freesurfer-tool
Use this skill whenever the user wants to process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline. Triggers include: 'freesurfer', 'recon-all', 'segment MRI', 'FreeSurfer processing', 'cortical segmentation', 'subcortical segmentation', 'run recon-all', 'freesurfer T1', 'process brain MRI with freesurfer', 'aseg aparc', or any request to run FreeSurfer on NIfTI MRI data for research analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill freesurfer-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.
# FreeSurfer Tool ## Overview FreeSurfer is the gold-standard open-source suite for automated reconstruction of the brain’s cortical surface from structural MRI, including skull-stripping, intensity normalization, Talairach registration, cortical parcellation (Desikan-Killiany / Destrieux atlases), subcortical segmentation (`aseg`), surface mesh generation, cortical thickness estimation, and statistics. This skill serves as the **NeuroClaw interface-layer wrapper** for FreeSurfer and strictly follows the hierarchical design: 1. Check whether FreeSurfer is installed (`recon-all --version`, `$FREESURFER_HOME` environment variable). 2. If not found → immediately invoke `dependency-planner` to plan and (after user confirmation) install the latest stable FreeSurfer release + license setup. 3. Collect and confirm: input NIfTI file(s), subject ID, output `SUBJECTS_DIR`, desired stages/flags (e.g. `-all`, `-autorecon1..3`, `-T2`, `-FLAIR`, `-parallel`). 4. Generate a clear, numbered execution plan including exact shell commands. 5. Present plan, estimated runtime, disk/RAM requirements, and risks → wait for explicit user confirmation (“YES” / “execute” / “proceed”). 6. On confirmation → de
- Overview
- Quick Reference (Common Use Cases)
- Installation Check & Setup
- Agent Reference Rule
- NeuroClaw recommended wrapper script
- Important Notes & Limitations
- When to Call This Skill
- Complementary / Related Skills
- Reference
- Post-Execution Verification (Harness Integration)
python skills/freesurfer-tool/scripts/freesurfer_processor.py \
What does the freesurfer-tool skill do?
Use this skill whenever the user wants to process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline. Triggers include: 'freesurfer', 'recon-all', 'segment MRI', 'FreeSurfer processing', 'cortical segmentation', 'subcortical segmentation', 'run recon-all', 'freesurfer T1', 'process brain MRI with freesurfer', 'aseg aparc', or any request to run FreeSurfer on NIfTI MRI data for research analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill freesurfer-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.