Pycortex Documentation

Pycortex is a software package for generating beautiful interactive 3D visualizations of fMRI data projected onto cortical surface models. It can also generate high quality 2D flattened cortical visualizations.

This documentation is still under development. Please report errors or bugs at https://github.com/gallantlab/pycortex/issues.

For a list of recent changes, please see the releases on GitHub.

User Guide

• Installation
  • Optional Dependencies
  • Demo
  • Basic Configuration
• Surface Segmentation and Flattening
  • Starting & Setting up Freesurfer
  • Importing Data Into Freesurfer
  • Creating Pial & White Matter Surfaces
• Surface Database
  • Anatomical scans
  • Cache
  • Surfaces
  • Transforms
  • Surface info
  • Views
  • overlays.svg
  • rois.svg
  • Example subject database entry
• Alignments
  • Automatic Alignment
  • Automatically Tweaking Alignments
  • Manual Alignment
• Surface-defined ROIs
• Transform formats
• Colormaps

Example Gallery

• Example Gallery
  • Datasets Examples
  • Examples with fsaverage
  • Importing Surfaces Examples
  • Quickflat Examples
  • Quickstart Examples
  • Surface Analysis Examples
  • Utility Examples
  • WebGL Examples

API Reference

• Python API Reference
  • Most commonly used modules
    • quickflat
    • webgl
    • dataset
  • All the other modules
    • align
    • anat
    • database
    • freesurfer
    • mapper
    • mni
    • polyutils
    • segment
    • surfinfo
    • utils
    • volume
    • xfm

Citation

If you use pycortex in published work, please cite the pycortex paper:

Gao JS, Huth AG, Lescroart MD and Gallant JL (2015) Pycortex: an interactive surface visualizer for fMRI. Front. Neuroinform. 9:23. doi: 10.3389/fninf.2015.00023

Indices and tables

• Index

• Module Index

• Search Page