nipype.interfaces.semtools.brains.utilities module

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GenerateEdgeMapImage

Link to code

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 unicode 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 (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.

minimumOutputRangean 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.

numberOfThreadsan integer (int or long)

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

Link to code

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 unicode 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 (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.

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

Link to code

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 unicode 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 (int or long)

number of histogram bin.

Maps to a command-line argument: --numberOfHistogramBins %d.

numberOfMatchPointsan integer (int or long)

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 unicode 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.