aslprep.utils.plotting module

Plotting functions and classes.

class ASLPlot(func_file, mask_file=None, data=None, confounds_file=None, seg_file=None, tr=None, usecols=None, units=None, vlines=None, spikes_files=None)

Bases: object

Generates the ASL Summary Plot.

confounds

func_file

mask_data

plot(figure=None)

Generate the plot.

seg_data

spikes

tr

class CBFPlot(cbf, ref_vol, label, outfile, vmax)

Bases: object

Generate the CBF Summary Plot.

This plot restricts CBF values to -20 (if there are negative values) or 0 (if not) to 100.

cbf

label

outfile

plot()

Generate the plot.

This plot restricts CBF values to -20 (if there are negative values) or 0 (if not) to 100.

ref_vol

vmax

class CBFtsPlot(cbf_file, confounds_file=None, seg_file=None, score_outlier_index=None, tr=None, units=None, vlines=None)

Bases: object

Generate the CBF time series Summary Plot.

cbf_file

fd_file

plot(figure=None)

Generate the plot.

seg_data

tr

confoundplotx(tseries, gs_ts, gs_dist=None, name=None, units=None, tr=None, hide_x=True, color='b', cutoff=None, ylims=None)

Generate a modified version of confoundplot from niworkflows.

TODO: Figure out what was modified and why. TODO: See if I can use the regular confoundplot instead.

plot_carpet(func, atlaslabels=None, detrend=True, size=(950, 800), subplot=None, output_file=None, legend=False, tr=None, lut=None)

Generate a carpet plot.

Plot an image representation of voxel intensities across time also know as the “carpet plot” or “Power plot”. See Jonathan Power Neuroimage 2017 Jul 1; 154:150-158.

Parameters:

• func (string) – Path to NIfTI or CIFTI ASL image

• atlaslabels (ndarray, optional) – A 3D array of integer labels from an atlas, resampled into img space. Required if func is a NIfTI image.

• detrend (boolean, optional) – Detrend and standardize the data prior to plotting.

• nskip (int, optional) – Number of volumes at the beginning of the scan marked as nonsteady state. Not used.

• size (tuple, optional) – Size of figure.

• subplot (matplotlib Subplot, optional) – Subplot to plot figure on.

• title (string, optional) – The title displayed on the figure.

• output_file (string, 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.

• legend (bool) – Whether to render the average functional series with atlaslabels as overlay.

• tr (float , optional) – Specify the TR, if specified it uses this value. If left as None, # of frames is plotted instead of time.

• lut (ndarray, optional) – Look up table for segmentations

plot_stat_map(cbf, ref_vol, plot_params=None, order=('z', 'x', 'y'), vmax=100, estimate_brightness=False, label=None, compress='auto')

Plot statistical map.