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# interfaces.semtools.brains.utilities

## GenerateEdgeMapImage

Link to code

Wraps command ** GenerateEdgeMapImage **

title: GenerateEdgeMapImage

category: BRAINS.Utilities

description: Automatic edgemap generation for edge-guided super-resolution reconstruction

version: 1.0

contributor: Ali Ghayoor

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    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
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputMRVolumes: (a list of items which are an existing file name)
            List of input structural MR volumes to create the maximum edgemap
            flag: --inputMRVolumes %s...
    inputMask: (an existing file name)
            Input mask file name. If set, image histogram percentiles will be
            calculated within the mask
            flag: --inputMask %s
    lowerPercentileMatching: (a float)
            Map lower quantile and below to minOutputRange. It should be a value
            between zero and one
            flag: --lowerPercentileMatching %f
    maximumOutputRange: (an integer (int or long))
            Map upper quantile and above to maximum output range. Default is 255
            that is the maximum range of unsigned char
            flag: --maximumOutputRange %d
    minimumOutputRange: (an integer (int or long))
            Map lower quantile and below to minimum output range. It should be a
            small number greater than zero. Default is 1
            flag: --minimumOutputRange %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputEdgeMap: (a boolean or a file name)
            output edgemap file name
            flag: --outputEdgeMap %s
    outputMaximumGradientImage: (a boolean or a file name)
            output gradient image file name
            flag: --outputMaximumGradientImage %s
    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
    upperPercentileMatching: (a float)
            Map upper quantile and above to maxOutputRange. It should be a value
            between zero and one
            flag: --upperPercentileMatching %f

Outputs:

    outputEdgeMap: (an existing file name)
            (required) output file name
    outputMaximumGradientImage: (an existing file name)
            output gradient image file name

## GeneratePurePlugMask

Link to code

Wraps command ** GeneratePurePlugMask **

title: GeneratePurePlugMask

category: BRAINS.Utilities

description: This program gets several modality image files and returns a binary mask that defines the pure plugs

version: 1.0

contributor: Ali Ghayoor

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    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
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputImageModalities: (a list of items which are an existing file
             name)
            List of input image file names to create pure plugs mask
            flag: --inputImageModalities %s...
    numberOfSubSamples: (a list of items which are an integer (int or
             long))
            Number of continous index samples taken at each direction of lattice
            space for each plug volume
            flag: --numberOfSubSamples %s
    outputMaskFile: (a boolean or a file name)
            Output binary mask file name
            flag: --outputMaskFile %s
    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
    threshold: (a float)
            threshold value to define class membership
            flag: --threshold %f

Outputs:

    outputMaskFile: (an existing file name)
            (required) Output binary mask file name

## HistogramMatchingFilter

Link to code

Wraps command ** HistogramMatchingFilter **

title: Write Out Image Intensities

category: BRAINS.Utilities

description: For Analysis

version: 0.1

contributor: University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    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
    histogramAlgorithm: ('OtsuHistogramMatching')
             histogram algrithm selection
            flag: --histogramAlgorithm %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputBinaryVolume: (an existing file name)
            inputBinaryVolume
            flag: --inputBinaryVolume %s
    inputVolume: (an existing file name)
            The Input image to be computed for statistics
            flag: --inputVolume %s
    numberOfHistogramBins: (an integer (int or long))
             number of histogram bin
            flag: --numberOfHistogramBins %d
    numberOfMatchPoints: (an integer (int or long))
             number of histogram matching points
            flag: --numberOfMatchPoints %d
    outputVolume: (a boolean or a file name)
            Output Image File Name
            flag: --outputVolume %s
    referenceBinaryVolume: (an existing file name)
            referenceBinaryVolume
            flag: --referenceBinaryVolume %s
    referenceVolume: (an existing file name)
            The Input image to be computed for statistics
            flag: --referenceVolume %s
    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
    verbose: (a boolean)
             verbose mode running for debbuging
            flag: --verbose
    writeHistogram: (a unicode string)
             decide if histogram data would be written with prefixe of the file
            name
            flag: --writeHistogram %s

Outputs:

    outputVolume: (an existing file name)
            Output Image File Name