mne.viz.plot_vector_source_estimates¶
-
mne.viz.
plot_vector_source_estimates
(stc, subject=None, hemi='lh', colormap='hot', time_label='auto', smoothing_steps=10, transparent=None, brain_alpha=0.4, overlay_alpha=None, vector_alpha=1.0, scale_factor=None, time_viewer=False, subjects_dir=None, figure=None, views='lat', colorbar=True, clim='auto', cortex='classic', size=800, background='black', foreground='white', initial_time=None, time_unit='s')[source]¶ Plot VectorSourceEstimate with PySurfer.
A “glass brain” is drawn and all dipoles defined in the source estimate are shown using arrows, depicting the direction and magnitude of the current moment at the dipole. Additionally, an overlay is plotted on top of the cortex with the magnitude of the current.
- Parameters
- stc
VectorSourceEstimate
The vector source estimate to plot.
- subject
str
|None
The subject name corresponding to FreeSurfer environment variable SUBJECT. If None stc.subject will be used. If that is None, the environment will be used.
- hemi
str
, ‘lh’ | ‘rh’ | ‘split’ | ‘both’ The hemisphere to display.
- colormap
str
|np.ndarray
offloat
, shape(n_colors, 3 | 4) Name of colormap to use or a custom look up table. If array, must be (n x 3) or (n x 4) array for with RGB or RGBA values between 0 and 255. This should be a sequential colormap.
- time_label
str
|callable()
|None
Format of the time label (a format string, a function that maps floating point time values to strings, or None for no label). The default is
time=%0.2f ms
.- smoothing_steps
int
The amount of smoothing
- transparentbool
If True, use a linear transparency between fmin and fmid.
- brain_alpha
float
Alpha value to apply globally to the surface meshes. Defaults to 0.4.
- overlay_alpha
float
Alpha value to apply globally to the overlay. Defaults to
brain_alpha
.- vector_alpha
float
Alpha value to apply globally to the vector glyphs. Defaults to 1.
- scale_factor
float
|None
Scaling factor for the vector glyphs. By default, an attempt is made to automatically determine a sane value.
- time_viewerbool
Display time viewer GUI.
- subjects_dir
str
The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR.
- figureinstance of
mayavi.core.api.Scene
|list
|int
|None
If None, a new figure will be created. If multiple views or a split view is requested, this must be a list of the appropriate length. If int is provided it will be used to identify the Mayavi figure by it’s id or create a new figure with the given id.
- views
str
|list
View to use. See
surfer.Brain
.- colorbarbool
If True, display colorbar on scene.
- clim
str
|dict
Colorbar properties specification. If ‘auto’, set clim automatically based on data percentiles. If dict, should contain:
kind
‘value’ | ‘percent’Flag to specify type of limits.
lims
list | np.ndarray | tuple of float, 3 elementsLeft, middle, and right bound for colormap.
Unlike
stc.plot
, it cannot usepos_lims
, as the surface plot must show the magnitude.- cortex
str
ortuple
specifies how binarized curvature values are rendered. either the name of a preset PySurfer cortex colorscheme (one of ‘classic’, ‘bone’, ‘low_contrast’, or ‘high_contrast’), or the name of mayavi colormap, or a tuple with values (colormap, min, max, reverse) to fully specify the curvature colors.
- size
float
ortuple
offloat
The size of the window, in pixels. can be one number to specify a square window, or the (width, height) of a rectangular window.
- backgroundmatplotlib color
Color of the background of the display window.
- foregroundmatplotlib color
Color of the foreground of the display window.
- initial_time
float
|None
The time to display on the plot initially.
None
to display the first time sample (default).- time_unit‘s’ | ‘ms’
Whether time is represented in seconds (“s”, default) or milliseconds (“ms”).
- stc
- Returns
- brain
surfer.Brain
A instance of
surfer.Brain
from PySurfer.
- brain
Notes
New in version 0.15.
If the current magnitude overlay is not desired, set
overlay_alpha=0
andsmoothing_steps=1
.