mne.viz.plot_volume_source_estimates#

mne.viz.plot_volume_source_estimates(stc, src, subject=None, subjects_dir=None, mode='stat_map', bg_img='T1.mgz', colorbar=True, colormap='auto', clim='auto', transparent=None, show=True, initial_time=None, initial_pos=None, verbose=None)[source]#

Plot Nutmeg style volumetric source estimates using nilearn.

Parameters:

stcVectorSourceEstimate

The vector source estimate to plot.

srcinstance of SourceSpaces | instance of SourceMorph

The source space. Can also be a SourceMorph to morph the STC to a new subject (see Examples).

Changed in version 0.18: Support for SpatialImage.

subjectstr | None

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

subjects_dirpath-like | None

The path to the directory containing the FreeSurfer subjects reconstructions. If None, defaults to the SUBJECTS_DIR environment variable.

mode'stat_map' | 'glass_brain'

The plotting mode to use. For 'glass_brain', activation absolute values are displayed after being transformed to a standard MNI brain.

bg_imginstance of SpatialImage | str

The background image used in the nilearn plotting function. Can also be a string to use the bg_img file in the subject’s MRI directory (default is 'T1.mgz'). Not used in “glass brain” plotting.

colorbarbool

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

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.

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 bounds for colormap.

pos_limslist | np.ndarray | tuple of float, 3 elements
Lower, middle, and upper bound for colormap. Positive values will be mirrored directly across zero during colormap construction to obtain negative control points.

Note

Only one of lims or pos_lims should be provided. Only sequential colormaps should be used with lims, and only divergent colormaps should be used with pos_lims.

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.

showbool

Show figures if True. Defaults to True.

initial_timefloat | None

The initial time to plot. Can be None (default) to use the time point with the maximal absolute value activation across all voxels or the initial_pos voxel (if initial_pos is None or not, respectively).

New in v0.19.

initial_posndarray, shape (3,) | None

The initial position to use (in m). Can be None (default) to use the voxel with the maximum absolute value activation across all time points or at initial_time (if initial_time is None or not, respectively).

New in v0.19.

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:

figinstance of Figure: The figure.

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.

In 'glass_brain' mode, values are transformed to the standard MNI brain using the FreeSurfer Talairach transformation $SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm.

New in v0.17.

Changed in version 0.19: MRI volumes are automatically transformed to MNI space in 'glass_brain' mode.

Examples

Passing a mne.SourceMorph as the src parameter can be useful for plotting in a different subject’s space (here, a 'sample' STC in 'fsaverage'’s space):

>>> morph = mne.compute_source_morph(src_sample, subject_to='fsaverage')  
>>> fig = stc_vol_sample.plot(morph)  