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
- args : a unicode 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 (int or long)
- 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 (int or long)
- 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 (int or long)
- 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.
- 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
- args : a unicode 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 (int or long)
- Number of continous 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.
- 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
- args : a unicode 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’
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 (int or long)
Maps to a command-line argument:
--numberOfHistogramBins %d.- numberOfMatchPoints : an integer (int or long)
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
Maps to a command-line argument:
--verbose.- writeHistogram : a unicode string
Maps to a command-line argument:
--writeHistogram %s.
- outputVolume : a pathlike object or string representing an existing file
- Output Image File Name.