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 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
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
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 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
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
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 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
histogramAlgorithm: ('OtsuHistogramMatching')
         histogram algrithm selection
        flag: --histogramAlgorithm %s
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
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