nilearn.plotting: Plotting Brain Data

Plotting

Plotting code for nilearn.

Functions

find_cut_slices(img[, direction, n_cuts, ...])	Find 'good' cross-section slicing positions along a given axis.
find_xyz_cut_coords(img[, mask_img, ...])	Find the center of the largest activation connected component.
find_parcellation_cut_coords(labels_img[, ...])	Return coordinates of center of mass of 3D parcellation atlas.
find_probabilistic_atlas_cut_coords(maps_img)	Return coordinates of center probabilistic atlas 4D image.
plot_anat([anat_img, cut_coords, ...])	Plot cuts of an anatomical image.
plot_carpet(img[, mask_img, mask_labels, ...])	Plot an image representation of voxel intensities across time.
plot_connectome(adjacency_matrix, node_coords)	Plot connectome on top of the brain glass schematics.
plot_contrast_matrix(contrast_def, design_matrix)	Create plot for contrast definition.
plot_design_matrix(design_matrix[, rescale, ...])	Plot a design matrix.
plot_design_matrix_correlation(design_matrix)	Compute and plot the correlation between regressor of a design matrix.
plot_epi([epi_img, cut_coords, output_file, ...])	Plot cuts of an EPI image.
plot_event(model_event[, cmap, output_file])	Create plot for event visualization.
plot_glass_brain(stat_map_img[, ...])	Plot 2d projections of an ROI/mask image (by default 3 projections: Frontal, Axial, and Lateral).
plot_img(img[, cut_coords, output_file, ...])	Plot cuts of a given image.
plot_img_on_surf(stat_map[, surf_mesh, ...])	Plot multiple views of plot_surf_stat_map in a single figure.
plot_markers(node_values, node_coords[, ...])	Plot network nodes (markers) on top of the brain glass schematics.
plot_matrix(mat[, title, labels, figure, ...])	Plot the given matrix.
plot_prob_atlas(maps_img[, bg_img, ...])	Plot a Probabilistic atlas onto the anatomical image by default MNI template.
plot_roi(roi_img[, bg_img, cut_coords, ...])	Plot cuts of an ROI/mask image.
plot_stat_map(stat_map_img[, bg_img, ...])	Plot cuts of an ROI/mask image.
plot_surf([surf_mesh, surf_map, bg_map, ...])	Plot surfaces with optional background and data.
plot_surf_contours([surf_mesh, roi_map, ...])	Plot contours of ROIs on a surface, optionally over a statistical map.
plot_surf_roi([surf_mesh, roi_map, bg_map, ...])	Plot ROI on a surface mesh with optional background.
plot_surf_stat_map([surf_mesh, stat_map, ...])	Plot a stats map on a surface mesh with optional background.
show()	Show all the figures generated by nilearn and/or matplotlib.
view_surf([surf_mesh, surf_map, bg_map, ...])	Insert a surface plot of a surface map into an HTML page.
view_img_on_surf(stat_map_img[, surf_mesh, ...])	Insert a surface plot of a statistical map into an HTML page.
view_connectome(adjacency_matrix, node_coords)	Insert a 3d plot of a connectome into an HTML page.
view_markers(marker_coords[, marker_color, ...])	Insert a 3d plot of markers in a brain into an HTML page.
view_img(stat_map_img[, bg_img, cut_coords, ...])	Interactive html viewer of a statistical map, with optional background.

Comparing images

Functions to compare volume or surface images.

Functions

plot_bland_altman(ref_img, src_img[, ...])	Create a Bland-Altman plot between 2 images.
plot_img_comparison(ref_imgs, src_imgs[, ...])	Create plots to compare two lists of images and measure correlation.

Interacting with figures

Display objects and utilities.

These objects are returned by plotting functions from the plotting module.

Classes

PlotlySurfaceFigure([figure, output_file, hemi])

Implementation of a surface figure obtained with plotly engine.

Axes

BaseAxes(ax, direction, coord[, radiological])	An MPL axis-like object that displays a 2D view of 3D volumes.
CutAxes(ax, direction, coord[, radiological])	An MPL axis-like object that displays a cut of 3D volumes.
GlassBrainAxes(ax, direction, coord[, ...])	An MPL axis-like object that displays a 2D projection of 3D volumes with a schematic view of the brain.

Projectors

OrthoProjector(cut_coords[, axes, black_bg, ...])	A class to create linked axes for plotting orthogonal projections of 3D maps.
LZRYProjector(cut_coords[, axes, black_bg, ...])	The LZRYProjector class enables ? visualization on the same figure through 2D projections with plot_glass_brain.
LYRZProjector(cut_coords[, axes, black_bg, ...])	The LYRZProjector class enables ? visualization on the same figure through 2D projections with plot_glass_brain.
LYRProjector(cut_coords[, axes, black_bg, ...])	The LYRProjector class enables ? visualization on the same figure through 2D projections with plot_glass_brain.
LZRProjector(cut_coords[, axes, black_bg, ...])	The LZRProjector class enables hemispheric sagittal visualization on the same figure through 2D projections with plot_glass_brain.
LRProjector(cut_coords[, axes, black_bg, ...])	The LRProjector class enables left-right visualization on the same figure through 2D projections with plot_glass_brain.
LProjector(cut_coords[, axes, black_bg, ...])	The LProjector class enables the visualization of left 2D projection with plot_glass_brain.
RProjector(cut_coords[, axes, black_bg, ...])	The RProjector class enables the visualization of right 2D projection with plot_glass_brain.
XZProjector(cut_coords[, axes, black_bg, ...])	The XZProjector class enables to combine sagittal and axial views on the same figure through 2D projections with plot_glass_brain.
YZProjector(cut_coords[, axes, black_bg, ...])	The YZProjector class enables to combine coronal and axial views on the same figure through 2D projections with plot_glass_brain.
YXProjector(cut_coords[, axes, black_bg, ...])	The YXProjector class enables to combine coronal and sagittal views on the same figure through 2D projections with plot_glass_brain.
XProjector(cut_coords[, axes, black_bg, ...])	The XProjector class enables sagittal visualization through 2D projections with plot_glass_brain.
YProjector(cut_coords[, axes, black_bg, ...])	The YProjector class enables coronal visualization through 2D projections with plot_glass_brain.
ZProjector(cut_coords[, axes, black_bg, ...])	The ZProjector class enables axial visualization through 2D projections with plot_glass_brain.

Slicers

BaseSlicer(cut_coords[, axes, black_bg, ...])	BaseSlicer implementation which main purpose is to auto adjust the axes size to the data with different layout of cuts.
OrthoSlicer(cut_coords[, axes, black_bg, ...])	Class to create 3 linked axes for plotting orthogonal cuts of 3D maps.
MosaicSlicer(cut_coords[, axes, black_bg, ...])	A class to create 3 Axes for plotting cuts of 3D maps, in multiple rows and columns.
TiledSlicer(cut_coords[, axes, black_bg, ...])	A class to create 3 axes for plotting orthogonal cuts of 3D maps, organized in a 2x2 grid.
XSlicer(cut_coords[, axes, black_bg, ...])	The XSlicer class enables sagittal visualization with plotting functions of Nilearn like nilearn.plotting.plot_img.
XZSlicer(cut_coords[, axes, black_bg, ...])	The XZSlicer class enables to combine sagittal and axial views on the same figure with plotting functions of Nilearn like nilearn.plotting.plot_img.
YXSlicer(cut_coords[, axes, black_bg, ...])	The YXSlicer class enables to combine coronal and sagittal views on the same figure with plotting functions of Nilearn like nilearn.plotting.plot_img.
YZSlicer(cut_coords[, axes, black_bg, ...])	The YZSlicer class enables to combine coronal and axial views on the same figure with plotting functions of Nilearn like nilearn.plotting.plot_img.
YSlicer(cut_coords[, axes, black_bg, ...])	The YSlicer class enables coronal visualization with plotting functions of Nilearn like nilearn.plotting.plot_img.
ZSlicer(cut_coords[, axes, black_bg, ...])	The ZSlicer class enables axial visualization with plotting functions of Nilearn like nilearn.plotting.plot_img.

Functions

get_projector(display_mode)	Retrieve a projector from a given display mode.
get_slicer(display_mode)	Retrieve a slicer from a given display mode.