This documentation is for development version 0.18.dev0.

mne.viz.plot_volume_source_estimates

mne.viz.plot_volume_source_estimates(stc, src, subject=None, subjects_dir=None, mode='stat_map', bg_img=None, colorbar=True, colormap='auto', clim='auto', transparent=None, show=True, verbose=None)[source]

Plot Nutmeg style volumetric source estimates using nilearn.

Parameters:
stc : VectorSourceEstimate

The vector source estimate to plot.

src : instance of SourceSpaces

The source space.

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.

subjects_dir : str

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

mode : str

The plotting mode to use. Either ‘stat_map’ (default) or ‘glass_brain’. For “glass_brain”, activation absolute values are displayed after being transformed to a standard MNI brain.

bg_img : Niimg-like object | None

The background image used in the nilearn plotting function. If None, it is the T1.mgz file that is found in the subjects_dir. Not used in “glass brain” plotting.

colorbar : boolean, optional

If True, display a colorbar on the right of the plots.

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. Default (‘auto’) uses ‘hot’ for one-sided data and ‘mne’ for two-sided data.

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.

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

Left, 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 with pos_lims.

transparent : bool | None

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

show : bool

Show figures if True. Defaults to True.

verbose : bool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Notes

Click on any of the anatomical slices to explore the time series. Clicking on any time point will bring up the corresponding anatomical map.

The left and right arrow keys can be used to navigate in time. To move in time by larger steps, use shift+left and shift+right.

New in version 0.17.