Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add CUHK-AIM-Group/NeuroClaw --skill freesurfer-toolgit clone --depth 1 https://github.com/CUHK-AIM-Group/NeuroClawWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/freesurfer-tool)<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/freesurfer-tool"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/freesurfer-tool/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/freesurfer-tool"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/freesurfer-tool.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00150 | $0.03053 |
| Opus 5 | $0.00075 | $0.01527 |
| Sonnet 5 | $0.00030 | $0.00611 |
| Haiku 4.5 | $0.00015 | $0.00305 |
Grade A, and why
freesurfer-tool scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
**Key design principle (2026 update)**: No direct `subprocess.run()` calls for long-running FreeSurfer commands. All shell execution is routed through `claw-shell` for centralized logging, timeout handling, real-time out How it starts
The opening of the file, as written. The whole thing — 286 lines — stays where its author put it; the contents beside it link to each section on GitHub.
FreeSurfer Tool
Overview
FreeSurfer is the gold-standard open-source suite for automated reconstruction of the brain’s cortical surface from structural MRI, including skull-stripping, intensity normalization, Talairach registration, cortical parcellation (Desikan-Killiany / Destrieux atlases), subcortical segmentation (aseg), surface mesh generation, cortical thickness estimation, and statistics.
This skill serves as the NeuroClaw interface-layer wrapper for FreeSurfer and strictly follows the hierarchical design:
- Check whether FreeSurfer is installed (
recon-all --version,$FREESURFER_HOMEenvironment variable). - If not found → immediately invoke
dependency-plannerto plan and (after user confirmation) install the latest stable FreeSurfer release + license setup. - Collect and confirm: input NIfTI file(s), subject ID, output
SUBJECTS_DIR, desired stages/flags (e.g.-all,-autorecon1..3,-T2,-FLAIR,-parallel). - Generate a clear, numbered execution plan including exact shell commands.
- Present plan, estimated runtime, disk/RAM requirements, and risks → wait for explicit user confirmation (“YES” / “execute” / “proceed”).
- On confirmation → delegate all shell command execution to the
claw-shellskill (environment setup,recon-allinvocation, logging, progress monitoring). - Report completion status, log location, output directory, and next steps.
Key design principle (2026 update): No direct subprocess.run() calls for long-running FreeSurfer commands. All shell execution is routed through claw-shell for centralized logging, timeout handling, real-time output streaming, and interruption safety.
Research use only.
Quick Reference (Common Use Cases)
| Task | Recommended recon-all flags / approach |
|---|---|
| Full pipeline (most common) | -all |
| Fast subcortical + basic surfaces | -autorecon1 -autorecon2 -autorecon3 |
| Cortical surfaces & parcellation | -autorecon2 -autorecon3 (after autorecon1 completed) |
| Improve pial surface with T2 | -T2 T2w.nii.gz |
| Use FLAIR for better segmentation | -FLAIR FLAIR.nii.gz |
| Enable multi-core acceleration | -parallel -openmp 8 (or match available cores) |
| Resume interrupted run | Omit -i and -all, specify stages only |
| Generate statistics only | -stats |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 286 lines · 150 tokens per session scan A f0c7f0cb3ba9
freesurfer-tool is a skill published in the GitHub repository CUHK-AIM-Group/NeuroClaw (84 stars, last pushed 4d ago), licensed MIT. It adds 150 tokens to every session and 3,053 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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