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# nipype.interfaces.semtools.brains.utilities module

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## GenerateEdgeMapImage

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `GenerateEdgeMapImage`.

> title: GenerateEdgeMapImage

> category: BRAINS.Utilities

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

> version: 1.0

> contributor: Ali Ghayoor

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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: `{}`)

> inputMRVolumesa list of items which are a pathlike object or string representing an existing file

>   List of input structural MR volumes to create the maximum edgemap. Maps to a command-line argument: `--inputMRVolumes %s...`.

> inputMaska pathlike object or string representing an existing file

>   Input mask file name. If set, image histogram percentiles will be calculated within the mask. Maps to a command-line argument: `--inputMask %s`.

> lowerPercentileMatchinga float

>   Map lower quantile and below to minOutputRange. It should be a value between zero and one. Maps to a command-line argument: `--lowerPercentileMatching %f`.

> maximumOutputRangean integer (int or long)

>   Map upper quantile and above to maximum output range. Default is 255 that is the maximum range of unsigned char. Maps to a command-line argument: `--maximumOutputRange %d`.

> minimumOutputRangean 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. Maps to a command-line argument: `--minimumOutputRange %d`.

> numberOfThreadsan integer (int or long)

>   Explicitly specify the maximum number of threads to use. Maps to a command-line argument: `--numberOfThreads %d`.

> outputEdgeMapa boolean or a pathlike object or string representing a file

>   Output edgemap file name. Maps to a command-line argument: `--outputEdgeMap %s`.

> outputMaximumGradientImagea boolean or a pathlike object or string representing a file

>   Output gradient image file name. Maps to a command-line argument: `--outputMaximumGradientImage %s`.

> upperPercentileMatchinga float

>   Map upper quantile and above to maxOutputRange. It should be a value between zero and one. Maps to a command-line argument: `--upperPercentileMatching %f`.

> outputEdgeMapa pathlike object or string representing an existing file

>   (required) output file name.

> outputMaximumGradientImagea pathlike object or string representing an existing file

>   Output gradient image file name.

## GeneratePurePlugMask

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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: `{}`)

> inputImageModalitiesa list of items which are a pathlike object or string representing an existing file

>   List of input image file names to create pure plugs mask. Maps to a command-line argument: `--inputImageModalities %s...`.

> numberOfSubSamplesa 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. Maps to a command-line argument: `--numberOfSubSamples %s`.

> outputMaskFilea boolean or a pathlike object or string representing a file

>   Output binary mask file name. Maps to a command-line argument: `--outputMaskFile %s`.

> thresholda float

>   Threshold value to define class membership. Maps to a command-line argument: `--threshold %f`.

> outputMaskFilea pathlike object or string representing an existing file

>   (required) Output binary mask file name.

## HistogramMatchingFilter

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `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

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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: `{}`)

> histogramAlgorithm‘OtsuHistogramMatching’

>   > histogram algrithm selection.

>   Maps to a command-line argument: `--histogramAlgorithm %s`.

> inputBinaryVolumea pathlike object or string representing an existing file

>   InputBinaryVolume. Maps to a command-line argument: `--inputBinaryVolume %s`.

> inputVolumea pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--inputVolume %s`.

> numberOfHistogramBinsan integer (int or long)

>   > number of histogram bin.

>   Maps to a command-line argument: `--numberOfHistogramBins %d`.

> numberOfMatchPointsan integer (int or long)

>   > number of histogram matching points.

>   Maps to a command-line argument: `--numberOfMatchPoints %d`.

> outputVolumea boolean or a pathlike object or string representing a file

>   Output Image File Name. Maps to a command-line argument: `--outputVolume %s`.

> referenceBinaryVolumea pathlike object or string representing an existing file

>   ReferenceBinaryVolume. Maps to a command-line argument: `--referenceBinaryVolume %s`.

> referenceVolumea pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--referenceVolume %s`.

> verbosea boolean

>   > verbose mode running for debbuging.

>   Maps to a command-line argument: `--verbose`.

> writeHistograma unicode string

>   > decide if histogram data would be written with prefixe of the file name.

>   Maps to a command-line argument: `--writeHistogram %s`.

> outputVolumea pathlike object or string representing an existing file

>   Output Image File Name.