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_anat#

nilearn.plotting.plot_anat(anat_img=<MNI152Template>, cut_coords=None, output_file=None, display_mode='ortho', figure=None, axes=None, title=None, annotate=True, threshold=None, draw_cross=True, black_bg='auto', dim='auto', cmap=<matplotlib.colors.LinearSegmentedColormap object>, colorbar=False, cbar_tick_format='%.2g', vmin=None, vmax=None, **kwargs)[source]#

Plot cuts of an anatomical image (by default 3 cuts: Frontal, Axial, and Lateral)

Parameters:
anat_imgNiimg-like object, optional

See Input and output: neuroimaging data representation. The anatomical image to be used as a background. If None is given, nilearn tries to find a T1 template. 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’}, optional

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

Default=’ortho’.

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), optional

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, optional

The title displayed on the figure. Default=None.

annotatebool, optional

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

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.

draw_crossbool, optional

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

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’.

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’.

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.gray`.

colorbarboolean, optional

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

cbar_tick_format: str, optional

Controls how to format the tick labels of the colorbar. Ex: use “%i” to display as integers. Default is ‘%.2g’ for 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.

Notes

Arrays should be passed in numpy convention: (x, y, z) ordered.

For visualization, non-finite values found in passed ‘anat_img’ are set to zero.

Examples using nilearn.plotting.plot_anat#

Intro to GLM Analysis: a single-session, single-subject fMRI dataset

Intro to GLM Analysis: a single-session, single-subject fMRI dataset

Intro to GLM Analysis: a single-session, single-subject fMRI dataset
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Plot Haxby masks

Plot Haxby masks
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