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=None, alpha=1.0, time_viewer=False, config_opts=None, subjects_dir=None, figure=None, views='lat', colorbar=True, clim='auto', cortex='classic', size=800, background='black', foreground='white', initial_time=None, time_unit=None)

Plot SourceEstimates with PySurfer

Note: PySurfer currently needs the SUBJECTS_DIR environment variable, which will automatically be set by this function. Plotting multiple SourceEstimates with different values for subjects_dir will cause PySurfer to use the wrong FreeSurfer surfaces when using methods of the returned Brain object. It is therefore recommended to set the SUBJECTS_DIR environment variable or always use the same value for subjects_dir (within the same Python session).

Parameters:

stc : SourceEstimates

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 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. If ‘auto’, either ‘hot’ or ‘mne’ will be chosen based on whether ‘lims’ or ‘pos_lims’ are specified in clim.

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 | None

If True, use a linear transparency between fmin and fmid. None will choose automatically based on colormap type.

alpha : float

Alpha value to apply globally to the overlay.

time_viewer : bool

Display time viewer GUI.

config_opts : dict

Deprecated parameter.

subjects_dir : str

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

figure : instance of mayavi.core.scene.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
: str

Flag to specify type of limits. ‘value’ or ‘percent’.

lims
: list | np.ndarray | tuple of float, 3 elements

Note: Only use this if ‘colormap’ is not ‘mne’. Left, middle, and right bound for colormap.

pos_lims
: list | np.ndarray | tuple of float, 3 elements

Note: Only use this if ‘colormap’ is ‘mne’. Left, middle, and right bound for colormap. Positive values will be mirrored directly across zero during colormap construction to obtain negative control points.

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 pair of floats

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 (expected by PySurfer) or milliseconds. The current default is ‘ms’, but will change to ‘s’ in MNE 0.14. To avoid a deprecation warning specify time_unit explicitly.

Returns:

brain : Brain

A instance of surfer.viz.Brain from PySurfer.