freesurfer-tool skillA
freesurfer-tool is agent-read markdown (skill) from cuhk-aim-group/neurodiscovery: 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 requ.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# 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”). …
Read the whole file at its exact version.
How to install
mdr add cuhk-aim-group/neurodiscovery/freesurfer-tool@git:20260506.86420c0mdr add cuhk-aim-group/neurodiscovery/freesurfer-tool@sha256:f0c7f0cb3ba914f1Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_mffov2s6w6wuqk6l)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260506.86420c0 latest | 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
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12789 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
cuhk-aim-group/neurodiscovery · 91 stars · license MIT · pushed 2026-09-22 · 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/f0c7f0cb3ba914f1ca677ff539885b92d0237d331f7480eac350295a3ff53eca
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