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PYSURFER

NAME

pysurfer − visualize cortical surface reconstruction from Freesurfer

DESCRIPTION

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

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

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