table of contents
- bullseye 0.11.0-1
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 |