qsiprep.interfaces.dipy module

Image tools interfaces

class qsiprep.interfaces.dipy.Patch2Self(**kwargs)[source]

Bases: SeriesPreprocReport, SimpleInterface

Mandatory Inputs:

  • bval_file (a pathlike object or string representing an existing file) – Bval file containing b-values.

  • in_file (a pathlike object or string representing an existing file) – 4D diffusion MRI data file.

Optional Inputs:

  • alpha (a float) – Regularization parameter for Ridge and Lasso. (Nipype default value: 1.0)

  • b0_denoising (a boolean) – Denoise the b=0 images too. (Nipype default value: True)

  • b0_threshold (a float) – Threshold to segregate b0s. (Nipype default value: 50.0)

  • clip_negative_vals (a boolean) – Sets negative values after denoising to 0. (Nipype default value: False)

  • mask (a pathlike object or string representing a file) – Mask image (unused).

  • model (a string) – Regression model for Patch2Self. (Nipype default value: ols)

  • nmse_text (a string or os.PathLike object)

  • out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: patch2self_report.svg)

  • shift_intensity (a boolean) – Shifts the distribution of intensities per volume to give non-negative values. (Nipype default value: True)

Outputs:

  • nmse_text (a string or os.PathLike object) – Nmse between input and output volumes.

  • noise_image (a pathlike object or string representing an existing file) – Residuals depicting suppressed noise.

  • out_file (a pathlike object or string representing an existing file) – Denoised version of the input image.

  • out_report (a pathlike object or string representing a file) – Filename for the visual report.

qsiprep.interfaces.dipy.popen_run(arg_list)[source]