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
). Ifsrc
contains aCase
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 (scalar) – Endpoints for the colormap. Need to be set explicitly if
cmap
is a LUT array.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 | sequence of str) – One or several views to show in the figure. The options are:
'lateral', 'medial', 'ventral', 'dorsal', 'rostral', 'parietal', 'frontal', 'caudal'
.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 (scalar) – Layout parameters (figure width/height, subplot width/height).
h (scalar) – Layout parameters (figure width/height, subplot width/height).
axw (scalar) – Layout parameters (figure width/height, subplot width/height).
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 throughsmoothing_steps
, the mask is added as data layer, otherwise it is added as label. To add a mask independently, use theBrain.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 instance containing the plot.
- Return type: