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='auto', subjects_dir=None, figure=None, views='lateral', colorbar=True, clim='auto', cortex='classic', size=800, background='black', foreground=None, initial_time=None, time_unit='s', show_traces='auto', src=None, volume_options=1.0, view_layout='vertical', add_data_kwargs=None, brain_kwargs=None, verbose=None)[source]#

Plot VectorSourceEstimate with PyVista.

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:

stcVectorSourceEstimate | MixedVectorSourceEstimate

The vector source estimate to plot.

subjectstr | None

The FreeSurfer subject name. If None, stc.subject will be used.

hemistr, ‘lh’ | ‘rh’ | ‘split’ | ‘both’

The hemisphere to display.

colormapstr | 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_labelstr | 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 'auto', which will use time=%0.2f ms if there is more than one time point.

smoothing_stepsint

The amount of smoothing.

transparentbool | None

If True: use a linear transparency between fmin and fmid and make values below fmin fully transparent (symmetrically for divergent colormaps). None will choose automatically based on colormap type.

brain_alphafloat

Alpha value to apply globally to the surface meshes. Defaults to 0.4.

overlay_alphafloat

Alpha value to apply globally to the overlay. Defaults to brain_alpha.

vector_alphafloat

Alpha value to apply globally to the vector glyphs. Defaults to 1.

scale_factorfloat | None

Scaling factor for the vector glyphs. By default, an attempt is made to automatically determine a sane value.

time_viewerbool | str

Display time viewer GUI. Can be “auto”, which is True for the PyVista backend and False otherwise.

Changed in version 0.20: Added “auto” option and default.

subjects_dirstr

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

figureinstance of Figure3D | 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 PyVista figure by it’s id or create a new figure with the given id.

viewsstr | list

View to use. Using multiple views (list) is not supported for mpl backend. See Brain.show_view for valid string options.

colorbarbool

If True, display colorbar on scene.

climstr | 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.

limslist | np.ndarray | tuple of float, 3 elements

Lower, middle, and upper bound for colormap.

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

cortexstr or tuple

Specifies how binarized curvature values are rendered. either the name of a preset Brain cortex colorscheme (one of ‘classic’, ‘bone’, ‘low_contrast’, or ‘high_contrast’), or the name of a colormap, or a tuple with values (colormap, min, max, reverse) to fully specify the curvature colors.

sizefloat 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.

backgroundmatplotlib color

Color of the background of the display window.

foregroundmatplotlib color | None

Color of the foreground of the display window. None will choose black or white based on the background color.

initial_timefloat | 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”).

show_tracesbool | str | float

If True, enable interactive picking of a point on the surface of the brain and plot its time course. This feature is only available with the PyVista 3d backend, and requires time_viewer=True. Defaults to ‘auto’, which will use True if and only if time_viewer=True, the backend is PyVista, and there is more than one time point. If float (between zero and one), it specifies what proportion of the total window should be devoted to traces (True is equivalent to 0.25, i.e., it will occupy the bottom 1/4 of the figure).

New in version 0.20.0.

srcinstance of SourceSpaces | None

The source space corresponding to the source estimate. Only necessary if the STC is a volume or mixed source estimate.

volume_optionsfloat | dict | None

Options for volumetric source estimate plotting, with key/value pairs:

• 'resolution'float | None

  Resolution (in mm) of volume rendering. Smaller (e.g., 1.) looks better at the cost of speed. None (default) uses the volume source space resolution, which is often something like 7 or 5 mm, without resampling.

• 'blending'str

  Can be “mip” (default) for maximum intensity projection or “composite” for composite blending using alpha values.

• 'alpha'float | None

  Alpha for the volumetric rendering. Defaults are 0.4 for vector source estimates and 1.0 for scalar source estimates.

• 'surface_alpha'float | None

  Alpha for the surface enclosing the volume(s). None (default) will use half the volume alpha. Set to zero to avoid plotting the surface.

• 'silhouette_alpha'float | None

  Alpha for a silhouette along the outside of the volume. None (default) will use 0.25 * surface_alpha.

• 'silhouette_linewidth'float

  The line width to use for the silhouette. Default is 2.

A float input (default 1.) or None will be used for the 'resolution' entry.

view_layoutstr

Can be “vertical” (default) or “horizontal”. When using “horizontal” mode, the PyVista backend must be used and hemi cannot be “split”.

add_data_kwargsdict | None

Additional arguments to brain.add_data (e.g., dict(time_label_size=10)).

brain_kwargsdict | None

Additional arguments to the mne.viz.Brain constructor (e.g., dict(silhouette=True)).

verbosebool | str | int | None

Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

Returns:

brainmne.viz.Brain

A instance of mne.viz.Brain.

Notes

New in version 0.15.

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

Examples using mne.viz.plot_vector_source_estimates#

Plotting the full vector-valued MNE solution

Plotting the full vector-valued MNE solution