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.
8.10.27. nilearn.plotting.view_img_on_surf¶
nilearn.plotting.view_img_on_surf(stat_map_img, surf_mesh='fsaverage5', threshold=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, black_bg=False, vmax=None, vmin=None, symmetric_cmap=True, colorbar=True, colorbar_height=0.5, colorbar_fontsize=25, title=None, title_fontsize=25)¶Insert a surface plot of a statistical map into an HTML page.
Parameters: stat_map_img : Niimg-like object, 3D
surf_mesh : str or dict, optional.
if ‘fsaverage5’, use fsaverage5 mesh from nilearn.datasets if ‘fsaverage’, use fsaverage mesh from nilearn.datasets if a dictionary, it should have the same structure as those returned by nilearn.datasets.fetch_surf_fsaverage, i.e. keys should be ‘infl_left’, ‘pial_left’, ‘sulc_left’, ‘infl_right’, ‘pial_right’, and ‘sulc_right’, containing inflated and pial meshes, and sulcal depth values for left and right hemispheres.
threshold : str, number or None, optional (default=None)
If None, no thresholding. If it is a number only values of amplitude greater than threshold will be shown. If it is a string it must finish with a percent sign, e.g. “25.3%”, and only values of amplitude above the given percentile will be shown.
cmap : str or matplotlib colormap, optional
black_bg : bool, optional (default=False)
If True, image is plotted on a black background. Otherwise on a white background.
vmax : float or None, optional (default=None)
upper bound for the colorbar. if None, use the absolute max of the brain map.
vmin : float, or None (default=None)
min value for mapping colors. If symmetric_cmap is True, vmin is always equal to -vmax and cannot be chosen. If symmetric_cmap is False, vmin defaults to the min of the image, or 0 when a threshold is used.
symmetric_cmap : bool, optional (default=True)
Make colormap symmetric (ranging from -vmax to vmax). You can set it to False if you are plotting only positive values.
colorbar : bool, optional (default=True)
add a colorbar
colorbar_height : float, optional (default=.5)
height of the colorbar, relative to the figure height
colorbar_fontsize : int, optional (default=25)
fontsize of the colorbar tick labels
title : str, optional (default=None)
title for the plot
title_fontsize : int, optional (default=25)
fontsize of the title
Returns: SurfaceView : plot of the stat map.
It can be saved as an html page or rendered (transparently) by the Jupyter notebook. Useful methods are :
- ‘resize’ to resize the plot displayed in a Jupyter notebook
- ‘save_as_html’ to save the plot to a file
- ‘open_in_browser’ to save the plot and open it in a web browser.
See also
nilearn.plotting.view_surf- plot from a surface map on a cortical mesh.
