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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})inputMRVolumes (a 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....inputMask (a 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.lowerPercentileMatching (a 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.maximumOutputRange (an 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.minimumOutputRange (an 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputEdgeMap (a boolean or a pathlike object or string representing a file) – Output edgemap file name. Maps to a command-line argument:
--outputEdgeMap %s.outputMaximumGradientImage (a boolean or a pathlike object or string representing a file) – Output gradient image file name. Maps to a command-line argument:
--outputMaximumGradientImage %s.upperPercentileMatching (a 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.- Outputs:
outputEdgeMap (a pathlike object or string representing an existing file) – (required) output file name.
outputMaximumGradientImage (a 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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})inputImageModalities (a 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....numberOfSubSamples (a list of items which are an integer) – Number of continuous index samples taken at each direction of lattice space for each plug volume. Maps to a command-line argument:
--numberOfSubSamples %s.outputMaskFile (a boolean or a pathlike object or string representing a file) – Output binary mask file name. Maps to a command-line argument:
--outputMaskFile %s.threshold (a float) – Threshold value to define class membership. Maps to a command-line argument:
--threshold %f.- Outputs:
outputMaskFile (a 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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line 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’) – Environment variables. (Nipype default value:
{})histogramAlgorithm (‘OtsuHistogramMatching’) – histogram algrithm selection. Maps to a command-line argument:
--histogramAlgorithm %s.inputBinaryVolume (a pathlike object or string representing an existing file) – InputBinaryVolume. Maps to a command-line argument:
--inputBinaryVolume %s.inputVolume (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--inputVolume %s.numberOfHistogramBins (an integer) – number of histogram bin. Maps to a command-line argument:
--numberOfHistogramBins %d.numberOfMatchPoints (an integer) – number of histogram matching points. Maps to a command-line argument:
--numberOfMatchPoints %d.outputVolume (a boolean or a pathlike object or string representing a file) – Output Image File Name. Maps to a command-line argument:
--outputVolume %s.referenceBinaryVolume (a pathlike object or string representing an existing file) – ReferenceBinaryVolume. Maps to a command-line argument:
--referenceBinaryVolume %s.referenceVolume (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--referenceVolume %s.verbose (a boolean) – verbose mode running for debugging. Maps to a command-line argument:
--verbose.writeHistogram (a string) – decide if histogram data would be written with prefixe of the file name. Maps to a command-line argument:
--writeHistogram %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Output Image File Name.