.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.semtools.brains.utilities
====================================


.. _nipype.interfaces.semtools.brains.utilities.GenerateEdgeMapImage:


.. index:: GenerateEdgeMapImage

GenerateEdgeMapImage
--------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/semtools/brains/utilities.py#L125>`__

Wraps the executable command `` GenerateEdgeMapImage ``.

title: GenerateEdgeMapImage

category: BRAINS.Utilities

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

version: 1.0

contributor: Ali Ghayoor

Inputs::

        [Optional]
        inputMask: (an existing file name)
                Input mask file name. If set, image histogram percentiles will be
                calculated within the mask
                argument: ``--inputMask %s``
        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
                argument: ``--maximumOutputRange %d``
        outputMaximumGradientImage: (a boolean or a file name)
                output gradient image file name
                argument: ``--outputMaximumGradientImage %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        numberOfThreads: (an integer (int or long))
                Explicitly specify the maximum number of threads to use.
                argument: ``--numberOfThreads %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
                argument: ``--minimumOutputRange %d``
        outputEdgeMap: (a boolean or a file name)
                output edgemap file name
                argument: ``--outputEdgeMap %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
        inputMRVolumes: (a list of items which are an existing file name)
                List of input structural MR volumes to create the maximum edgemap
                argument: ``--inputMRVolumes %s...``
        lowerPercentileMatching: (a float)
                Map lower quantile and below to minOutputRange. It should be a value
                between zero and one
                argument: ``--lowerPercentileMatching %f``
        upperPercentileMatching: (a float)
                Map upper quantile and above to maxOutputRange. It should be a value
                between zero and one
                argument: ``--upperPercentileMatching %f``

Outputs::

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

.. _nipype.interfaces.semtools.brains.utilities.GeneratePurePlugMask:


.. index:: GeneratePurePlugMask

GeneratePurePlugMask
--------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/semtools/brains/utilities.py#L175>`__

Wraps the executable 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::

        [Optional]
        outputMaskFile: (a boolean or a file name)
                Output binary mask file name
                argument: ``--outputMaskFile %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
                argument: ``--numberOfSubSamples %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        inputImageModalities: (a list of items which are an existing file
                  name)
                List of input image file names to create pure plugs mask
                argument: ``--inputImageModalities %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
        threshold: (a float)
                threshold value to define class membership
                argument: ``--threshold %f``

Outputs::

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

.. _nipype.interfaces.semtools.brains.utilities.HistogramMatchingFilter:


.. index:: HistogramMatchingFilter

HistogramMatchingFilter
-----------------------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/semtools/brains/utilities.py#L55>`__

Wraps the executable 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::

        [Optional]
        outputVolume: (a boolean or a file name)
                Output Image File Name
                argument: ``--outputVolume %s``
        writeHistogram: (a unicode string)
                 decide if histogram data would be written with prefixe of the file
                name
                argument: ``--writeHistogram %s``
        verbose: (a boolean)
                 verbose mode running for debbuging
                argument: ``--verbose ``
        histogramAlgorithm: ('OtsuHistogramMatching')
                 histogram algrithm selection
                argument: ``--histogramAlgorithm %s``
        inputBinaryVolume: (an existing file name)
                inputBinaryVolume
                argument: ``--inputBinaryVolume %s``
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        referenceVolume: (an existing file name)
                The Input image to be computed for statistics
                argument: ``--referenceVolume %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
        referenceBinaryVolume: (an existing file name)
                referenceBinaryVolume
                argument: ``--referenceBinaryVolume %s``
        numberOfMatchPoints: (an integer (int or long))
                 number of histogram matching points
                argument: ``--numberOfMatchPoints %d``
        numberOfHistogramBins: (an integer (int or long))
                 number of histogram bin
                argument: ``--numberOfHistogramBins %d``
        inputVolume: (an existing file name)
                The Input image to be computed for statistics
                argument: ``--inputVolume %s``

Outputs::

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