The command-line interface

Introduction

The command-line program pysurfer is designed to largely replicate Freesufer’s tksurfer command-line interface in the format and style of arguments it accepts. Like tksurfer, invoking it will initialize a visualization in an external window and begin an IPython session in the terminal, through which the visualization can be manipulated.

Initializing a simple visualization session is quite easy. Simply call pysurfer with three positional arguments: the subject_id, the hemisphere, and the surface geometry to visualize:

pysurfer fsaverage lh inflated

which will open a viewing session that looks like this:

Manipulating the visualization

Once the viewer window is open, there are two ways to manipulate the visualization. To see other angles, zoom in or out, and translate the brain, simply click and drag with your mouse. See the Mayavi documentation for more information about using the mouse and keyboard to interact with a Mayavi scence.

When pysurfer finishes loading the visualization, it initializes an IPython session in terminal, which allows for a more comprehensive interaction with the scene. The IPython interactive namespace will include a brain variable, which is bound to the Brain object underlying the visualization. For convenience, the b variable is also mapped to this object. (As a reminder, you can always type whos in an IPython prompt to see the contents of the interactive namespace.) See the Brain documentation for full information about how to control the visualization in this way.

Other command-line options

As in tksurfer, most aspects of the visualization can be initialized from the command-line. To get a full documentation of the command-line interface, simply type pysurfer at a terminal prompt and hit enter.