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.plot_roi#

nilearn.plotting.plot_roi(roi_img, bg_img=<MNI152Template>, cut_coords=None, output_file=None, display_mode='ortho', figure=None, axes=None, title=None, annotate=True, draw_cross=True, black_bg='auto', threshold=0.5, alpha=0.7, cmap=<matplotlib.colors.LinearSegmentedColormap object>, dim='auto', colorbar=False, cbar_tick_format='%i', vmin=None, vmax=None, resampling_interpolation='nearest', view_type='continuous', linewidths=2.5, radiological=False, **kwargs)[source]#

Plot cuts of an ROI/mask image.

By default 3 cuts: Frontal, Axial, and Lateral.

Parameters:

roi_imgNiimg-like object

See Input and output: neuroimaging data representation. The ROI/mask image, it could be binary mask or an atlas or ROIs with integer values.

bg_imgNiimg-like object, optional

See Input and output: neuroimaging data representation. The background image to plot on top of. If nothing is specified, the MNI152 template will be used. To turn off background image, just pass “bg_img=None”. Default=MNI152TEMPLATE.

cut_coordsNone, a tuple of float, or int, optional

The MNI coordinates of the point where the cut is performed.

If display_mode is ‘ortho’ or ‘tiled’, this should be a 3-tuple: (x, y, z)

For display_mode == “x”, “y”, or “z”, then these are the coordinates of each cut in the corresponding direction.

If None is given, the cuts are calculated automatically.

If display_mode is ‘mosaic’, and the number of cuts is the same for all directions, cut_coords can be specified as an integer. It can also be a length 3 tuple specifying the number of cuts for every direction if these are different.

Note

If display_mode is “x”, “y” or “z”, cut_coords can be an integer, in which case it specifies the number of cuts to perform.

output_filestr, or None, optional

The name of an image file to export the plot to. Valid extensions are .png, .pdf, .svg. If output_file is not None, the plot is saved to a file, and the display is closed.

display_mode{“ortho”, “tiled”, “mosaic”, “x”, “y”, “z”, “yx”, “xz”, “yz”}, default=”ortho”

Choose the direction of the cuts:

“x”: sagittal

“y”: coronal

“z”: axial

“ortho”: three cuts are performed in orthogonal directions

“tiled”: three cuts are performed and arranged in a 2x2 grid

“mosaic”: three cuts are performed along multiple rows and columns

figureint, or matplotlib.figure.Figure, or None, optional

Matplotlib figure used or its number. If None is given, a new figure is created.

axesmatplotlib.axes.Axes, or 4 tupleof float: (xmin, ymin, width, height), default=None

The axes, or the coordinates, in matplotlib figure space, of the axes used to display the plot. If None, the complete figure is used.

titlestr, or None, default=None

The title displayed on the figure.

annotatebool, default=True

If annotate is True, positions and left/right annotation are added to the plot.

draw_crossbool, default=True

If draw_cross is True, a cross is drawn on the plot to indicate the cut position.

black_bgbool, or “auto”, optional

If True, the background of the image is set to be black. If you wish to save figures with a black background, you will need to pass facecolor=”k”, edgecolor=”k” to matplotlib.pyplot.savefig. Default=’auto’.

thresholda number, None, or ‘auto’, optional

If None is given, the image is not thresholded. If a number is given, it is used to threshold the image: values below the threshold (in absolute value) are plotted as transparent. If “auto” is given, the threshold is determined magically by analysis of the image. Default=0.5.

alphafloat between 0 and 1, default=0.7

Alpha sets the transparency of the color inside the filled contours.

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=`plt.cm.gist_ncar`.

dimfloat, or “auto”, optional

Dimming factor applied to background image. By default, automatic heuristics are applied based upon the background image intensity. Accepted float values, where a typical span is between -2 and 2 (-2 = increase contrast; 2 = decrease contrast), but larger values can be used for a more pronounced effect. 0 means no dimming. Default=’auto’.

colorbarboolean, default=False

If True, display a colorbar on the right of the plots.

cbar_tick_format: str, default=”%.2g” (scientific notation)

Controls how to format the tick labels of the colorbar. Ex: use “%.2g” to use scientific notation.

vminfloat, optional

Lower bound of the colormap. If None, the min of the image is used. Passed to matplotlib.pyplot.imshow.

vmaxfloat, optional

Upper bound of the colormap. If None, the max of the image is used. Passed to matplotlib.pyplot.imshow.

resampling_interpolationstr, optional

Interpolation to use when resampling the image to the destination space. Can be:

“continuous”: use 3rd-order spline interpolation

“nearest”: use nearest-neighbor mapping.

Note

“nearest” is faster but can be noisier in some cases.

Default=’nearest’.

view_type{‘continuous’, ‘contours’}, default=’continuous’

By default view_type == ‘continuous’, rois are shown as continuous colors. If view_type == ‘contours’, maps are shown as contours. For this type, label denoted as 0 is considered as background and not shown.

linewidthsfloat, optional

Set the boundary thickness of the contours. Only reflects when view_type=contours. Default=2.5.

radiologicalbool, default=False

Invert x axis and R L labels to plot sections as a radiological view. If False (default), the left hemisphere is on the left of a coronal image. If True, left hemisphere is on the right.

kwargs: extra keyword arguments, optional

Extra keyword arguments ultimately passed to matplotlib.pyplot.imshow via add_overlay.

Returns:

displayOrthoSlicer or None: An instance of the OrthoSlicer class. If output_file is defined, None is returned.

Examples using `nilearn.plotting.plot_roi`#

Clustering methods to learn a brain parcellation from fMRI

Understanding parameters of the first-level model

Simple example of NiftiMasker use

Understanding NiftiMasker and mask computation

Computing a Region of Interest (ROI) mask manually

nilearn.plotting.plot_roi#

Examples using nilearn.plotting.plot_roi#

Examples using `nilearn.plotting.plot_roi`#