nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection module

Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.

N4ITKBiasFieldCorrection

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: N4ITKBiasFieldCorrection.

title: N4ITK MRI Bias correction

category: Filtering

description: Performs image bias correction using N4 algorithm. This module is based on the ITK filters contributed in the following publication: Tustison N, Gee J “N4ITK: Nick’s N3 ITK Implementation For MRI Bias Field Correction”, The Insight Journal 2009 January-June, http://hdl.handle.net/10380/3053

version: 9

documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/N4ITKBiasFieldCorrection

contributor: Nick Tustison (UPenn), Andrey Fedorov (SPL, BWH), Ron Kikinis (SPL, BWH)

acknowledgements: The development of this module was partially supported by NIH grants R01 AA016748-01, R01 CA111288 and U01 CA151261 as well as by NA-MIC, NAC, NCIGT and the Slicer community.

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • bsplineorder (an integer) – Order of B-spline used in the approximation. Larger values will lead to longer execution times, may result in overfitting and poor result. Maps to a command-line argument: --bsplineorder %d.

  • convergencethreshold (a float) – Stopping criterion for the iterative bias estimation. Larger values will lead to smaller execution time. Maps to a command-line argument: --convergencethreshold %f.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • histogramsharpening (a list of items which are a float) – A vector of up to three values. Non-zero values correspond to Bias Field Full Width at Half Maximum, Wiener filter noise, and Number of histogram bins. Maps to a command-line argument: --histogramsharpening %s.

  • inputimage (a pathlike object or string representing an existing file) – Input image where you observe signal inhomegeneity. Maps to a command-line argument: --inputimage %s.

  • iterations (a list of items which are an integer) – Maximum number of iterations at each level of resolution. Larger values will increase execution time, but may lead to better results. Maps to a command-line argument: --iterations %s.

  • maskimage (a pathlike object or string representing an existing file) – Binary mask that defines the structure of your interest. NOTE: This parameter is OPTIONAL. If the mask is not specified, the module will use internally Otsu thresholding to define this mask. Better processing results can often be obtained when a meaningful mask is defined. Maps to a command-line argument: --maskimage %s.

  • meshresolution (a list of items which are a float) – Resolution of the initial bspline grid defined as a sequence of three numbers. The actual resolution will be defined by adding the bspline order (default is 3) to the resolution in each dimension specified here. For example, 1,1,1 will result in a 4x4x4 grid of control points. This parameter may need to be adjusted based on your input image. In the multi-resolution N4 framework, the resolution of the bspline grid at subsequent iterations will be doubled. The number of resolutions is implicitly defined by Number of iterations parameter (the size of this list is the number of resolutions). Maps to a command-line argument: --meshresolution %s.

  • outputbiasfield (a boolean or a pathlike object or string representing a file) – Recovered bias field (OPTIONAL). Maps to a command-line argument: --outputbiasfield %s.

  • outputimage (a boolean or a pathlike object or string representing a file) – Result of processing. Maps to a command-line argument: --outputimage %s.

  • shrinkfactor (an integer) – Defines how much the image should be upsampled before estimating the inhomogeneity field. Increase if you want to reduce the execution time. 1 corresponds to the original resolution. Larger values will significantly reduce the computation time. Maps to a command-line argument: --shrinkfactor %d.

  • splinedistance (a float) – An alternative means to define the spline grid, by setting the distance between the control points. This parameter is used only if the grid resolution is not specified. Maps to a command-line argument: --splinedistance %f.

  • weightimage (a pathlike object or string representing an existing file) – Weight Image. Maps to a command-line argument: --weightimage %s.

Outputs:

  • outputbiasfield (a pathlike object or string representing an existing file) – Recovered bias field (OPTIONAL).

  • outputimage (a pathlike object or string representing an existing file) – Result of processing.