mne.viz.plot_source_estimates¶
-
mne.viz.
plot_source_estimates
(stc, subject=None, surface='inflated', hemi='lh', colormap='auto', time_label='auto', smoothing_steps=10, transparent=True, alpha=1.0, 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', backend='auto', spacing='oct6', title=None, verbose=None)[source]¶ Plot SourceEstimate with PySurfer.
By default this function uses
mayavi.mlab
to plot the source estimates. If Mayavi is not installed, the plotting is done withmatplotlib.pyplot
(much slower, decimated source space by default).- Parameters
- stc
SourceEstimate
The source estimates 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.
- surface
str
The type of surface (inflated, white etc.).
- 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. The default (‘auto’) uses ‘hot’ for one-sided data and ‘mne’ for two-sided data.
- 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.
- alpha
float
Alpha value to apply globally to the overlay. Has no effect with mpl backend.
- 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
| instance ofmatplotlib.figure.Figure
|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. If an instance of matplotlib figure, mpl backend is used for plotting.
- views
str
|list
View to use. See
surfer.Brain
. Supported views: [‘lat’, ‘med’, ‘ros’, ‘cau’, ‘dor’ ‘ven’, ‘fro’, ‘par’]. Using multiple views is not supported for mpl backend.- 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.
pos_lims
list | np.ndarray | tuple of float, 3 elementsLeft, middle, and right bound for colormap. Positive values will be mirrored directly across zero during colormap construction to obtain negative control points.
Note
Only sequential colormaps should be used with
lims
, and only divergent colormaps should be used withpos_lims
.- 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. Has no effect with mpl backend.
- 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. Has no effect with mpl backend.
- backgroundmatplotlib color
Color of the background of the display window.
- foregroundmatplotlib color
Color of the foreground of the display window. Has no effect with mpl backend.
- 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”).
- backend‘auto’ | ‘mayavi’ | ‘matplotlib’
Which backend to use. If
'auto'
(default), tries to plot with mayavi, but resorts to matplotlib if mayavi is not available.New in version 0.15.0.
- spacing
str
The spacing to use for the source space. Can be
'ico#'
for a recursively subdivided icosahedron,'oct#'
for a recursively subdivided octahedron, or'all'
for all points. In general, you can speed up the plotting by selecting a sparser source space. Has no effect with mayavi backend. Defaults to ‘oct6’.New in version 0.15.0.
- title
str
|None
Title for the figure. If None, the subject name will be used.
New in version 0.17.0.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more).
- stc
- Returns
- figureinstance of
surfer.Brain
|matplotlib.figure.Figure
An instance of
surfer.Brain
from PySurfer or matplotlib figure.
- figureinstance of