fmriprep-tool skillA
fmriprep-tool is agent-read markdown (skill) from cuhk-aim-group/neurodiscovery: 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..
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
# 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
mdr add cuhk-aim-group/neurodiscovery/fmriprep-tool@git:20260505.e9ddd22mdr add cuhk-aim-group/neurodiscovery/fmriprep-tool@sha256:8a463617afe6d1d3Pin 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_ahhxkaaidien5lu3)
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Versions
| 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
- 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
cuhk-aim-group/neurodiscovery · 91 stars · license MIT · pushed 2026-09-22 · 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
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