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freesurfer-tool

Automate end-to-end FreeSurfer processing for structural MRI data.

78|3|Updated Mar 25, 2026
Search Tags:#automation#workflow#neuroimaging#freesurfer#recon-all#cortical#MRI
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill freesurfer-tool
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: freesurfer-tool
Source: https://github.com/CUHK-AIM-Group/NeuroClaw/tree/main/skills/freesurfer-tool
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroClaw --skill freesurfer-tool

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates end-to-end FreeSurfer processing for structural MRI data by providing a safe wrapper that verifies installation, validates inputs, builds an execution plan, and delegates all long-running commands to claw-shell, ensuring reproducible and auditable runs.

Core Features & Use Cases

  • Environment checks and installation planning via dependency-planner.
  • Input validation for MRI data and subject configuration.
  • Execution planning with exact shell commands and safety guardrails.
  • Post-execution verification and logging through harness-core.

Quick Start

Provide a structural MRI NIfTI file and a subject ID to initiate a planned FreeSurfer run, and confirm execution to hand off to claw-shell.

Frequently Asked Questions about freesurfer-tool

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

FAQPage Schema
How do I automate FreeSurfer recon-all processing for structural MRI data?▼

You can automate FreeSurfer recon-all processing by providing a structural MRI NIfTI file and subject ID to generate an execution plan with safety guardrails, then delegating the long-running commands to claw-shell for reproducible runs.

What is the best way to ensure FreeSurfer environment dependencies are installed before running cortical reconstruction?▼

The best way to verify FreeSurfer environment dependencies is through automated environment checks and installation planning, which validate your setup and generate a dependency plan before initiating cortical reconstruction.

Does this FreeSurfer workflow wrapper support configurable processing stages for structural MRI data?▼

Yes, this FreeSurfer workflow wrapper supports configurable processing stages, allowing you to build a customized execution plan with exact shell commands and safety guardrails before delegating structural MRI processing.

How do I validate MRI data inputs before starting a FreeSurfer recon-all pipeline?▼

To validate MRI data inputs before starting a FreeSurfer recon-all pipeline, the wrapper performs automated input validation for your structural MRI NIfTI files and subject configuration during the execution planning phase.

Why does FreeSurfer processing fail without centralized logging and post-execution verification?▼

FreeSurfer processing lacks reproducibility and auditability without centralized logging and post-execution verification, which ensure that delegated long-running commands are tracked and validated against expected structural MRI outputs.

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