fsl-tool

Orchestrate FSL neuroimaging workflows with installation checks and user-confirmed execution plans.

78|3|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill fsl-tool
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: fsl-tool
Source: https://github.com/CUHK-AIM-Group/NeuroClaw/tree/main/skills/fsl-tool
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill fsl-tool

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill provides a safe, unified interface to manage FSL-based neuroimaging analyses across structural, functional, and diffusion MRI. It shields users from installation fragility and manual command composition by validating environment readiness and generating an executable plan.

Core Features & Use Cases

  • Environment check and dependency planning if FSL is absent
  • Generation of a concrete shell command execution plan
  • Safe, auditable execution via claw-shell with explicit user confirmation
  • Suitable for preprocessing, registration, and model-fitting tasks in structural, functional, and diffusion MRI workflows
  • Use Case: Neuroimaging study preprocessing with T1w, fMRI, and DTI data

Quick Start

Request a full FSL preprocessing pipeline on your dataset (e.g., T1w.nii.gz) and confirm execution to begin.

Frequently Asked Questions about fsl-tool

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

FAQPage Schema
How do I automate an FSL preprocessing pipeline for neuroimaging data?

To automate an FSL preprocessing pipeline for neuroimaging data, request the workflow on your dataset, review the generated shell command execution plan with parameter explanations, and confirm execution to run it safely via claw-shell.

How do I check if FSL is installed before running fMRI or DTI analysis?

To check if FSL is installed before running fMRI or DTI analysis, the interface automatically validates environment readiness using fslversion, generating a dependency plan if the installation is missing.

What is the best way to safely execute FSL commands for brain extraction and tractography?

The best way to safely execute FSL commands for brain extraction and tractography is by routing the generated execution plan through claw-shell, requiring explicit user confirmation before any structural or diffusion MRI processing begins.

Can I use this interface for structural, functional, and diffusion MRI workflows?

Yes, you can use this unified interface for structural, functional, and diffusion MRI workflows, covering typical research pipeline tasks including preprocessing, brain extraction, normalization, and tractography scenarios.

Why does my FSL workflow require explicit approval before executing shell commands?

Your FSL workflow requires explicit approval before executing shell commands to ensure safe, auditable execution, allowing you to review a concrete plan with parameter explanations before routing commands through claw-shell.

Do I need a local FSL installation to run neuroimaging pipelines through this interface?

Yes, you need a local FSL installation to run neuroimaging pipelines. The interface checks for FSL availability using fslversion and provides dependency planning if the required environment is absent.