.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PYSURFER "1" "June 2018" "pysurfer 0.7" "User Commands"
.SH NAME
pysurfer \- visualize cortical surface reconstruction from Freesurfer
.SH DESCRIPTION
usage: pysurfer subject_id hemisphere surface [options]
.PP
PySurfer is a package for visualization and interaction with cortical
surface representations of neuroimaging data from Freesurfer.
.PP
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.
.PP
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.
.SS "positional arguments:"
.TP
subject_id
subject id as in subjects dir
.TP
hemi
hemisphere to load
.TP
surf
surface mesh (e.g. 'pial', 'inflated')
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-morphometry\fR MEAS
load morphometry file (e.g. thickness, curvature)
.TP
\fB\-annotation\fR ANNOT
load annotation (by name or filepath)
.TP
\fB\-label\fR LABEL
load label (by name or filepath
.TP
\fB\-borders\fR
only show label/annot borders
.TP
\fB\-overlay\fR FILE
load scalar overlay file
.TP
\fB\-range\fR MIN MAX
overlay threshold and saturation point
.TP
\fB\-min\fR MIN
overlay threshold
.TP
\fB\-max\fR MAX
overlay saturation point
.TP
\fB\-sign\fR {abs,pos,neg}
overlay sign
.TP
\fB\-name\fR NAME
name to use for the overlay
.TP
\fB\-size\fR [SIZE]
size of the display window (in pixels)
.TP
\fB\-background\fR COLOR
background color for display
.TP
\fB\-foreground\fR COLOR
foreground color for display
.TP
\fB\-cortex\fR COLOR
colormap or color for rendering the cortex
.TP
\fB\-alpha\fR COLOR
specifies opacity for the cortical surface
.TP
\fB\-title\fR TITLE
title to use for the figure
.TP
\fB\-views\fR [VIEWS [VIEWS ...]]
view list (space\-separated) to use