wmh-segmentation

wmh-segmentation is a skill for Claude Code, Codex from CUHK-AIM-Group/NeuroClaw. It costs 137 tokens per session (1,651 once invoked), scanned B, original, MIT.

An automated tool for marking white matter hyperintensities, bright areas often seen in brain MRI, in a FLAIR scan using a matching T1-weighted scan. It produces a NIfTI image mask showing the detected areas.

In plain words
What is it for?
Use it to segment white matter hyperintensities from FLAIR and T1-weighted MRI scans for research analysis.
Why use it?
Manually outlining these areas is time-consuming and difficult to apply consistently. The workflow checks the required MRI inputs and prepares the model to run in a container.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to segment white matter hyperintensities from FLAIR and T1-weighted MRI scans for research analysis.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/cuhk-aim-group/neuroclaw/wmh-segmentation
Install

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.

Any agent
npx skills add CUHK-AIM-Group/NeuroClaw --skill wmh-segmentation
Clone the repo
git clone --depth 1 https://github.com/CUHK-AIM-Group/NeuroClaw

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for wmh-segmentation

README.md
[![agentmods](https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/wmh-segmentation/github.svg)](https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/wmh-segmentation)
Your own site
<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/wmh-segmentation"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/wmh-segmentation/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.

agentmods 80×15 button for wmh-segmentation

Your own site · 80×15
<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/wmh-segmentation"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/wmh-segmentation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 137 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,651 The whole file, excluding the scripts and references it only reads on demand.
Security scan B 2 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 20 findings, up to high

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • high Privilege Escalation · line 46
    Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
    Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
  • high Privilege Escalation · line 48
    Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
    Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
  • high Privilege Escalation · line 71
    Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
    Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
  • high Privilege Escalation · line 73
    Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
    Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
  • medium MCP Rug Pull · line 33
    Docker image references without a specific tag (:latest is implicit) or digest (@sha256:...) can be silently replaced by a malicious image.
    Fix: Pin the image: image:tag or image@sha256:abc123
  • medium Privilege Escalation · line 46
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 51
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 52
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 53
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 49
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 50
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 71
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 74
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 75
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 76
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 77
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium Privilege Escalation · line 78
    Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
    Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
  • medium MCP Rug Pull · line 84
    Docker image references without a specific tag (:latest is implicit) or digest (@sha256:...) can be silently replaced by a malicious image.
    Fix: Pin the image: image:tag or image@sha256:abc123
  • medium MCP Rug Pull · line 99
    Docker image references without a specific tag (:latest is implicit) or digest (@sha256:...) can be silently replaced by a malicious image.
    Fix: Pin the image: image:tag or image@sha256:abc123
  • low Tool Misuse · line 96
    Tool parameters are crafted to achieve unintended or unsafe behavior. Parameter abuse can bypass intended safety checks (e.g. shell=True, --force, dangerous glob patterns).
    Fix: Validate all tool parameters against an allowlist. Reject dangerous parameter values (shell=True, --force, -rf /) and use safe defaults.
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00137 $0.01651
Opus 5 $0.00068 $0.00826
Sonnet 5 $0.00027 $0.00330
Haiku 4.5 $0.00014 $0.00165

Measured 9d ago against content hash a7cce033e4d9, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade B, and why

wmh-segmentation scanned grade B with 2 findings 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 9d 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.

Asks for rootmediumPrivilege escalation

A mod that escalates privileges can change anything on the machine, not only the project.

sudo gpg --dearmor -o /usr/share/keyrings/nvidia-container-toolkit-keyring.gpg

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

curl -fsSL https://nvidia.github.io/libnvidia-container/gpgkey | \
skills/wmh-segmentation/SKILL.md · 133 lines

How it starts

The opening of the file, as written. The whole thing — 133 lines — stays where its author put it; the contents beside it link to each section on GitHub.

WMH Segmentation (MARS-WMH nnU-Net)

Overview

MARS-WMH is the state-of-the-art, clinically-validated deep-learning tool (nnU-Net architecture) for segmenting brain white matter hyperintensities of presumed vascular origin. It takes a FLAIR image (recommended 1 mm isotropic) and a co-registered or registrable T1w image (1 mm isotropic, no contrast) and outputs a precise WMH segmentation mask in NIfTI format (returned in the original input resolution).

This skill serves as the NeuroClaw interface-layer wrapper for the official MARS-WMH Docker container (ghcr.io/miac-research/wmh-nnunet:latest) and strictly follows the hierarchical design:

  1. Check whether Docker (with NVIDIA Container Toolkit) is installed (docker --version + nvidia-smi via claw-shell).
  2. If nvidia-smi fails → immediately print the exact NVIDIA Container Toolkit installation commands and instruct the user to run them manually before retry.
  3. If paths not provided → interactively ask the user for FLAIR and T1w full paths and confirm they exist on disk.
  4. If paths provided → verify file existence and readability.
  5. Prepare clean working directory, copy inputs, generate exact Docker pull/tag + run commands.
  6. Generate a numbered execution plan.
  7. Present the plan, estimated runtime (~5–15 min on GPU), requirements and risks → wait for explicit user confirmation (“YES” / “execute” / “proceed”).
  8. On confirmation → delegate all shell execution to claw-shell.
  9. Report completion, exact output mask location, and next steps.

Key design principle (2026 update): All Docker execution is routed through claw-shell.

Quick Reference (Common Use Cases)

Task Recommended approach
Standard WMH segmentation Default Docker run (nnU-Net, GPU)
Already co-registered images Add --skipRegistration flag
CPU-only fallback Remove --gpus all (slow)

Read the full file on GitHub · 133 lines

Changes

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.

  1. 9d ago First seen · 133 lines · 137 tokens per session scan B a7cce033e4d9

Subscribe to this mod's changes

wmh-segmentation is a skill published in the GitHub repository CUHK-AIM-Group/NeuroClaw (85 stars, last pushed 6d ago), licensed MIT. It adds 137 tokens to every session and 1,651 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it B with 2 findings (asks for root, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

Related

Other skills, from other repositories

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…

anthropics/knowledge-work-plugins · 123 tokens

matlab

Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.

K-Dense-AI/scientific-agent-skills · 42 tokens

exploratory-data-analysis

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…

K-Dense-AI/scientific-agent-skills · 83 tokens

phylogenetics

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills · 68 tokens

research-engineer

An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.

davila7/claude-code-templates · 43 tokens

mapping-to-snomed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…

maziyarpanahi/openmed · 205 tokens