with exact command, flags, estimated runtime, and risks. 5. Present the plan and wait for explicit user confirmation (“YES” / “execute” / “proceed”). 6. On confirmation → delegate the entire pipeline execution to `claw-shell`. 7. After completion, summarize outputs, highlight QC reports, and suggest next steps (e.g., feeding results into analysis or paper-writing). **Research use only.** ## Quick Reference | Task | Recommended
- Overview
- Quick Reference
- Common Shell Command Examples
- Installation (Handled by dependency-planner)
- NeuroClaw recommended wrapper script
- Important Notes & Limitations
- When to Call This Skill
- Post-Execution Verification (Harness Integration)
- Complementary / Related Skills
- More Advanced Features
Standard full pipeline (most common) fmriprep \ participant \ Anatomical preprocessing only fmriprep /data/bids /data/fmriprep_output participant --anat-only Use Singularity instead of Docker (common on clusters) singularity run --cleanenv \ fmriprep --version
What does the fmriprep-tool skill do?
Use this skill whenever the user wants to perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep. Triggers include: 'fmriprep', 'fMRIPrep', 'fMRI preprocessing', 'BIDS fMRI', 'run fmriprep', 'preprocess bold', 'BOLD preprocessing', 'anatomical preprocessing', or any request involving BIDS-organized fMRI datasets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill fmriprep-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.