nipype.interfaces.slicer.legacy.segmentation module

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OtsuThresholdSegmentation

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: OtsuThresholdSegmentation.

title: Otsu Threshold Segmentation

category: Legacy.Segmentation

description: This filter creates a labeled image from a grayscale image. First, it calculates an optimal threshold that separates the image into foreground and background. This threshold separates those two classes so that their intra-class variance is minimal (see http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a connected component algorithm to generate unique labels for each connected region of the foreground. Finally, the resulting image is relabeled to provide consecutive numbering.

version: 1.0

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

contributor: Bill Lorensen (GE)

acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Optional Inputs:

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

  • brightObjects (a boolean) – Segmenting bright objects on a dark background or dark objects on a bright background. Maps to a command-line argument: --brightObjects.

  • 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: {})

  • faceConnected (a boolean) – This is an advanced parameter. Adjacent voxels are face connected. This affects the connected component algorithm. If this parameter is false, more regions are likely to be identified. Maps to a command-line argument: --faceConnected.

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

  • minimumObjectSize (an integer) – Minimum size of object to retain. This parameter can be used to get rid of small regions in noisy images. Maps to a command-line argument: --minimumObjectSize %d.

  • numberOfBins (an integer) – This is an advanced parameter. The number of bins in the histogram used to model the probability mass function of the two intensity distributions. Small numbers of bins may result in a more conservative threshold. The default should suffice for most applications. Experimentation is the only way to see the effect of varying this parameter. Maps to a command-line argument: --numberOfBins %d.

  • outputVolume (a boolean or a pathlike object or string representing a file) – Output filtered. Maps to a command-line argument: %s (position: -1).

Outputs:

outputVolume (a pathlike object or string representing an existing file) – Output filtered.