freesurfer

What problem does it solve?

It helps you understand, route, and plan FreeSurfer cortical surface reconstruction and anatomical processing tasks without guessing command details or making unsafe assumptions.

Core Features & Use Cases

• Surface reconstruction guidance: Focuses on FreeSurfer surface reconstruction, segmentation artifacts to watch for, and expected outputs from cortical workflows like recon-all.
• Documentation-first assistance: Points you to high-value local reference materials (e.g., command registration, install/FAQ, recon-all step tables, file formats, coordinate systems) so your next steps are evidence-based.
• QC and workflow routing: Supports planning inspection steps (surfaces, parcellations, coordinate assumptions) and routing outputs to downstream tool families such as MNE or Nilearn.

Quick Start

Use the freesurfer skill for a question about what recon-all steps produce which cortical surface outputs and what QC checks to run before continuing.