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.
- srcinstance 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_imgNiimg-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.
- colorbarbool, optional
If True, display a colorbar on the right of the plots.
- colormap
str
|np.ndarray
offloat
, 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 elementsLeft, middle, and right bound for colormap.
pos_lims
list | np.ndarray | tuple of float, 3 elementsLeft, 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 withpos_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.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more).
- stc
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.