interfaces.semtools.brains.utilities¶
GenerateEdgeMapImage¶
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]
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
lowerPercentileMatching: (a float)
Map lower quantile and below to minOutputRange. It should be a value
between zero and one
argument: ``--lowerPercentileMatching %f``
outputMaximumGradientImage: (a boolean or a file name)
output gradient image file name
argument: ``--outputMaximumGradientImage %s``
inputMask: (an existing file name)
Input mask file name. If set, image histogram percentiles will be
calculated within the mask
argument: ``--inputMask %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
argument: ``--inputMRVolumes %s...``
upperPercentileMatching: (a float)
Map upper quantile and above to maxOutputRange. It should be a value
between zero and one
argument: ``--upperPercentileMatching %f``
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``
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``
numberOfThreads: (an integer (int or long))
Explicitly specify the maximum number of threads to use.
argument: ``--numberOfThreads %d``
Outputs:
outputMaximumGradientImage: (an existing file name)
output gradient image file name
outputEdgeMap: (an existing file name)
(required) output file name
GeneratePurePlugMask¶
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]
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``
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 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
threshold: (a float)
threshold value to define class membership
argument: ``--threshold %f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
outputMaskFile: (a boolean or a file name)
Output binary mask file name
argument: ``--outputMaskFile %s``
Outputs:
outputMaskFile: (an existing file name)
(required) Output binary mask file name
HistogramMatchingFilter¶
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]
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 ``
numberOfMatchPoints: (an integer (int or long))
number of histogram matching points
argument: ``--numberOfMatchPoints %d``
histogramAlgorithm: ('OtsuHistogramMatching')
histogram algrithm selection
argument: ``--histogramAlgorithm %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``
inputVolume: (an existing file name)
The Input image to be computed for statistics
argument: ``--inputVolume %s``
inputBinaryVolume: (an existing file name)
inputBinaryVolume
argument: ``--inputBinaryVolume %s``
numberOfHistogramBins: (an integer (int or long))
number of histogram bin
argument: ``--numberOfHistogramBins %d``
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
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
referenceBinaryVolume: (an existing file name)
referenceBinaryVolume
argument: ``--referenceBinaryVolume %s``
Outputs:
outputVolume: (an existing file name)
Output Image File Name