interfaces.semtools.brains.utilities

GenerateEdgeMapImage

Link to code

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]
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...``
inputMask: (an existing file name)
        Input mask file name. If set, image histogram percentiles will be
        calculated within the mask
        argument: ``--inputMask %s``
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``
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``
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``
outputEdgeMap: (a boolean or a file name)
        output edgemap file name
        argument: ``--outputEdgeMap %s``
outputMaximumGradientImage: (a boolean or a file name)
        output gradient image file name
        argument: ``--outputMaximumGradientImage %s``
numberOfThreads: (an integer (int or long))
        Explicitly specify the maximum number of threads to use.
        argument: ``--numberOfThreads %d``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
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', nipype default value: {})
        Environment variables

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 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]
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...``
threshold: (a float)
        threshold value to define class membership
        argument: ``--threshold %f``
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``
outputMaskFile: (a boolean or a file name)
        Output binary mask file name
        argument: ``--outputMaskFile %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
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', nipype default value: {})
        Environment variables

Outputs:

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

HistogramMatchingFilter

Link to code

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]
inputVolume: (an existing file name)
        The Input image to be computed for statistics
        argument: ``--inputVolume %s``
referenceVolume: (an existing file name)
        The Input image to be computed for statistics
        argument: ``--referenceVolume %s``
outputVolume: (a boolean or a file name)
        Output Image File Name
        argument: ``--outputVolume %s``
referenceBinaryVolume: (an existing file name)
        referenceBinaryVolume
        argument: ``--referenceBinaryVolume %s``
inputBinaryVolume: (an existing file name)
        inputBinaryVolume
        argument: ``--inputBinaryVolume %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``
writeHistogram: (a unicode string)
         decide if histogram data would be written with prefixe of the file
        name
        argument: ``--writeHistogram %s``
histogramAlgorithm: ('OtsuHistogramMatching')
         histogram algrithm selection
        argument: ``--histogramAlgorithm %s``
verbose: (a boolean)
         verbose mode running for debbuging
        argument: ``--verbose ``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
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', nipype default value: {})
        Environment variables

Outputs:

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