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_connectome#

nilearn.plotting.view_connectome(adjacency_matrix, node_coords, edge_threshold=None, edge_cmap=<matplotlib.colors.LinearSegmentedColormap object>, symmetric_cmap=True, linewidth=6.0, node_color='auto', node_size=3.0, colorbar=True, colorbar_height=0.5, colorbar_fontsize=25, title=None, title_fontsize=25)[source]#

Insert a 3d plot of a connectome into an HTML page.

Parameters:
adjacency_matrixndarray, shape=(n_nodes, n_nodes)

The weights of the edges.

node_coordsndarray, shape=(n_nodes, 3)

The coordinates of the nodes in MNI space.

node_colorcolor or sequence of colors, optional

Color(s) of the nodes. Default=’auto’.

edge_thresholdstr, number or None, optional

If None, no thresholding. If it is a number only connections 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 connections of amplitude above the given percentile will be shown.

edge_cmapstr or matplotlib colormap, optional

Colormap to use. Default=cm.bwr.

symmetric_cmapbool, optional

Make colormap symmetric (ranging from -vmax to vmax). Default=True.

linewidthfloat, optional

Width of the lines that show connections. Default=6.0.

node_sizefloat, optional

Size of the markers showing the seeds in pixels. Default=3.0.

colorbarbool, optional

Add a colorbar. Default=True.

colorbar_heightfloat, optional

Height of the colorbar, relative to the figure height. Default=0.5.

colorbar_fontsizeint, optional

Fontsize of the colorbar tick labels. Default=25.

titlestr, optional

Title for the plot.

title_fontsizeint, optional

Fontsize of the title. Default=25.

Returns:
ConnectomeViewplot of the connectome.

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.plot_connectome

projected views of a connectome in a glass brain.

nilearn.plotting.view_markers

interactive plot of colored markers

nilearn.plotting.view_surf, nilearn.plotting.view_img_on_surf

interactive view of statistical maps or surface atlases on the cortical surface.

Examples using nilearn.plotting.view_connectome#

Loading and plotting of a cortical surface atlas

Loading and plotting of a cortical surface atlas

Loading and plotting of a cortical surface atlas
Extracting signals of a probabilistic atlas of functional regions

Extracting signals of a probabilistic atlas of functional regions

Extracting signals of a probabilistic atlas of functional regions
Computing a connectome with sparse inverse covariance

Computing a connectome with sparse inverse covariance

Computing a connectome with sparse inverse covariance
Extract signals on spheres and plot a connectome

Extract signals on spheres and plot a connectome

Extract signals on spheres and plot a connectome