Introduction

PySurfer is a Python based program for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data.

PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets.

Contents

• Installation and Dependencies
• Examples
  • Basic Visualization
  • Display fMRI Activation
  • Display a Conjunction Map
  • Display Activation Contours
  • Plot Activation Foci
  • Display Volume Data
  • Plot a label generated at an activation foci
  • Display ROI Labels
  • Plot MEG inverse solution
  • Overlay Morphometry Data
  • Display ROI Values
  • Using Annotation Files
  • Display Probabilistic Labels
  • Show the different brain views
  • Make a multiview image
  • Animate brain and save movie
  • Save a set of views
• Documentation
  • The command-line interface
  • Customizing the Visualization
  • The Config File

Authors

Michael Waskom, Stanford University

Alexandre Gramfort, Harvard Med. School MGH Martinos Center - INRIA

Scott Burns, Harvard Med. School MGH Martinos Center

Martin Luessi, Harvard Med. School MGH Martinos Center

License

The PySurfer source code is available under the simplified BSD license

Support

If you have problems installing the software or questions about usage, documentation or something else related to PySurfer, you can post to the NiPy mailing list. Please preface the subject line with “[PySurfer]”.

Mailing list:nipy-devel@neuroimaging.scipy.org [subscription, archive]

Contribute

https://github.com/nipy/PySurfer/