nipype.interfaces.semtools.filtering.featuredetection module

Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.

CannyEdge

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: CannyEdge.

title: Canny Edge Detection

category: Filtering.FeatureDetection

description: Get the distance from a voxel to the nearest voxel of a given tissue type.

version: 0.1.0.(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was written by Hans J. Johnson.

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: {})

inputVolumea pathlike object or string representing an existing file

Required: input tissue label image. Maps to a command-line argument: --inputVolume %s.

lowerThresholda float

Threshold is the lowest allowed value in the output image. Its data type is the same as the data type of the output image. Any values below the Threshold level will be replaced with the OutsideValue parameter value, whose default is zero. . Maps to a command-line argument: --lowerThreshold %f.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

upperThresholda float

Threshold is the lowest allowed value in the output image. Its data type is the same as the data type of the output image. Any values below the Threshold level will be replaced with the OutsideValue parameter value, whose default is zero. . Maps to a command-line argument: --upperThreshold %f.

variancea float

Variance and Maximum error are used in the Gaussian smoothing of the input image. See itkDiscreteGaussianImageFilter for information on these parameters. Maps to a command-line argument: --variance %f.

outputVolumea pathlike object or string representing an existing file

Required: output image.

CannySegmentationLevelSetImageFilter

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: CannySegmentationLevelSetImageFilter.

title: Canny Level Set Image Filter

category: Filtering.FeatureDetection

description: The CannySegmentationLevelSet is commonly used to refine a manually generated manual mask.

version: 0.3.0

license: CC

contributor: Regina Kim

acknowledgements: This command module was derived from Insight/Examples/Segmentation/CannySegmentationLevelSetImageFilter.cxx (copyright) Insight Software Consortium. See http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation for more detailed descriptions.

advectionWeighta float

Controls the smoothness of the resulting mask, small number are more smooth, large numbers allow more sharp corners. . Maps to a command-line argument: --advectionWeight %f.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

cannyThresholda float

Canny Threshold Value. Maps to a command-line argument: --cannyThreshold %f.

cannyVariancea float

Canny variance. Maps to a command-line argument: --cannyVariance %f.

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: {})

initialModela pathlike object or string representing an existing file

Maps to a command-line argument: --initialModel %s.

initialModelIsovaluea float

The identification of the input model iso-surface. (for a binary image with 0s and 1s use 0.5) (for a binary image with 0s and 255’s use 127.5). Maps to a command-line argument: --initialModelIsovalue %f.

inputVolumea pathlike object or string representing an existing file

Maps to a command-line argument: --inputVolume %s.

maxIterationsan integer

The. Maps to a command-line argument: --maxIterations %d.

outputSpeedVolumea boolean or a pathlike object or string representing a file

Maps to a command-line argument: --outputSpeedVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Maps to a command-line argument: --outputVolume %s.

outputSpeedVolume : a pathlike object or string representing an existing file outputVolume : a pathlike object or string representing an existing file

DilateImage

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: DilateImage.

title: Dilate Image

category: Filtering.FeatureDetection

description: Uses mathematical morphology to dilate the input images.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputRadiusan integer

Required: input neighborhood radius. Maps to a command-line argument: --inputRadius %d.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

DilateMask

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: DilateMask.

title: Dilate Image

category: Filtering.FeatureDetection

description: Uses mathematical morphology to dilate the input images.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputBinaryVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputBinaryVolume %s.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

lowerThresholda float

Required: lowerThreshold value. Maps to a command-line argument: --lowerThreshold %f.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

sizeStructuralElementan integer

Size of structural element. sizeStructuralElement=1 means that 3x3x3 structuring element for 3D. Maps to a command-line argument: --sizeStructuralElement %d.

outputVolumea pathlike object or string representing an existing file

Required: output image.

DistanceMaps

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: DistanceMaps.

title: Mauerer Distance

category: Filtering.FeatureDetection

description: Get the distance from a voxel to the nearest voxel of a given tissue type.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputLabelVolumea pathlike object or string representing an existing file

Required: input tissue label image. Maps to a command-line argument: --inputLabelVolume %s.

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputTissueLabelan integer

Required: input integer value of tissue type used to calculate distance. Maps to a command-line argument: --inputTissueLabel %d.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

DumpBinaryTrainingVectors

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: DumpBinaryTrainingVectors.

title: Erode Image

category: Filtering.FeatureDetection

description: Uses mathematical morphology to erode the input images.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputHeaderFilenamea pathlike object or string representing an existing file

Required: input header file name. Maps to a command-line argument: --inputHeaderFilename %s.

inputVectorFilenamea pathlike object or string representing an existing file

Required: input vector filename. Maps to a command-line argument: --inputVectorFilename %s.

ErodeImage

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: ErodeImage.

title: Erode Image

category: Filtering.FeatureDetection

description: Uses mathematical morphology to erode the input images.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputRadiusan integer

Required: input neighborhood radius. Maps to a command-line argument: --inputRadius %d.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

FlippedDifference

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: FlippedDifference.

title: Flip Image

category: Filtering.FeatureDetection

description: Difference between an image and the axially flipped version of that image.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

GenerateBrainClippedImage

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: GenerateBrainClippedImage.

title: GenerateBrainClippedImage

category: Filtering.FeatureDetection

description: Automatic FeatureImages using neural networks

version: 1.0

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Eun Young Kim

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: {})

inputImga pathlike object or string representing an existing file

Input volume 1, usually t1 image. Maps to a command-line argument: --inputImg %s.

inputMska pathlike object or string representing an existing file

Input volume 2, usually t2 image. Maps to a command-line argument: --inputMsk %s.

numberOfThreadsan integer

Explicitly specify the maximum number of threads to use. Maps to a command-line argument: --numberOfThreads %d.

outputFileNamea boolean or a pathlike object or string representing a file

(required) output file name. Maps to a command-line argument: --outputFileName %s.

outputFileNamea pathlike object or string representing an existing file

(required) output file name.

GenerateSummedGradientImage

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: GenerateSummedGradientImage.

title: GenerateSummedGradient

category: Filtering.FeatureDetection

description: Automatic FeatureImages using neural networks

version: 1.0

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Greg Harris, Eun Young Kim

MaximumGradienta boolean

If set this flag, it will compute maximum gradient between two input volumes instead of sum of it. Maps to a command-line argument: --MaximumGradient.

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: {})

inputVolume1a pathlike object or string representing an existing file

Input volume 1, usually t1 image. Maps to a command-line argument: --inputVolume1 %s.

inputVolume2a pathlike object or string representing an existing file

Input volume 2, usually t2 image. Maps to a command-line argument: --inputVolume2 %s.

numberOfThreadsan integer

Explicitly specify the maximum number of threads to use. Maps to a command-line argument: --numberOfThreads %d.

outputFileNamea boolean or a pathlike object or string representing a file

(required) output file name. Maps to a command-line argument: --outputFileName %s.

outputFileNamea pathlike object or string representing an existing file

(required) output file name.

GenerateTestImage

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: GenerateTestImage.

title: DownSampleImage

category: Filtering.FeatureDetection

description: Down sample image for testing

version: 1.0

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: Eun Young Kim

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: {})

inputVolumea pathlike object or string representing an existing file

Input volume 1, usually t1 image. Maps to a command-line argument: --inputVolume %s.

lowerBoundOfOutputVolumea float

Maps to a command-line argument: --lowerBoundOfOutputVolume %f.

outputVolumea boolean or a pathlike object or string representing a file

(required) output file name. Maps to a command-line argument: --outputVolume %s.

outputVolumeSizea float

Output Volume Size. Maps to a command-line argument: --outputVolumeSize %f.

upperBoundOfOutputVolumea float

Maps to a command-line argument: --upperBoundOfOutputVolume %f.

outputVolumea pathlike object or string representing an existing file

(required) output file name.

GradientAnisotropicDiffusionImageFilter

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: GradientAnisotropicDiffusionImageFilter.

title: GradientAnisopropicDiffusionFilter

category: Filtering.FeatureDetection

description: Image Smoothing using Gradient Anisotropic Diffuesion Filer

contributor: This tool was developed by Eun Young Kim by modifying ITK Example

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

conductancea float

Conductance for diffusion process. Maps to a command-line argument: --conductance %f.

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: {})

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

numberOfIterationsan integer

Optional value for number of Iterations. Maps to a command-line argument: --numberOfIterations %d.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

timeStepa float

Time step for diffusion process. Maps to a command-line argument: --timeStep %f.

outputVolumea pathlike object or string representing an existing file

Required: output image.

HammerAttributeCreator

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: HammerAttributeCreator.

title: HAMMER Feature Vectors

category: Filtering.FeatureDetection

description: Create the feature vectors used by HAMMER.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This was extracted from the Hammer Registration source code, and wrapped up by Hans J. Johnson.

Scalean integer

Determine Scale of Ball. Maps to a command-line argument: --Scale %d.

Strengtha float

Determine Strength of Edges. Maps to a command-line argument: --Strength %f.

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: {})

inputCSFVolumea pathlike object or string representing an existing file

Required: input CSF posterior image. Maps to a command-line argument: --inputCSFVolume %s.

inputGMVolumea pathlike object or string representing an existing file

Required: input grey matter posterior image. Maps to a command-line argument: --inputGMVolume %s.

inputWMVolumea pathlike object or string representing an existing file

Required: input white matter posterior image. Maps to a command-line argument: --inputWMVolume %s.

outputVolumeBasea string

Required: output image base name to be appended for each feature vector. Maps to a command-line argument: --outputVolumeBase %s.

NeighborhoodMean

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: NeighborhoodMean.

title: Neighborhood Mean

category: Filtering.FeatureDetection

description: Calculates the mean, for the given neighborhood size, at each voxel of the T1, T2, and FLAIR.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputRadiusan integer

Required: input neighborhood radius. Maps to a command-line argument: --inputRadius %d.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

NeighborhoodMedian

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: NeighborhoodMedian.

title: Neighborhood Median

category: Filtering.FeatureDetection

description: Calculates the median, for the given neighborhood size, at each voxel of the input image.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Required: input brain mask image. Maps to a command-line argument: --inputMaskVolume %s.

inputRadiusan integer

Required: input neighborhood radius. Maps to a command-line argument: --inputRadius %d.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

STAPLEAnalysis

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: STAPLEAnalysis.

title: Dilate Image

category: Filtering.FeatureDetection

description: Uses mathematical morphology to dilate the input images.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Mark Scully and Jeremy Bockholt.

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: {})

inputDimensionan integer

Required: input image Dimension 2 or 3. Maps to a command-line argument: --inputDimension %d.

inputLabelVolumea list of items which are a pathlike object or string representing an existing file

Required: input label volume. Maps to a command-line argument: --inputLabelVolume %s....

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

TextureFromNoiseImageFilter

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: TextureFromNoiseImageFilter.

title: TextureFromNoiseImageFilter

category: Filtering.FeatureDetection

description: Calculate the local noise in an image.

version: 0.1.0.$Revision: 1 $(alpha)

documentation-url: http:://www.na-mic.org/

license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt

contributor: This tool was developed by Eunyoung Regina Kim

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: {})

inputRadiusan integer

Required: input neighborhood radius. Maps to a command-line argument: --inputRadius %d.

inputVolumea pathlike object or string representing an existing file

Required: input image. Maps to a command-line argument: --inputVolume %s.

outputVolumea boolean or a pathlike object or string representing a file

Required: output image. Maps to a command-line argument: --outputVolume %s.

outputVolumea pathlike object or string representing an existing file

Required: output image.

TextureMeasureFilter

Link to code

Bases: SEMLikeCommandLine

Wrapped executable: TextureMeasureFilter.

title: Canny Level Set Image Filter

category: Filtering.FeatureDetection

description: The CannySegmentationLevelSet is commonly used to refine a manually generated manual mask.

version: 0.3.0

license: CC

contributor: Regina Kim

acknowledgements: This command module was derived from Insight/Examples/Segmentation/CannySegmentationLevelSetImageFilter.cxx (copyright) Insight Software Consortium. See http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation for more detailed descriptions.

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

distancean integer

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

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: {})

inputMaskVolumea pathlike object or string representing an existing file

Maps to a command-line argument: --inputMaskVolume %s.

inputVolumea pathlike object or string representing an existing file

Maps to a command-line argument: --inputVolume %s.

insideROIValuea float

Maps to a command-line argument: --insideROIValue %f.

outputFilenamea boolean or a pathlike object or string representing a file

Maps to a command-line argument: --outputFilename %s.

outputFilename : a pathlike object or string representing an existing file