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_carpet

nilearn.plotting.plot_carpet(img, mask_img=None, mask_labels=None, t_r=None, detrend=True, output_file=None, figure=None, axes=None, vmin=None, vmax=None, title=None, cmap='gray', cmap_labels=<matplotlib.colors.LinearSegmentedColormap object>, standardize=True)[source]

Plot an image representation of voxel intensities across time.

This figure is also known as a “grayplot” or “Power plot”.

Parameters:
imgNiimg-like object

See Input and output: neuroimaging data representation. 4D image.

mask_imgNiimg-like object or None, default=None

Limit plotted voxels to those inside the provided mask. If a 3D atlas is provided, voxels will be grouped by atlas value and a colorbar will be added to the left side of the figure with atlas labels. If not specified, a new mask will be derived from data. See Input and output: neuroimaging data representation.

mask_labelsdict or None, default=None

If mask_img corresponds to an atlas, then this dictionary maps values from the mask_img to labels. Dictionary keys are labels and values are values within the atlas.

t_rfloat or None, default=None

Repetition time, in seconds (sampling period). Set to None if not provided.

Note

If t_r is not provided, it will be inferred from img’s header (img.header.get_zooms()[-1]).

Added in version 0.9.1: Prior to this, t_r would be inferred from img without user input.

detrendbool, default=True

Detrend and z-score the data prior to plotting.

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.

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 tuple of 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.

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.

titlestr, or None, default=None

The title displayed on the figure.

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=`gray`.

cmap_labelsmatplotlib.colors.Colormap, or str, default=`plt.cm.gist_ncar`

If mask_img corresponds to an atlas, then cmap_labels can be used to define the colormap for coloring the labels placed on the side of the carpet plot.

standardizebool, default=True

If standardize is True, the data are centered and normed: their mean is put to 0 and their variance is put to 1 in the time dimension.

Note

Added to control passing value to standardize of signal.clean to call new behavior since passing “zscore” or True (default) is deprecated. This parameter will be deprecated in version 0.13 and removed in version 0.15.

Returns:
figurematplotlib.figure.Figure

Figure object with carpet plot.

Notes

This figure was originally developed in Power[1].

In cases of long acquisitions (>800 volumes), the data will be downsampled to have fewer than 800 volumes before being plotted.

References

Examples using nilearn.plotting.plot_carpet

Visualizing global patterns with a carpet plot

Visualizing global patterns with a carpet plot