nireports.interfaces.dmri module

Diffusion MRI -specific visualization.

class nireports.interfaces.dmri.DWIHeatmap(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.SimpleInterface

Prepare an fMRI summary plot for the report.

Mandatory Inputs

  • b_indices (a dictionary with keys which are an integer and with values which are a list of items which are an integer) – Index of b values.

  • in_file (a pathlike object or string representing an existing file) – A DWI file.

  • mask_file (a pathlike object or string representing an existing file) – A 3D mask.

  • scalarmap (a pathlike object or string representing an existing file) – A DWI-derived scalar map.

Optional Inputs

  • bins (a tuple of the form: (an integer, an integer)) – Bins. (Nipype default value: (150, 11))

  • colormap (a string) – Colormap of the heatmap. (Nipype default value: YlGn)

  • scalarmap_label (a string) – Set the label designating the scalar map.

  • sigma (a float) – Standard deviation of the noise (for SNR conversions).

  • subsample (an integer) – A number of samples if subsampling the data.

  • threshold (a float) – A DWI intensity threshold.

Outputs

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