Pycortex Guide

Purpose

Encodes domain knowledge for using pycortex — a Python library for visualizing fMRI and volumetric neuroimaging data on cortical surfaces. Covers data creation, 2D flatmap rendering, interactive 3D WebGL viewers, volume-to-surface mapping, subject database management, FreeSurfer/fMRIPrep integration, and surface geometry analysis.

When to Use This Skill

Activate when the user:

• Wants to visualize fMRI data on cortical surfaces
• Mentions pycortex, import cortex, flatmaps, or cortical surface visualization
• Needs to create Volume, Vertex, or Dataset objects for brain data
• Wants to generate 2D flatmaps or 3D interactive brain viewers
• Needs to import FreeSurfer or fMRIPrep subjects into pycortex
• Works with volume-to-surface mapping or cortical ROIs
• Needs to align functional data to anatomical surfaces
• Wants to compute surface properties (curvature, thickness, geodesic distance)

Reference Files