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, 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 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_dirstr

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

modestr

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_imginstance of SpatialImage | 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.

colorbarbool, optional

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. 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 version 0.19.

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 version 0.19.

verbosebool, 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.

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 version 0.17.

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)