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.view_surf¶

nilearn.plotting.view_surf(surf_mesh=None, surf_map=None, bg_map=None, hemi='left', threshold=None, cmap='RdBu_r', black_bg=False, vmax=None, vmin=None, bg_on_data=False, darkness=0.7, symmetric_cmap=True, colorbar=True, colorbar_height=0.5, colorbar_fontsize=25, title=None, title_fontsize=25)[source]¶

Insert a surface plot of a surface map into an HTML page.

Parameters:

surf_meshstr or list of two numpy.ndarray or a InMemoryMesh, or a PolyMesh, or None, default=None

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, or a InMemoryMesh object with “coordinates” and “faces” attributes, or a PolyMesh object, or None. If None is passed, then surf_map must be a SurfaceImage instance and the mesh from that SurfaceImage instance will be used.

surf_mapstr or numpy.ndarray, or SurfaceImage or None, default=None

Data to be displayed on the surface mesh. Can be a file (valid formats are .gii, .mgz, .nii, .nii.gz, or Freesurfer specific files such as .thickness, .area, .curv, .sulc, .annot, .label) or a Numpy array. If None is passed for surf_mesh then surf_map must be a SurfaceImage instance and its the mesh will be used for plotting.

bg_mapstr or pathlib.Path or numpy.ndarray or SurfaceImage or None, default=None

Background image to be plotted on the mesh underneath the surf_data in grayscale, most likely a sulcal depth map for realistic shading. If the map contains values outside [0, 1], it will be rescaled such that all values are in [0, 1]. Otherwise, it will not be modified. If a str or pathlib.Path is passed, it should be loadable to a numpy.ndarray by load_surf_data. If a numpy.ndarray is passed, if should have a shape (n_vertices, ), with n_vertices matching that of the underlying mesh used for plotting.

hemi{“left”, “right”, “both”}, default=”left”

Hemisphere to display. It is only used if surf_map is SurfaceImage and / or surf_mesh is PolyMesh. Otherwise a warning will be displayed.

Added in version 0.11.0.

bg_on_databool, default=False

If True and a bg_map is specified, the surf_data data is multiplied by the background image, so that e.g. sulcal depth is jointly visible with surf_data. Otherwise, the background image will only be visible where there is no surface data (either because surf_data contains nans or because is was thresholded).

Note

This non-uniformly changes the surf_data values according to e.g the sulcal depth.

darknessfloat between 0 and 1, optional

Specifying the darkness of the background image:

1 indicates that the original values of the background are used
0.5 indicates that the background values
are reduced by half before being applied.

Default=1.

thresholdstr, number or None, 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.

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=”RdBu_r”

black_bgbool, default=False

If True, image is plotted on a black background. Otherwise on a white background.

symmetric_cmapbool, default=True

Make colormap symmetric (ranging from -vmax to vmax). Set it to False if you are plotting a surface atlas.

vmaxfloat or None, default=None

upper bound for the colorbar. if None, use the absolute max of the brain map.

vminfloat 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.

colorbarbool, default=True

Add a colorbar or not.

colorbar_heightfloat, default=0.5

Height of the colorbar, relative to the figure height.

colorbar_fontsizeint, default=25

Fontsize of the colorbar tick labels.

titlestr, default=None

Title for the plot.

title_fontsizeint, default=25

Fontsize of the title.

Returns:

SurfaceViewplot 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.

Examples using `nilearn.plotting.view_surf`¶

Working with Surface images

Loading and plotting of a cortical surface atlas

Making a surface plot of a 3D statistical map

nilearn.plotting.view_surf¶

Examples using nilearn.plotting.view_surf¶

Examples using `nilearn.plotting.view_surf`¶