aslprep.interfaces.plotting module

Plotting interfaces.

class ASLCarpetPlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Create a combined carpet/line plot for ASL time series data.

Copy the x-form matrices from hdr_file to out_file.

Mandatory Inputs:

in_nifti (a pathlike object or string representing an existing file) – Input ASL (4D NIfTI file).

Optional Inputs:

  • confounds_file (a pathlike object or string representing an existing file) – BIDS’ _confounds.tsv file.

  • confounds_list (a list of at least 1 items which are a string or a tuple of the form: (a string, a string or None) or a tuple of the form: (a string, a string or None, a string or None) or None) – List of headers to extract from the confounds_file.

  • drop_trs (an integer) – Dummy scans. (Nipype default value: 0)

  • in_cifti (a pathlike object or string representing an existing file) – Input ASL (CIFTI dense timeseries).

  • in_segm (a pathlike object or string representing an existing file) – Volumetric segmentation corresponding to in_nifti.

  • str_or_tuple (a string or a tuple of the form: (a string, a string or None) or a tuple of the form: (a string, a string or None, a string or None))

  • tr (a float or None) – The repetition time. (Nipype default value: None)

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.

class CBFByTissueTypePlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Prepare an CBF summary plot for the report.

Mandatory Inputs:

  • img_type (‘cbf’ or ‘att’ or ‘abat’ or ‘abv’) – Image type.

  • in_file (a pathlike object or string representing an existing file)

  • seg_file (a pathlike object or string representing an existing file) – Segmentation file.

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.

class CBFSummaryPlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Prepare an CBF summary plot for the report.

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

Mandatory Inputs:

  • in_file (a pathlike object or string representing an existing file) – Image to plot.

  • label (a string) – Label.

  • ref_vol (a pathlike object or string representing an existing file) – Reference volume to use as underlay.

  • vmax (a float) – Maximum value for figure. (Nipype default value: 100)

Optional Inputs:

vmin (a float) – Minimum value for figure. (Nipype default value: -20)

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.