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.
- class nipype.interfaces.semtools.brains.utilities.GenerateEdgeMapImage(command=None, terminal_output=None, write_cmdline=False, **inputs)¶
Bases:
SEMLikeCommandLineWrapped 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¶
- 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.
Outputs¶
- 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.
- class nipype.interfaces.semtools.brains.utilities.GeneratePurePlugMask(command=None, terminal_output=None, write_cmdline=False, **inputs)¶
Bases:
SEMLikeCommandLineWrapped 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¶
- 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 continuous 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.
Outputs¶
- outputMaskFilea pathlike object or string representing an existing file
(required) Output binary mask file name.
- class nipype.interfaces.semtools.brains.utilities.HistogramMatchingFilter(command=None, terminal_output=None, write_cmdline=False, **inputs)¶
Bases:
SEMLikeCommandLineWrapped 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¶
- 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 algorithm 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 debugging.
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.
Outputs¶
- outputVolumea pathlike object or string representing an existing file
Output Image File Name.