pysurfer − visualize cortical surface reconstruction from Freesurfer
22:18:01: Warning: Mismatch between the program and library build versions detected. The library used 3.0 (wchar_t,compiler with C++ ABI 1010,wx containers,compatible with 2.8), and wxPython used 3.0 (wchar_t,compiler with C++ ABI 1009,wx containers,compatible with 2.8). 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 |
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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