lyman.visualizations.CarpetPlot

class lyman.visualizations.CarpetPlot(data, seg, mc_params=None, smooth_fwhm=5, percent_change=True, vlim=None, title=None)

__init__(self, data, seg, mc_params=None, smooth_fwhm=5, percent_change=True, vlim=None, title=None)

Heatmap rendering of an fMRI timeseries for quality control.

The Freesurfer segmentation is used to organize data by different components of the brain.

Instantiating the class will load, preprocess, and plot the data.

Parameters

datafilename or nibabel image

4D time series data to plot.

wmparcfilename or nibabel image

Freesurfer wmparc image in functional space.

mc_paramsfilename or DataFrame, optional

Text file or array of realignment parameters. If present, the time series of framewise displacements will be shown at the top of the figure.

smooth_fwhmfloat or None, optional

Size of the smoothing kernel, in mm, to apply. Smoothing is restricted within the mask for each component (cortex, cerebellum, etc.). Smoothing reduces white noise and makes global image artifacts much more apparent. Set to None to skip smoothing.

percent_changebool, optional

If True, convert data to percent signal change over time.

vlimNone or int, optional

Colormap limits (will be symmetric around 0).

titlestring

Title to show at the top of the plot.

Attributes

figmatplotlib Figure

axesdict of matplotlib Axes

segdatadict of arrays with data in the main plot

fd1d array of framewise displacements