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# nipype.interfaces.semtools.segmentation.specialized module

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## BRAINSABC

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSABC`.

> title: Intra-subject registration, bias Correction, and tissue classification (BRAINS)

> category: Segmentation.Specialized

> description: Atlas-based tissue segmentation method. This is an algorithmic extension of work done by XXXX at UNC and Utah XXXX need more description here.

> argsa unicode string

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

> atlasDefinitiona pathlike object or string representing an existing file

>   Contains all parameters for Atlas. Maps to a command-line argument: `--atlasDefinition %s`.

> atlasToSubjectInitialTransforma boolean or a pathlike object or string representing a file

>   The initial transform from atlas to the subject. Maps to a command-line argument: `--atlasToSubjectInitialTransform %s`.

> atlasToSubjectTransforma boolean or a pathlike object or string representing a file

>   The transform from atlas to the subject. Maps to a command-line argument: `--atlasToSubjectTransform %s`.

> atlasToSubjectTransformType‘Identity’ or ‘Rigid’ or ‘Affine’ or ‘BSpline’ or ‘SyN’

>   > What type of linear transform type do you want to use to register the atlas to the reference subject image.

>   Maps to a command-line argument: `--atlasToSubjectTransformType %s`.

> atlasWarpingOffa boolean

>   Deformable registration of atlas to subject. Maps to a command-line argument: `--atlasWarpingOff`.

> debuglevelan integer (int or long)

>   Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. Maps to a command-line argument: `--debuglevel %d`.

> defaultSuffixa unicode string

>   Maps to a command-line argument: `--defaultSuffix %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: `{}`)

> filterIterationan integer (int or long)

>   Filter iterations. Maps to a command-line argument: `--filterIteration %d`.

> filterMethod‘None’ or ‘CurvatureFlow’ or ‘GradientAnisotropicDiffusion’ or ‘Median’

>   Filter method for preprocessing of registration. Maps to a command-line argument: `--filterMethod %s`.

> filterTimeStepa float

>   Filter time step should be less than (PixelSpacing/(1^(DIM+1)), value is set to negative, then allow automatic setting of this value. . Maps to a command-line argument: `--filterTimeStep %f`.

> gridSizea list of items which are an integer (int or long)

>   Grid size for atlas warping with BSplines. Maps to a command-line argument: `--gridSize %s`.

> implicitOutputsa boolean or a list of items which are a pathlike object or string representing a file

>   Outputs to be made available to NiPype. Needed because not all BRAINSABC outputs have command line arguments. Maps to a command-line argument: `--implicitOutputs %s...`.

> inputVolumeTypesa list of items which are a unicode string

>   The list of input image types corresponding to the inputVolumes. Maps to a command-line argument: `--inputVolumeTypes %s`.

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

>   The list of input image files to be segmented. Maps to a command-line argument: `--inputVolumes %s...`.

> interpolationMode‘BSpline’ or ‘NearestNeighbor’ or ‘WindowedSinc’ or ‘Linear’ or ‘ResampleInPlace’ or ‘Hamming’ or ‘Cosine’ or ‘Welch’ or ‘Lanczos’ or ‘Blackman’

>   Type of interpolation to be used when applying transform to moving volume. Options are Linear, NearestNeighbor, BSpline, WindowedSinc, or ResampleInPlace. The ResampleInPlace option will create an image with the same discrete voxel values and will adjust the origin and direction of the physical space interpretation. Maps to a command-line argument: `--interpolationMode %s`.

> maxBiasDegreean integer (int or long)

>   Maximum bias degree. Maps to a command-line argument: `--maxBiasDegree %d`.

> maxIterationsan integer (int or long)

>   Filter iterations. Maps to a command-line argument: `--maxIterations %d`.

> medianFilterSizea list of items which are an integer (int or long)

>   The radius for the optional MedianImageFilter preprocessing in all 3 directions. Maps to a command-line argument: `--medianFilterSize %s`.

> numberOfSubSamplesInEachPlugAreaa 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: `--numberOfSubSamplesInEachPlugArea %s`.

> numberOfThreadsan integer (int or long)

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

> outputDira boolean or a pathlike object or string representing a directory

>   Ouput directory. Maps to a command-line argument: `--outputDir %s`.

> outputDirtyLabelsa boolean or a pathlike object or string representing a file

>   Output Dirty Label Image. Maps to a command-line argument: `--outputDirtyLabels %s`.

> outputFormat‘NIFTI’ or ‘Meta’ or ‘Nrrd’

>   Output format. Maps to a command-line argument: `--outputFormat %s`.

> outputLabelsa boolean or a pathlike object or string representing a file

>   Output Label Image. Maps to a command-line argument: `--outputLabels %s`.

> outputVolumesa boolean or a list of items which are a pathlike object or string representing a file

>   Corrected Output Images: should specify the same number of images as inputVolume, if only one element is given, then it is used as a file pattern where %s is replaced by the imageVolumeType, and %d by the index list location. Maps to a command-line argument: `--outputVolumes %s...`.

> posteriorTemplatea unicode string

>   Filename template for Posterior output files. Maps to a command-line argument: `--posteriorTemplate %s`.

> purePlugsThresholda float

>   If this threshold value is greater than zero, only pure samples are used to compute the distributions in EM classification, and only pure samples are used for KNN training. The default value is set to 0, that means not using pure plugs. However, a value of 0.2 is suggested if you want to activate using pure plugs option. Maps to a command-line argument: `--purePlugsThreshold %f`.

> restoreStatea pathlike object or string representing an existing file

>   The initial state for the registration process. Maps to a command-line argument: `--restoreState %s`.

> saveStatea boolean or a pathlike object or string representing a file

>   (optional) Filename to which save the final state of the registration. Maps to a command-line argument: `--saveState %s`.

> subjectIntermodeTransformType‘Identity’ or ‘Rigid’ or ‘Affine’ or ‘BSpline’

>   > What type of linear transform type do you want to use to register the atlas to the reference subject image.

>   Maps to a command-line argument: `--subjectIntermodeTransformType %s`.

> useKNNa boolean

>   Use the KNN stage of estimating posteriors. Maps to a command-line argument: `--useKNN`.

> writeLessa boolean

>   Does not write posteriors and filtered, bias corrected images. Maps to a command-line argument: `--writeLess`.

> atlasToSubjectInitialTransforma pathlike object or string representing an existing file

>   The initial transform from atlas to the subject.

> atlasToSubjectTransforma pathlike object or string representing an existing file

>   The transform from atlas to the subject.

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

>   Outputs to be made available to NiPype. Needed because not all BRAINSABC outputs have command line arguments.

> outputDira pathlike object or string representing an existing directory

>   Ouput directory.

> outputDirtyLabelsa pathlike object or string representing an existing file

>   Output Dirty Label Image.

> outputLabelsa pathlike object or string representing an existing file

>   Output Label Image.

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

>   Corrected Output Images: should specify the same number of images as inputVolume, if only one element is given, then it is used as a file pattern where %s is replaced by the imageVolumeType, and %d by the index list location.

> saveStatea pathlike object or string representing an existing file

>   (optional) Filename to which save the final state of the registration.

## BRAINSConstellationDetector

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSConstellationDetector`.

> title: Brain Landmark Constellation Detector (BRAINS)

> category: Segmentation.Specialized

> description: This program will find the mid-sagittal plane, a constellation of landmarks in a volume, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (labeled at the origin of the image physical space.) Part of this work is an extention of the algorithms originally described by Dr. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, NeuroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030. (http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c)

> version: 1.0

> documentation-url: http://www.nitrc.org/projects/brainscdetector/

> BackgroundFillValuea unicode string

>   Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number. Maps to a command-line argument: `--BackgroundFillValue %s`.

> LLSModela pathlike object or string representing an existing file

>   Linear least squares model filename in HD5 format. Maps to a command-line argument: `--LLSModel %s`.

> acLowerBounda float

>   , When generating a resampled output image, replace the image with the BackgroundFillValue everywhere below the plane This Far in physical units (millimeters) below (inferior to) the AC point (as found by the model.) The oversize default was chosen to have no effect. Based on visualizing a thousand masks in the IPIG study, we recommend a limit no smaller than 80.0 mm., . Maps to a command-line argument: `--acLowerBound %f`.

> argsa unicode string

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

> atlasLandmarkWeightsa pathlike object or string representing an existing file

>   Weights associated with atlas landmarks to be used for BRAINSFit registration initialization, . Maps to a command-line argument: `--atlasLandmarkWeights %s`.

> atlasLandmarksa pathlike object or string representing an existing file

>   Atlas landmarks to be used for BRAINSFit registration initialization, . Maps to a command-line argument: `--atlasLandmarks %s`.

> atlasVolumea pathlike object or string representing an existing file

>   Atlas volume image to be used for BRAINSFit registration. Maps to a command-line argument: `--atlasVolume %s`.

> cutOutHeadInOutputVolumea boolean

>   , Flag to cut out just the head tissue when producing an (un)transformed clipped volume., . Maps to a command-line argument: `--cutOutHeadInOutputVolume`.

> debuga boolean

>   , Show internal debugging information., . Maps to a command-line argument: `--debug`.

> 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: `{}`)

> forceACPointa list of items which are a float

>   , Use this flag to manually specify the AC point from the original image on the command line., . Maps to a command-line argument: `--forceACPoint %s`.

> forceHoughEyeDetectorReportFailurea boolean

>   , Flag indicates whether the Hough eye detector should report failure, . Maps to a command-line argument: `--forceHoughEyeDetectorReportFailure`.

> forcePCPointa list of items which are a float

>   , Use this flag to manually specify the PC point from the original image on the command line., . Maps to a command-line argument: `--forcePCPoint %s`.

> forceRPPointa list of items which are a float

>   , Use this flag to manually specify the RP point from the original image on the command line., . Maps to a command-line argument: `--forceRPPoint %s`.

> forceVN4Pointa list of items which are a float

>   , Use this flag to manually specify the VN4 point from the original image on the command line., . Maps to a command-line argument: `--forceVN4Point %s`.

> houghEyeDetectorModean integer (int or long)

>   , This flag controls the mode of Hough eye detector. By default, value of 1 is for T1W images, while the value of 0 is for T2W and PD images., . Maps to a command-line argument: `--houghEyeDetectorMode %d`.

> inputLandmarksEMSPa pathlike object or string representing an existing file

>   , The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (in .fcsv) with the landmarks in the estimated MSP aligned space to be loaded. The detector will only process landmarks not enlisted on the file., . Maps to a command-line argument: `--inputLandmarksEMSP %s`.

> inputTemplateModela pathlike object or string representing an existing file

>   User-specified template model., . Maps to a command-line argument: `--inputTemplateModel %s`.

> inputVolumea pathlike object or string representing an existing file

>   Input image in which to find ACPC points. Maps to a command-line argument: `--inputVolume %s`.

> interpolationMode‘NearestNeighbor’ or ‘Linear’ or ‘ResampleInPlace’ or ‘BSpline’ or ‘WindowedSinc’ or ‘Hamming’ or ‘Cosine’ or ‘Welch’ or ‘Lanczos’ or ‘Blackman’

>   Type of interpolation to be used when applying transform to moving volume. Options are Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc. Maps to a command-line argument: `--interpolationMode %s`.

> mspQualityLevelan integer (int or long)

>   , Flag cotrols how agressive the MSP is estimated. 0=quick estimate (9 seconds), 1=normal estimate (11 seconds), 2=great estimate (22 seconds), 3=best estimate (58 seconds), NOTE: -1= Prealigned so no estimate!., . Maps to a command-line argument: `--mspQualityLevel %d`.

> numberOfThreadsan integer (int or long)

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

> otsuPercentileThresholda float

>   , This is a parameter to FindLargestForegroundFilledMask, which is employed when acLowerBound is set and an outputUntransformedClippedVolume is requested., . Maps to a command-line argument: `--otsuPercentileThreshold %f`.

> outputLandmarksInACPCAlignedSpacea boolean or a pathlike object or string representing a file

>   , The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the output image space (the detected RP, AC, PC, and VN4) in it to be written., . Maps to a command-line argument: `--outputLandmarksInACPCAlignedSpace %s`.

> outputLandmarksInInputSpacea boolean or a pathlike object or string representing a file

>   , The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the original image space (the detected RP, AC, PC, and VN4) in it to be written., . Maps to a command-line argument: `--outputLandmarksInInputSpace %s`.

> outputMRMLa boolean or a pathlike object or string representing a file

>   , The filename for the new subject-specific scene definition file in the same format produced by Slicer3 (in .mrml format). Only the components that were specified by the user on command line would be generated. Compatible components include inputVolume, outputVolume, outputLandmarksInInputSpace, outputLandmarksInACPCAlignedSpace, and outputTransform., . Maps to a command-line argument: `--outputMRML %s`.

> outputResampledVolumea boolean or a pathlike object or string representing a file

>   ACPC-aligned output image in a resampled unifor space. Currently this is a 1mm, 256^3, Identity direction image. Maps to a command-line argument: `--outputResampledVolume %s`.

> outputTransforma boolean or a pathlike object or string representing a file

>   The filename for the original space to ACPC alignment to be written (in .h5 format)., . Maps to a command-line argument: `--outputTransform %s`.

> outputUntransformedClippedVolumea boolean or a pathlike object or string representing a file

>   Output image in which to store neck-clipped input image, with the use of –acLowerBound and maybe –cutOutHeadInUntransformedVolume. Maps to a command-line argument: `--outputUntransformedClippedVolume %s`.

> outputVerificationScripta boolean or a pathlike object or string representing a file

>   , The filename for the Slicer3 script that verifies the aligned landmarks against the aligned image file. This will happen only in conjunction with saveOutputLandmarks and an outputVolume., . Maps to a command-line argument: `--outputVerificationScript %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   ACPC-aligned output image with the same voxels, but updated origin, and direction cosign so that the AC point would fall at the physical location (0.0,0.0,0.0), and the mid-sagital plane is the plane where physical L/R coordinate is 0.0. Maps to a command-line argument: `--outputVolume %s`.

> rVN4a float

>   , Search radius for VN4 in unit of mm, . Maps to a command-line argument: `--rVN4 %f`.

> raca float

>   , Search radius for AC in unit of mm, . Maps to a command-line argument: `--rac %f`.

> rescaleIntensitiesa boolean

>   , Flag to turn on rescaling image intensities on input., . Maps to a command-line argument: `--rescaleIntensities`.

> rescaleIntensitiesOutputRangea list of items which are an integer (int or long)

>   , This pair of integers gives the lower and upper bounds on the signal portion of the output image. Out-of-field voxels are taken from BackgroundFillValue., . Maps to a command-line argument: `--rescaleIntensitiesOutputRange %s`.

> resultsDira boolean or a pathlike object or string representing a directory

>   , The directory for the debuging images to be written., . Maps to a command-line argument: `--resultsDir %s`.

> rmpja float

>   , Search radius for MPJ in unit of mm, . Maps to a command-line argument: `--rmpj %f`.

> rpca float

>   , Search radius for PC in unit of mm, . Maps to a command-line argument: `--rpc %f`.

> trimRescaledIntensitiesa float

>   , Turn on clipping the rescaled image one-tailed on input. Units of standard deviations above the mean. Very large values are very permissive. Non-positive value turns clipping off. Defaults to removing 0.00001 of a normal tail above the mean., . Maps to a command-line argument: `--trimRescaledIntensities %f`.

> verbosea boolean

>   , Show more verbose output, . Maps to a command-line argument: `--verbose`.

> writeBranded2DImagea boolean or a pathlike object or string representing a file

>   , The filename for the 2D .png branded midline debugging image. This will happen only in conjunction with requesting an outputVolume., . Maps to a command-line argument: `--writeBranded2DImage %s`.

> writedebuggingImagesLevelan integer (int or long)

>   , This flag controls if debugging images are produced. By default value of 0 is no images. Anything greater than zero will be increasing level of debugging images., . Maps to a command-line argument: `--writedebuggingImagesLevel %d`.

> outputLandmarksInACPCAlignedSpacea pathlike object or string representing an existing file

>   , The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the output image space (the detected RP, AC, PC, and VN4) in it to be written., .

> outputLandmarksInInputSpacea pathlike object or string representing an existing file

>   , The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the original image space (the detected RP, AC, PC, and VN4) in it to be written., .

> outputMRMLa pathlike object or string representing an existing file

>   , The filename for the new subject-specific scene definition file in the same format produced by Slicer3 (in .mrml format). Only the components that were specified by the user on command line would be generated. Compatible components include inputVolume, outputVolume, outputLandmarksInInputSpace, outputLandmarksInACPCAlignedSpace, and outputTransform., .

> outputResampledVolumea pathlike object or string representing an existing file

>   ACPC-aligned output image in a resampled unifor space. Currently this is a 1mm, 256^3, Identity direction image.

> outputTransforma pathlike object or string representing an existing file

>   The filename for the original space to ACPC alignment to be written (in .h5 format)., .

> outputUntransformedClippedVolumea pathlike object or string representing an existing file

>   Output image in which to store neck-clipped input image, with the use of –acLowerBound and maybe –cutOutHeadInUntransformedVolume.

> outputVerificationScripta pathlike object or string representing an existing file

>   , The filename for the Slicer3 script that verifies the aligned landmarks against the aligned image file. This will happen only in conjunction with saveOutputLandmarks and an outputVolume., .

> outputVolumea pathlike object or string representing an existing file

>   ACPC-aligned output image with the same voxels, but updated origin, and direction cosign so that the AC point would fall at the physical location (0.0,0.0,0.0), and the mid-sagital plane is the plane where physical L/R coordinate is 0.0.

> resultsDira pathlike object or string representing an existing directory

>   , The directory for the debuging images to be written., .

> writeBranded2DImagea pathlike object or string representing an existing file

>   , The filename for the 2D .png branded midline debugging image. This will happen only in conjunction with requesting an outputVolume., .

## BRAINSCreateLabelMapFromProbabilityMaps

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSCreateLabelMapFromProbabilityMaps`.

> title: Create Label Map From Probability Maps (BRAINS)

> category: Segmentation.Specialized

> description: Given A list of Probability Maps, generate a LabelMap.

> argsa unicode string

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

> cleanLabelVolumea boolean or a pathlike object or string representing a file

>   The foreground labels volume. Maps to a command-line argument: `--cleanLabelVolume %s`.

> dirtyLabelVolumea boolean or a pathlike object or string representing a file

>   The labels prior to cleaning. Maps to a command-line argument: `--dirtyLabelVolume %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: `{}`)

> foregroundPriorsa list of items which are an integer (int or long)

>   A list: For each Prior Label, 1 if foreground, 0 if background. Maps to a command-line argument: `--foregroundPriors %s`.

> inclusionThresholda float

>   Tolerance for inclusion. Maps to a command-line argument: `--inclusionThreshold %f`.

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

>   The list of proobabilityimages. Maps to a command-line argument: `--inputProbabilityVolume %s...`.

> nonAirRegionMaska pathlike object or string representing an existing file

>   A mask representing the ‘NonAirRegion’ – Just force pixels in this region to zero. Maps to a command-line argument: `--nonAirRegionMask %s`.

> priorLabelCodesa list of items which are an integer (int or long)

>   A list of PriorLabelCode values used for coding the output label images. Maps to a command-line argument: `--priorLabelCodes %s`.

> cleanLabelVolumea pathlike object or string representing an existing file

>   The foreground labels volume.

> dirtyLabelVolumea pathlike object or string representing an existing file

>   The labels prior to cleaning.

## BRAINSCut

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSCut`.

> title: BRAINSCut (BRAINS)

> category: Segmentation.Specialized

> description: Automatic Segmentation using neural networks

> version: 1.0

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

> contributor: Vince Magnotta, Hans Johnson, Greg Harris, Kent Williams, Eunyoung Regina Kim

> NoTrainingVectorShufflinga boolean

>   If this flag is on, there will be no shuffling. Maps to a command-line argument: `--NoTrainingVectorShuffling`.

> applyModela boolean

>   Apply the neural net. Maps to a command-line argument: `--applyModel`.

> argsa unicode string

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

> computeSSEOna boolean

>   Compute Sum of Square Error (SSE) along the trained model until the number of iteration given in the modelConfigurationFilename file. Maps to a command-line argument: `--computeSSEOn`.

> createVectorsa boolean

>   Create vectors for training neural net. Maps to a command-line argument: `--createVectors`.

> 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: `{}`)

> generateProbabilitya boolean

>   Generate probability map. Maps to a command-line argument: `--generateProbability`.

> histogramEqualizationa boolean

>   A Histogram Equalization process could be added to the creating/applying process from Subject To Atlas. Default is false, which genreate input vectors without Histogram Equalization. . Maps to a command-line argument: `--histogramEqualization`.

> method‘RandomForest’ or ‘ANN’

>   Maps to a command-line argument: `--method %s`.

> modelConfigurationFilenamea pathlike object or string representing an existing file

>   XML File defining BRAINSCut parameters. Maps to a command-line argument: `--modelConfigurationFilename %s`.

> modelFilenamea unicode string

>   > model file name given from user (not by xml configuration file) .

>   Maps to a command-line argument: `--modelFilename %s`.

> multiStructureThresholda boolean

>   MultiStructureThreshold module to deal with overlaping area. Maps to a command-line argument: `--multiStructureThreshold`.

> netConfigurationa pathlike object or string representing an existing file

>   XML File defining BRAINSCut parameters. OLD NAME. PLEASE USE modelConfigurationFilename instead. Maps to a command-line argument: `--netConfiguration %s`.

> numberOfTreesan integer (int or long)

>   > Random tree: number of trees. This is to be used when only one model with specified depth wish to be created. .

>   Maps to a command-line argument: `--numberOfTrees %d`.

> randomTreeDepthan integer (int or long)

>   > Random tree depth. This is to be used when only one model with specified depth wish to be created. .

>   Maps to a command-line argument: `--randomTreeDepth %d`.

> trainModela boolean

>   Train the neural net. Maps to a command-line argument: `--trainModel`.

> trainModelStartIndexan integer (int or long)

>   Starting iteration for training. Maps to a command-line argument: `--trainModelStartIndex %d`.

> validatea boolean

>   Validate data set.Just need for the first time run ( This is for validation of xml file and not working yet ). Maps to a command-line argument: `--validate`.

> verbosean integer (int or long)

>   Print out some debugging information. Maps to a command-line argument: `--verbose %d`.

## BRAINSMultiSTAPLE

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSMultiSTAPLE`.

> title: Create best representative label map)

> category: Segmentation.Specialized

> description: given a list of label map images, create a representative/average label map.

> 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: `{}`)

> inputCompositeT1Volumea pathlike object or string representing an existing file

>   Composite T1, all label maps transofrmed into the space for this image. Maps to a command-line argument: `--inputCompositeT1Volume %s`.

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

>   The list of proobabilityimages. Maps to a command-line argument: `--inputLabelVolume %s...`.

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

>   Transforms to apply to label volumes. Maps to a command-line argument: `--inputTransform %s...`.

> labelForUndecidedPixelsan integer (int or long)

>   Label for undecided pixels. Maps to a command-line argument: `--labelForUndecidedPixels %d`.

> outputConfusionMatrixa boolean or a pathlike object or string representing a file

>   Confusion Matrix. Maps to a command-line argument: `--outputConfusionMatrix %s`.

> outputMultiSTAPLEa boolean or a pathlike object or string representing a file

>   The MultiSTAPLE average of input label volumes. Maps to a command-line argument: `--outputMultiSTAPLE %s`.

> resampledVolumePrefixa unicode string

>   If given, write out resampled volumes with this prefix. Maps to a command-line argument: `--resampledVolumePrefix %s`.

> skipResamplinga boolean

>   Omit resampling images into reference space. Maps to a command-line argument: `--skipResampling`.

> outputConfusionMatrixa pathlike object or string representing an existing file

>   Confusion Matrix.

> outputMultiSTAPLEa pathlike object or string representing an existing file

>   The MultiSTAPLE average of input label volumes.

## BRAINSROIAuto

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSROIAuto`.

> title: Foreground masking (BRAINS)

> category: Segmentation.Specialized

> description: This program is used to create a mask over the most prominant forground region in an image. This is accomplished via a combination of otsu thresholding and a closing operation. More documentation is available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ForegroundMasking.

> version: 2.4.1

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

> contributor: Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu

> acknowledgements: Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3); Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard)

> ROIAutoDilateSizea float

>   This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the final dilation size to capture a bit of background outside the tissue region. At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better. Maps to a command-line argument: `--ROIAutoDilateSize %f`.

> argsa unicode string

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

> closingSizea float

>   The Closing Size (in millimeters) for largest connected filled mask. This value is divided by image spacing and rounded to the next largest voxel number. Maps to a command-line argument: `--closingSize %f`.

> cropOutputa boolean

>   The inputVolume cropped to the region of the ROI mask. Maps to a command-line argument: `--cropOutput`.

> 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

>   The input image for finding the largest region filled mask. Maps to a command-line argument: `--inputVolume %s`.

> maskOutputa boolean

>   The inputVolume multiplied by the ROI mask. Maps to a command-line argument: `--maskOutput`.

> numberOfThreadsan integer (int or long)

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

> otsuPercentileThresholda float

>   Parameter to the Otsu threshold algorithm. Maps to a command-line argument: `--otsuPercentileThreshold %f`.

> outputROIMaskVolumea boolean or a pathlike object or string representing a file

>   The ROI automatically found from the input image. Maps to a command-line argument: `--outputROIMaskVolume %s`.

> outputVolumea boolean or a pathlike object or string representing a file

>   The inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumePixelType‘float’ or ‘short’ or ‘ushort’ or ‘int’ or ‘uint’ or ‘uchar’

>   The output image Pixel Type is the scalar datatype for representation of the Output Volume. Maps to a command-line argument: `--outputVolumePixelType %s`.

> thresholdCorrectionFactora float

>   A factor to scale the Otsu algorithm’s result threshold, in case clipping mangles the image. Maps to a command-line argument: `--thresholdCorrectionFactor %f`.

> outputROIMaskVolumea pathlike object or string representing an existing file

>   The ROI automatically found from the input image.

> outputVolumea pathlike object or string representing an existing file

>   The inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask.

## BinaryMaskEditorBasedOnLandmarks

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BinaryMaskEditorBasedOnLandmarks`.

> title: BRAINS Binary Mask Editor Based On Landmarks(BRAINS)

> category: Segmentation.Specialized

> version: 1.0

> documentation-url: http://www.nitrc.org/projects/brainscdetector/

> 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: `{}`)

> inputBinaryVolumea pathlike object or string representing an existing file

>   Input binary image in which to be edited. Maps to a command-line argument: `--inputBinaryVolume %s`.

> inputLandmarkNamesa list of items which are a unicode string

>   > A target input landmark name to be edited. This should be listed in the inputLandmakrFilename Given. .

>   Maps to a command-line argument: `--inputLandmarkNames %s`.

> inputLandmarkNamesForObliquePlanea list of items which are a unicode string

>   > Three subset landmark names of inputLandmarksFilename for a oblique plane computation. The plane computed for binary volume editing. .

>   Maps to a command-line argument: `--inputLandmarkNamesForObliquePlane %s`.

> inputLandmarksFilenamea pathlike object or string representing an existing file

>   > The filename for the landmark definition file in the same format produced by Slicer3 (.fcsv). .

>   Maps to a command-line argument: `--inputLandmarksFilename %s`.

> outputBinaryVolumea boolean or a pathlike object or string representing a file

>   Output binary image in which to be edited. Maps to a command-line argument: `--outputBinaryVolume %s`.

> setCutDirectionForLandmarka list of items which are a unicode string

>   Setting the cutting out direction of the input binary image to the one of anterior, posterior, left, right, superior or posterior. (ENUMERATION: ANTERIOR, POSTERIOR, LEFT, RIGHT, SUPERIOR, POSTERIOR) . Maps to a command-line argument: `--setCutDirectionForLandmark %s`.

> setCutDirectionForObliquePlanea list of items which are a unicode string

>   If this is true, the mask will be thresholded out to the direction of inferior, posterior, and/or left. Default behavrior is that cutting out to the direction of superior, anterior and/or right. . Maps to a command-line argument: `--setCutDirectionForObliquePlane %s`.

> outputBinaryVolumea pathlike object or string representing an existing file

>   Output binary image in which to be edited.

## ESLR

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `ESLR`.

> title: Clean Contiguous Label Map (BRAINS)

> category: Segmentation.Specialized

> description: From a range of label map values, extract the largest contiguous region of those labels

> argsa unicode string

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

> closingSizean integer (int or long)

>   The closing size for hole filling. Maps to a command-line argument: `--closingSize %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: `{}`)

> highan integer (int or long)

>   The higher bound of the labels to be used. Maps to a command-line argument: `--high %d`.

> inputVolumea pathlike object or string representing an existing file

>   Input Label Volume. Maps to a command-line argument: `--inputVolume %s`.

> lowan integer (int or long)

>   The lower bound of the labels to be used. Maps to a command-line argument: `--low %d`.

> numberOfThreadsan integer (int or long)

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

> openingSizean integer (int or long)

>   The opening size for hole filling. Maps to a command-line argument: `--openingSize %d`.

> outputVolumea boolean or a pathlike object or string representing a file

>   Output Label Volume. Maps to a command-line argument: `--outputVolume %s`.

> preserveOutsidea boolean

>   For values outside the specified range, preserve those values. Maps to a command-line argument: `--preserveOutside`.

> safetySizean integer (int or long)

>   The safetySize size for the clipping region. Maps to a command-line argument: `--safetySize %d`.

> outputVolumea pathlike object or string representing an existing file

>   Output Label Volume.