This documentation is for development version 0.18.dev0.

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 of float, 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

transparent : bool

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_viewer : bool

Display time viewer GUI.

subjects_dir : str

The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR.

figure : instance 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.

colorbar : bool

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 elements

Left, middle, and right bound for colormap.

Unlike stc.plot, it cannot use pos_lims, as the surface plot must show the magnitude.

cortex : str or tuple

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 or tuple of float

The size of the window, in pixels. can be one number to specify a square window, or the (width, height) of a rectangular window.

background : matplotlib color

Color of the background of the display window.

foreground : matplotlib 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”).

Returns:
brain : surfer.Brain

A instance of surfer.Brain from PySurfer.

Notes

New in version 0.15.

If the current magnitude overlay is not desired, set overlay_alpha=0 and smoothing_steps=1.