nipype.interfaces.semtools.brains.utilities module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
GenerateEdgeMapImage¶
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 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
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
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
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¶
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 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
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¶
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 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
number of histogram bin.
Maps to a command-line argument:
--numberOfHistogramBins %d
.- numberOfMatchPointsan integer
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 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.