fmriprep-tool

Name: fmriprep-tool
Availability: InStock
Author: CUHK-AIM-Group

Generate and execute fMRIPrep preprocessing plans for BIDS datasets.

78|3|Updated Mar 25, 2026

Search Tags:#preprocessing #reproducibility #neuroimaging #qc #fmriprep #bids #claw-shell

Ready to run

npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill fmriprep-tool

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: fmriprep-tool
Source: https://github.com/CUHK-AIM-Group/NeuroClaw/tree/main/skills/fmriprep-tool
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill fmriprep-tool

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Streamlines standardized preprocessing of fMRI and anatomical MRI data by coordinating fMRIPrep with dependency checks, containerized execution, and QC-ready outputs to reduce setup friction and ensure reproducibility.

Core Features & Use Cases

Dependency verification and safe installation planning via dependency-planner, ensuring Docker/Singularity readiness.
Automatic detection of BIDS-formatted input and output directories, followed by generation of a clear, step-by-step execution plan with exact commands, flags, and estimated runtime.
End-to-end orchestration through claw-shell after user confirmation, plus automatic post-run QC reporting and output summarization.

Quick Start

Provide a complete fMRIPrep preprocessing plan for a given BIDS dataset and confirm before execution.

Frequently Asked Questions about fmriprep-tool

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I run fMRIPrep preprocessing on a BIDS dataset end to end?▼

To run fMRIPrep preprocessing on a BIDS dataset, you provide the input and output directories to generate an execution plan with exact commands, confirm the plan, and orchestrate the containerized run automatically.

Do I need Docker or Singularity installed before running fMRI preprocessing?▼

Yes, you need Docker or Singularity installed before running fMRI preprocessing, as the workflow includes dependency verification to ensure container readiness and reproducible execution.

How does BIDS validation work before generating an fMRIPrep execution plan?▼

BIDS validation works by automatically detecting BIDS-formatted input and output directories, verifying the dataset structure before generating a clear, step-by-step execution plan with exact commands and estimated runtime.

Can I review the exact fMRIPrep commands before execution starts?▼

Yes, you can review exact fMRIPrep commands before execution starts, because the tool generates a detailed execution plan with specific flags and estimated runtime that requires your confirmation before gated execution through claw-shell.

Does fMRIPrep preprocessing provide quality control outputs automatically?▼

Yes, fMRIPrep preprocessing provides quality control outputs automatically, including post-run QC reporting and output summarization to verify the standardized results of your neuroimaging workflow.