nipype.interfaces.slicer.filtering.extractskeleton module

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ExtractSkeleton

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: ExtractSkeleton.

title: Extract Skeleton

category: Filtering

description: Extract the skeleton of a binary object. The skeleton can be limited to being a 1D curve or allowed to be a full 2D manifold. The branches of the skeleton can be pruned so that only the maximal center skeleton is returned.

version: 0.1.0.$Revision: 2104 $(alpha)

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

contributor: Pierre Seroul (UNC), Martin Styner (UNC), Guido Gerig (UNC), Stephen Aylward (Kitware)

acknowledgements: The original implementation of this method was provided by ETH Zurich, Image Analysis Laboratory of Profs Olaf Kuebler, Gabor Szekely and Guido Gerig. Martin Styner at UNC, Chapel Hill made enhancements. Wrapping for Slicer was provided by Pierre Seroul and Stephen Aylward at Kitware, Inc.

Optional Inputs:

  • InputImageFileName (a pathlike object or string representing an existing file) – Input image. Maps to a command-line argument: %s (position: -2).

  • OutputImageFileName (a boolean or a pathlike object or string representing a file) – Skeleton of the input image. Maps to a command-line argument: %s (position: -1).

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

  • dontPrune (a boolean) – Return the full skeleton, not just the maximal skeleton. Maps to a command-line argument: --dontPrune.

  • 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: {})

  • numPoints (an integer) – Number of points used to represent the skeleton. Maps to a command-line argument: --numPoints %d.

  • pointsFile (a string) – Name of the file to store the coordinates of the central (1D) skeleton points. Maps to a command-line argument: --pointsFile %s.

  • type (‘1D’ or ‘2D’) – Type of skeleton to create. Maps to a command-line argument: --type %s.

Outputs:

OutputImageFileName (a pathlike object or string representing an existing file) – Skeleton of the input image.