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 (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 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 instance containing the plot.

Return type:

Brain