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nilearn-tool SKILL.md skillA

nilearn-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/nilearn-tool@git:20260506.86420c0

Pins git:20260506.86420c0 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/nilearn-tool/SKILL.md
Versions recorded: 5
Latest version: git:20260506.86420c0, committed May 6, 2026
First version recorded: Mar 28, 2026
Size: 10,884 bytes
Repository stars: 93
License: MIT

Use this skill whenever any NeuroClaw fMRI modality skill needs to execute concrete Nilearn operations: ROI/atlas time-series extraction, confounds handling (fMRIPrep), seed-based connectivity maps, ROI-to-ROI connectivity matrices, and optional GLM/decoding utilities. This is the dedicated base/tool skill that contains Nilearn usage patterns and lightweight wrappers. Never called directly by the user.

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

# Nilearn Tool (Base/Tool Layer)

## Overview
`nilearn-tool` is the **NeuroClaw base/tool skill** that implements concrete **Nilearn** workflows for turning **preprocessed BOLD** into features (ROI time series, connectivity matrices, seed maps) and optional statistical modeling (GLM).

It is **never called directly by the user**. It is delegated to by `fmri-skill` (or other interface/modality skills) and executed via `claw-shell`.

**Research use only.**

## Agent Reference Rule

When the agent needs Nilearn-based implementation code, it should first consult the curated snippets in `skills/nilearn-tool/scripts/` instead of copying directly from long tutorial scripts with hard-coded paths.

Reference snippets available:
- `scripts/preprocess_bold_reference.py` -> dummy removal, smoothing, band-pass filtering, MNI resampling
- `scripts/connectome_reference.py` -> atlas ROI extraction and ROI-to-ROI connectivity export
- `scripts/zalff_summary_reference.py` -> MNI resampling, zALFF summary, atlas-level regional export
- `scripts/task_glm_reference.py` -> first-level task GLM with design matrix and contrast maps
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add cuhk-aim-group/neurodiscovery/nilearn-tool@sha256:74b02eed697228cc

The line at the top of this page pins the label git:20260506.86420c0, 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_jubvn3rlckvmd4z3.svg)](https://markdownregistry.com/a/art_jubvn3rlckvmd4z3)

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

Versions

The registry has recorded 5 versions of this file, between Mar 28, 2026 and May 6, 2026, about one every 10 days.

version	committed	commit	size	audit
git:20260506.86420c0 latest	2026-05-06	86420c0	10,884 B	A	view · diff
git:20260505.e9ddd22	2026-05-05	e9ddd22	10,883 B	A	view · diff
git:20260413.5f89017	2026-04-13	5f89017	10,826 B	A	view · diff
git:20260404.fa7f354	2026-04-04	fa7f354	6,252 B	A	view · diff
git:20260328.891ed93	2026-03-28	891ed93	4,640 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 (10884 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_jubvn3rlckvmd4z3
GET https://markdownregistry.com/api/v1/resolve?ref=cuhk-aim-group/neurodiscovery/nilearn-tool
GET https://markdownregistry.com/api/v1/blob/74b02eed697228cc62c265fdc432ad5aa7017d129c3513fe2b5e84998bab796e

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.