nilearn.plotting: Plotting Brain Data

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.

nilearn.plotting: 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, masker)	Create plots to compare two lists of images and measure correlation.

nilearn.plotting.displays: 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.