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freesurfer-tool SKILL.md skillA

freesurfer-tool from cuhk-aim-group/neurodiscovery is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add cuhk-aim-group/neurodiscovery/freesurfer-tool@git:20261014.f405841

Pins git:20261014.f405841 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: cuhk-aim-group/neurodiscovery
Path: skills/freesurfer-tool/SKILL.md
Versions recorded: 6
Latest version: git:20261014.f405841, committed Oct 14, 2026
First version recorded: Mar 28, 2026
Size: 4,356 bytes
Repository stars: 93
License: MIT

Plan or run FreeSurfer recon-all from structural MRI, resume an existing subject, or validate surfaces, segmentations and statistics.

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# FreeSurfer Tool

Choose the reconstruction stage requested by the user. Preserve provided image,
subject and output paths. This document supplies methods; loading it does not
execute reconstruction, install a license, delegate work or invoke verification.

## Inputs and environment

For a new full subject, require the actual local T1w image. Optional T2w or FLAIR
must exist when supplied; report an invalid optional path rather than silently
ignoring it. Do not replace unavailable anatomy with examples or synthetic data.
Check the FreeSurfer installation, setup script and license before execution.
Run environment setup and the command in the same shell/process environment.
Use an available shell executor, including `claw-shell` when exposed; when asked
for code, give a runnable external command rather than an unresolved tool call.

## New subject versus continuation

For an unused subject directory, initialize and run the complete workflow:

```bash
export SUBJECTS_DIR="$OUT/subjects"
source "$FREESURFER_HOME/SetUpFreeSurfer.sh"
mkdir -p "$SUBJECTS_DIR"
recon-all -sd "$SUBJECTS_DIR" -s "$SUBJECT" -i "$T1W" -all
```
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add cuhk-aim-group/neurodiscovery/freesurfer-tool@sha256:5417fcd095c83122

The line at the top of this page pins the label git:20261014.f405841, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_mffov2s6w6wuqk6l.svg)](https://markdownregistry.com/a/art_mffov2s6w6wuqk6l)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 6 versions of this file, between Mar 28, 2026 and Oct 14, 2026, about one every 40 days.

version	committed	commit	size	audit
git:20261014.f405841 latest	2026-10-14	f405841	4,356 B	A	view · diff
git:20260506.86420c0	2026-05-06	86420c0	12,789 B	A	view · diff
git:20260505.e9ddd22	2026-05-05	e9ddd22	12,798 B	A	view · diff
git:20260505.1bbc12b	2026-05-05	1bbc12b	12,741 B	A	view · diff
git:20260404.fa7f354	2026-04-04	fa7f354	11,981 B	A	view · diff
git:20260328.891ed93	2026-03-28	891ed93	10,312 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (4356 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

cuhk-aim-group/neurodiscovery · 93 stars · license MIT · pushed 2026-10-23 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_mffov2s6w6wuqk6l
GET https://markdownregistry.com/api/v1/resolve?ref=cuhk-aim-group/neurodiscovery/freesurfer-tool
GET https://markdownregistry.com/api/v1/blob/5417fcd095c83122a2ca8acb59832931b58dc9739c74d50a8d4b57f615042b4d

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.