Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

nilearn.plotting.plot_surf_contours#

nilearn.plotting.plot_surf_contours(surf_mesh, roi_map, axes=None, figure=None, levels=None, labels=None, colors=None, legend=False, cmap='tab20', title=None, output_file=None, **kwargs)[source]#

Plot contours of ROIs on a surface, optionally over a statistical map.

Parameters:

surf_meshstr or list of two numpy.ndarray: Surface mesh geometry, can be a file (valid formats are .gii or Freesurfer specific files such as .orig, .pial, .sphere, .white, .inflated) or a list of two Numpy arrays, the first containing the x-y-z coordinates of the mesh vertices, the second containing the indices (into coords) of the mesh faces.
roi_mapstr or numpy.ndarray or list of numpy.ndarray: ROI map to be displayed on the surface mesh, can be a file (valid formats are .gii, .mgz, or Freesurfer specific files such as .thickness, .area, .curv, .sulc, .annot, .label) or a Numpy array with a value for each vertex of the surf_mesh. The value at each vertex one inside the ROI and zero inside ROI, or an integer giving the label number for atlases.
axesinstance of matplotlib axes, None, optional: The axes instance to plot to. The projection must be ‘3d’ (e.g., figure, axes = plt.subplots(subplot_kw={‘projection’: ‘3d’}), where axes should be passed.). If None, uses axes from figure if available, else creates new axes.
figureint, or matplotlib.figure.Figure, or None, optional: Matplotlib figure used or its number. If None is given, a new figure is created.
levelslist of integers, or None, optional: A list of indices of the regions that are to be outlined. Every index needs to correspond to one index in roi_map. If None, all regions in roi_map are used.
labelslist of strings or None, or None, optional: A list of labels for the individual regions of interest. Provide None as list entry to skip showing the label of that region. If None no labels are used.
colorslist of matplotlib color names or RGBA values, or None, optional: Colors to be used.
legendboolean, optional, default=False: Whether to plot a legend of region’s labels.
cmapmatplotlib.colors.Colormap, or str, optional: The colormap to use. Either a string which is a name of a matplotlib colormap, or a matplotlib colormap object. Default=’tab20’.
titlestr, or None, default=None: The title displayed on the figure.
output_filestr, or None, optional: The name of an image file to export the plot to. Valid extensions are .png, .pdf, .svg. If output_file is not None, the plot is saved to a file, and the display is closed.
kwargs: extra keyword arguments, optional: Extra keyword arguments passed to plot_surf.