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qsiprep-tool SKILL.md skillA

qsiprep-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/qsiprep-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/qsiprep-tool/SKILL.md
Versions recorded: 5
Latest version: git:20260506.86420c0, committed May 6, 2026
First version recorded: Mar 25, 2026
Size: 11,440 bytes
Repository stars: 93
License: MIT

Use this skill whenever the user wants to run QSIPrep (BIDS App) for diffusion MRI (DWI) preprocessing with best-practice workflows (topup/eddy, denoising/unringing options, susceptibility/motion correction, coregistration/normalization, QC reports) on BIDS datasets. This skill is the NeuroClaw interface-layer wrapper for QSIPrep: it checks installation (Docker/Singularity/conda), generates an execution plan with exact commands and resource estimates, waits for explicit confirmation, then…

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

# QSIPrep Tool (Interface Layer)

## Overview
QSIPrep is a BIDS-App pipeline for **diffusion MRI (DWI) preprocessing** that emphasizes:
- Robust distortion/motion/eddy-current correction
- Interoperable derivatives for downstream modeling (DTI/DKI/CSD, tractography, connectome, etc.)
- Strong QC reporting (HTML)

This skill is the **NeuroClaw interface-layer wrapper** for QSIPrep and strictly follows the NeuroClaw safety pattern:

1. Check whether QSIPrep is available (preferred: Docker/Singularity image; alternative: conda).
2. If missing → invoke `dependency-planner` to produce an installation plan.
3. Verify inputs (must be BIDS-compliant; detect DWI + fieldmaps/reverse-PE b0 if present).
4. Generate a clear numbered plan with **exact commands**, runtime/resource estimates, and risks.
5. Wait for explicit user confirmation (“YES” / “execute” / “proceed”).
6. On confirmation → delegate all commands to `claw-shell`.
7. Summarize outputs (derivatives paths + QC report location) and suggest next steps.

**Research use only.**

---

## What QSIPrep Typically Does (High-Level)
- Validates BIDS layout (or skips if requested)
- Creates brain mask(s)
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add cuhk-aim-group/neurodiscovery/qsiprep-tool@sha256:0a7426a49d216d22

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_avzroj7ctgkmp6t3.svg)](https://markdownregistry.com/a/art_avzroj7ctgkmp6t3)

4 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 6, 2026, about one every 11 days.

version	committed	commit	size	audit
git:20260506.86420c0 latest	2026-05-06	86420c0	11,440 B	A	view · diff
git:20260505.e9ddd22	2026-05-05	e9ddd22	11,449 B	A	view · diff
git:20260404.fa7f354	2026-04-04	fa7f354	11,373 B	A	view · diff
git:20260328.891ed93	2026-03-28	891ed93	8,822 B	A	view · diff
git:20260325.a465181	2026-03-25	a465181	9,164 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 (11440 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_avzroj7ctgkmp6t3
GET https://markdownregistry.com/api/v1/resolve?ref=cuhk-aim-group/neurodiscovery/qsiprep-tool
GET https://markdownregistry.com/api/v1/blob/0a7426a49d216d22b5aca7aa9063802d2cefdf2df836665e68a80b93499173dc

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.