eelbrain.plot.brain.brain

eelbrain.plot.brain.brain(src, cmap=None, vmin=None, vmax=None, surf='inflated', views='lateral', hemi=None, colorbar=False, time_label='ms', w=None, h=None, axw=None, axh=None, foreground=None, background=None, parallel=True, cortex='classic', title=None, smoothing_steps=None, mask=True, subjects_dir=None, name=None, pos=None)

Create a Brain object with a data layer

Parameters:

src : NDVar ([case,] source, [time]) | SourceSpace | str

Data to plot; can be specified as NDVar with source-space data, SourceSpace dimension, or as subject name (str). If src contains a Case dimension, the average across cases is taken. If it contains integer data, it is plotted as annotation, otherwise as data layer.

cmap : str | array

Colormap (name of a matplotlib colormap) or LUT array. If src is an integer NDVar, cmap can be a color dictionary mapping label IDs to colors.

vmin, vmax : scalar

Endpoints for the colormap. Need to be set explicitly if cmap is a LUT array.

surf : ‘inflated’ | ‘pial’ | ‘smoothwm’ | ‘sphere’ | ‘white’

Freesurfer surface to use as brain geometry.

views : str | iterator of str

View or views to show in the figure. Options are: ‘rostral’, ‘parietal’, ‘frontal’, ‘ventral’, ‘lateral’, ‘caudal’, ‘medial’, ‘dorsal’.

hemi : ‘lh’ | ‘rh’ | ‘both’ | ‘split’

Which hemispheres to plot (default based on data).

colorbar : bool

Add a colorbar to the figure (use .plot_colorbar() to plot a colorbar separately).

time_label : str

Label to show time point. Use 'ms' or 's' to display time in milliseconds or in seconds, or supply a custom format string to format time values (in seconds; default is 'ms').

w, h, axw, axh : scalar

Layout parameters (figure width/height, subplot width/height).

foreground : mayavi color

Figure foreground color (i.e., the text color).

background : mayavi color

Figure background color.

parallel : bool

Set views to parallel projection (default True).

cortex : str | tuple | dict

Mark gyri and sulci on the cortex. Presets: 'classic' (default), 'high_contrast', 'low_contrast', 'bone'. Can also be a single color (e.g. 'red', (0.1, 0.4, 1.)) or a tuple of two colors for gyri and sulci (e.g. ['red', 'blue'] or [(1, 0, 0), (0, 0, 1)]). For all options see the PySurfer documentation.

title : str

title for the window (default is based on the subject name and src).

smoothing_steps : None | int

Number of smoothing steps if data is spatially undersampled (pysurfer Brain.add_data() argument).

mask : bool | matplotlib color

Shade areas that are not in src. Can be matplotlib color, including alpha (e.g., (1, 1, 1, 0.5) for semi-transparent white). If smoothing is enabled through smoothing_steps, the mask is added as data layer, otherwise it is added as label. To add a mask independently, use the Brain.add_mask() method.

subjects_dir : None | str

Override the subjects_dir associated with the source space dimension.

name : str

Equivalent to title, for consistency with other plotting functions.

pos : tuple of int

Position of the new window on the screen.

Returns:

brain : Brain

Brain instance containing the plot.