eelbrain.plot.brain.annot

eelbrain.plot.brain.annot(annot, subject='fsaverage', surf='smoothwm', borders=False, alpha=0.7, hemi=None, views=('lat', 'med'), w=None, h=None, axw=None, axh=None, foreground=None, background=None, parallel=True, cortex='classic', title=None, subjects_dir=None, name=None)

Plot the parcellation in an annotation file

Parameters

  • annot (str) – Name of the annotation (e.g., “PALS_B12_LOBES”).

  • subject (str) – Name of the subject (default ‘fsaverage’).

  • surf ('inflated' | 'pial' | 'smoothwm' | 'sphere' | 'white') – Freesurfer surface to use as brain geometry.

  • borders (bool | int) – Show only label borders (PySurfer Brain.add_annotation() argument).

  • alpha (scalar) – Alpha of the annotation (1=opaque, 0=transparent, default 0.7).

  • hemi ('lh' | 'rh' | 'both' | 'split') – Which hemispheres to plot (default includes hemisphere with more than one label in the annot file).

  • 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'.

  • 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 the parcellation name).

  • subjects_dir (None | str) – Override the default subjects_dir.

  • name (str) – Equivalent to title, for consistency with other plotting functions.

Returns

brain – PySurfer Brain instance.

Return type

surfer.Brain

Notes

The Brain object that is returned has a plot_legend() method to plot the color legend.

See also

eelbrain.plot.brain.annot_legend

plot a corresponding legend without the brain