interfaces.slicer.legacy.segmentation

OtsuThresholdSegmentation

Link to code

Wraps command **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.

Inputs:

[Mandatory]

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
brightObjects: (a boolean)
        Segmenting bright objects on a dark background or dark objects on a
        bright background.
        flag: --brightObjects
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
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.
        flag: --faceConnected
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
inputVolume: (an existing file name)
        Input volume to be segmented
        flag: %s, position: -2
minimumObjectSize: (an integer (int or long))
        Minimum size of object to retain. This parameter can be used to get
        rid of small regions in noisy images.
        flag: --minimumObjectSize %d
numberOfBins: (an integer (int or long))
        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.
        flag: --numberOfBins %d
outputVolume: (a boolean or a file name)
        Output filtered
        flag: %s, position: -1
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

outputVolume: (an existing file name)
        Output filtered