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fmriprep-tool SKILL.md skillA

fmriprep-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/fmriprep-tool@git:20260505.e9ddd22

Pins git:20260505.e9ddd22 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/fmriprep-tool/SKILL.md
Versions recorded: 5
Latest version: git:20260505.e9ddd22, committed May 5, 2026
First version recorded: Mar 25, 2026
Size: 9,048 bytes
Repository stars: 93
License: MIT

Use this skill whenever the user wants to perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep. Triggers include: 'fmriprep', 'fMRIPrep', 'fMRI preprocessing', 'BIDS fMRI', 'run fmriprep', 'preprocess bold', 'BOLD preprocessing', 'anatomical preprocessing', or any request involving BIDS-organized fMRI datasets.

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

# fMRIPrep Tool

## Overview

fMRIPrep is a robust, standardized preprocessing pipeline for BIDS-compliant functional and anatomical MRI data. It performs best-practice steps including anatomical segmentation, functional motion correction, susceptibility distortion correction, coregistration, normalization to standard space, and generates comprehensive QC reports.

This skill serves as the **NeuroClaw interface-layer wrapper** for fMRIPrep and strictly follows the hierarchical design:

1. Check whether fMRIPrep and its dependencies (Docker or Singularity) are installed.
2. If missing → invoke `dependency-planner` to generate a safe installation plan.
3. Detect input BIDS dataset structure and confirm output directory.
4. Generate a clear, numbered execution plan with exact command, flags, estimated runtime, and risks.
5. Present the plan and wait for explicit user confirmation (“YES” / “execute” / “proceed”).
6. On confirmation → delegate the entire pipeline execution to `claw-shell`.
7. After completion, summarize outputs, highlight QC reports, and suggest next steps (e.g., feeding results into analysis or paper-writing).

**Research use only.**

## Quick Reference
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add cuhk-aim-group/neurodiscovery/fmriprep-tool@sha256:8a463617afe6d1d3

The line at the top of this page pins the label git:20260505.e9ddd22, 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_ahhxkaaidien5lu3.svg)](https://markdownregistry.com/a/art_ahhxkaaidien5lu3)

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

Versions

The registry has recorded 5 versions of this file, between Mar 25, 2026 and May 5, 2026, about one every 10 days.

version	committed	commit	size	audit
git:20260505.e9ddd22 latest	2026-05-05	e9ddd22	9,048 B	A	view · diff
git:20260404.fa7f354	2026-04-04	fa7f354	8,972 B	A	view · diff
git:20260328.891ed93	2026-03-28	891ed93	6,636 B	A	view · diff
git:20260325.72d2cbf	2026-03-25	72d2cbf	6,758 B	A	view · diff
git:20260325.6f1b393	2026-03-25	6f1b393	6,879 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 (9048 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_ahhxkaaidien5lu3
GET https://markdownregistry.com/api/v1/resolve?ref=cuhk-aim-group/neurodiscovery/fmriprep-tool
GET https://markdownregistry.com/api/v1/blob/8a463617afe6d1d3911026783f0889cb3fe1afd0014acfcd797c6336ec527aa1

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.