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PYSURFER(1) User Commands PYSURFER(1)

NAME

pysurfer - visualize cortical surface reconstruction from Freesurfer

DESCRIPTION

usage: pysurfer subject_id hemisphere surface [options]

PySurfer is a package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer.

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, and, 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.

The visualization interface is exposed through methods on the `brain' variable that will exist in IPython namespace when the program finishes loading. Please see the PySurfer documentation for more information about how to interact with the Brain object.

positional arguments:

subject_id
subject id as in subjects dir
hemi
hemisphere to load
surf
surface mesh (e.g. 'pial', 'inflated')

optional arguments:

-h, --help
show this help message and exit
-morphometry MEAS
load morphometry file (e.g. thickness, curvature)
-annotation ANNOT
load annotation (by name or filepath)
-label LABEL
load label (by name or filepath
-borders
only show label/annot borders
-overlay FILE
load scalar overlay file
-range MIN MAX
overlay threshold and saturation point
-min MIN
overlay threshold
-max MAX
overlay saturation point
-sign {abs,pos,neg}
overlay sign
-name NAME
name to use for the overlay
-size [SIZE]
size of the display window (in pixels)
-background COLOR
background color for display
-foreground COLOR
foreground color for display
-cortex COLOR
colormap or color for rendering the cortex
-alpha COLOR
specifies opacity for the cortical surface
-title TITLE
title to use for the figure
-views [VIEWS [VIEWS ...]]
view list (space-separated) to use
June 2018 pysurfer 0.7