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# nipype.interfaces.semtools.utilities.brains module

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## BRAINSAlignMSP

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSAlignMSP`.

> title: Align Mid Saggital Brain (BRAINS)

> category: Utilities.BRAINS

> description: Resample an image into ACPC alignement ACPCDetect

> 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`.

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

>   , The image to be output., . Maps to a command-line argument: `--OutputresampleMSP %s`.

> 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: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   , The Image to be resampled, . 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)., . 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`.

> 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 results to be written., . Maps to a command-line argument: `--resultsDir %s`.

> 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`.

> 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`.

> OutputresampleMSPa pathlike object or string representing an existing file

>   , The image to be output., .

> resultsDira pathlike object or string representing an existing directory

>   , The directory for the results to be written., .

## BRAINSClipInferior

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSClipInferior`.

> title: Clip Inferior of Center of Brain (BRAINS)

> category: Utilities.BRAINS

> description: This program will read the inputVolume as a short int image, write the BackgroundFillValue everywhere inferior to the lower bound, and write the resulting clipped short int image in the outputVolume.

> version: 1.0

> 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`.

> acLowerBounda float

>   , When the input image to the output image, replace the image with the BackgroundFillValue everywhere below the plane This Far in physical units (millimeters) below (inferior to) the AC point (assumed to be the voxel field middle.) 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`.

> 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 image to make a clipped short int copy from. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer (int or long)

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

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

>   Output image, a short int copy of the upper portion of the input image, filled with BackgroundFillValue. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Output image, a short int copy of the upper portion of the input image, filled with BackgroundFillValue.

## BRAINSConstellationModeler

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSConstellationModeler`.

> title: Generate Landmarks Model (BRAINS)

> category: Utilities.BRAINS

> description: Train up a model for BRAINSConstellationDetector

> 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`.

> 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: `{}`)

> inputTrainingLista pathlike object or string representing an existing file

>   , Setup file, giving all parameters for training up a template model for each landmark., . Maps to a command-line argument: `--inputTrainingList %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)., . 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`.

> optimizedLandmarksFilenameExtendera unicode string

>   , If the trainingList is (indexFullPathName) and contains landmark data filenames [path]/[filename].fcsv , make the optimized landmarks filenames out of [path]/[filename](thisExtender) and the optimized version of the input trainingList out of (indexFullPathName)(thisExtender) , when you rewrite all the landmarks according to the saveOptimizedLandmarks flag., . Maps to a command-line argument: `--optimizedLandmarksFilenameExtender %s`.

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

>   , The full filename of the output model file., . Maps to a command-line argument: `--outputModel %s`.

> 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 results to be written., . Maps to a command-line argument: `--resultsDir %s`.

> saveOptimizedLandmarksa boolean

>   , Flag to make a new subject-specific landmark definition file in the same format produced by Slicer3 with the optimized landmark (the detected RP, AC, and PC) in it. Useful to tighten the variances in the ConstellationModeler., . Maps to a command-line argument: `--saveOptimizedLandmarks`.

> 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`.

> 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`.

> outputModela pathlike object or string representing an existing file

>   , The full filename of the output model file., .

> resultsDira pathlike object or string representing an existing directory

>   , The directory for the results to be written., .

## BRAINSEyeDetector

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSEyeDetector`.

> title: Eye Detector (BRAINS)

> category: Utilities.BRAINS

> 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`.

> debugDira unicode string

>   A place for debug information. Maps to a command-line argument: `--debugDir %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

>   The input volume. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer (int or long)

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

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

>   The output volume. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   The output volume.

## BRAINSInitializedControlPoints

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSInitializedControlPoints`.

> title: Initialized Control Points (BRAINS)

> category: Utilities.BRAINS

> description: Outputs bspline control points as landmarks

> version: 0.1.0.$Revision: 916 $(alpha)

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

> contributor: Mark Scully

> acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for Mark Scully and Hans Johnson at the University of Iowa.

> 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: `{}`)

> inputVolumea pathlike object or string representing an existing file

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

> numberOfThreadsan integer (int or long)

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

> outputLandmarksFilea unicode string

>   Output filename. Maps to a command-line argument: `--outputLandmarksFile %s`.

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

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

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

>   The permutation order for the images. The default is 0,1,2 (i.e. no permutation). Maps to a command-line argument: `--permuteOrder %s`.

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

>   The number of subdivisions of the BSpline Grid to be centered on the image space. Each dimension must have at least 3 subdivisions for the BSpline to be correctly computed. . Maps to a command-line argument: `--splineGridSize %s`.

> outputVolumea pathlike object or string representing an existing file

>   Output Volume.

## BRAINSLandmarkInitializer

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSLandmarkInitializer`.

> title: BRAINSLandmarkInitializer

> category: Utilities.BRAINS

> description: Create transformation file (*mat) from a pair of landmarks (*fcsv) files.

> version: 1.0

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

> contributor: Eunyoung Regina Kim

> 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: `{}`)

> inputFixedLandmarkFilenamea pathlike object or string representing an existing file

>   Input fixed landmark. *.fcsv. Maps to a command-line argument: `--inputFixedLandmarkFilename %s`.

> inputMovingLandmarkFilenamea pathlike object or string representing an existing file

>   Input moving landmark. *.fcsv. Maps to a command-line argument: `--inputMovingLandmarkFilename %s`.

> inputWeightFilenamea pathlike object or string representing an existing file

>   Input weight file name for landmarks. Higher weighted landmark will be considered more heavily. Weights are propotional, that is the magnitude of weights will be normalized by its minimum and maximum value. . Maps to a command-line argument: `--inputWeightFilename %s`.

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

>   Output transform file name (ex: ./outputTransform.mat) . Maps to a command-line argument: `--outputTransformFilename %s`.

> outputTransformFilenamea pathlike object or string representing an existing file

>   Output transform file name (ex: ./outputTransform.mat) .

## BRAINSLinearModelerEPCA

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSLinearModelerEPCA`.

> title: Landmark Linear Modeler (BRAINS)

> category: Utilities.BRAINS

> description: Training linear model using EPCA. Implementation based on my MS thesis, “A METHOD FOR AUTOMATED LANDMARK CONSTELLATION DETECTION USING EVOLUTIONARY PRINCIPAL COMPONENTS AND STATISTICAL SHAPE MODELS”

> 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: `{}`)

> inputTrainingLista pathlike object or string representing an existing file

>   Input Training Landmark List Filename, . Maps to a command-line argument: `--inputTrainingList %s`.

> numberOfThreadsan integer (int or long)

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

## BRAINSLmkTransform

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSLmkTransform`.

> title: Landmark Transform (BRAINS)

> category: Utilities.BRAINS

> description: This utility program estimates the affine transform to align the fixed landmarks to the moving landmarks, and then generate the resampled moving image to the same physical space as that of the reference image.

> 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: `{}`)

> inputFixedLandmarksa pathlike object or string representing an existing file

>   Input Fixed Landmark list file in fcsv, . Maps to a command-line argument: `--inputFixedLandmarks %s`.

> inputMovingLandmarksa pathlike object or string representing an existing file

>   Input Moving Landmark list file in fcsv, . Maps to a command-line argument: `--inputMovingLandmarks %s`.

> inputMovingVolumea pathlike object or string representing an existing file

>   The filename of input moving volume. Maps to a command-line argument: `--inputMovingVolume %s`.

> inputReferenceVolumea pathlike object or string representing an existing file

>   The filename of the reference volume. Maps to a command-line argument: `--inputReferenceVolume %s`.

> numberOfThreadsan integer (int or long)

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

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

>   The filename for the estimated affine transform, . Maps to a command-line argument: `--outputAffineTransform %s`.

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

>   The filename of the output resampled volume. Maps to a command-line argument: `--outputResampledVolume %s`.

> outputAffineTransforma pathlike object or string representing an existing file

>   The filename for the estimated affine transform, .

> outputResampledVolumea pathlike object or string representing an existing file

>   The filename of the output resampled volume.

## BRAINSMush

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSMush`.

> title: Brain Extraction from T1/T2 image (BRAINS)

> category: Utilities.BRAINS

> description: This program: 1) generates a weighted mixture image optimizing the mean and variance and 2) produces a mask of the brain volume

> version: 0.1.0.$Revision: 1.4 $(alpha)

> documentation-url: http:://mri.radiology.uiowa.edu

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

> contributor: This tool is a modification by Steven Dunn of a program developed by Greg Harris and Ron Pierson.

> acknowledgements: This work was developed by the University of Iowa Departments of Radiology and Psychiatry. This software was supported in part of NIH/NINDS award NS050568.

> argsa unicode string

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

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

>   Size of the cubic bounding box mask used when no brain mask is present. Maps to a command-line argument: `--boundingBoxSize %s`.

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

>   XYZ point-coordinate for the start of the cubic bounding box mask used when no brain mask is present. Maps to a command-line argument: `--boundingBoxStart %s`.

> desiredMeana float

>   Desired mean within the mask for weighted sum of both images. Maps to a command-line argument: `--desiredMean %f`.

> desiredVariancea float

>   Desired variance within the mask for weighted sum of both images. Maps to a command-line argument: `--desiredVariance %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: `{}`)

> inputFirstVolumea pathlike object or string representing an existing file

>   Input image (1) for mixture optimization. Maps to a command-line argument: `--inputFirstVolume %s`.

> inputMaskVolumea pathlike object or string representing an existing file

>   Input label image for mixture optimization. Maps to a command-line argument: `--inputMaskVolume %s`.

> inputSecondVolumea pathlike object or string representing an existing file

>   Input image (2) for mixture optimization. Maps to a command-line argument: `--inputSecondVolume %s`.

> lowerThresholdFactora float

>   Lower threshold factor for defining the brain mask. Maps to a command-line argument: `--lowerThresholdFactor %f`.

> lowerThresholdFactorPrea float

>   Lower threshold factor for finding an initial brain mask. Maps to a command-line argument: `--lowerThresholdFactorPre %f`.

> numberOfThreadsan integer (int or long)

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

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

>   The brain volume mask generated from the MUSH image. Maps to a command-line argument: `--outputMask %s`.

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

>   The MUSH image produced from the T1 and T2 weighted images. Maps to a command-line argument: `--outputVolume %s`.

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

>   Output Weights File. Maps to a command-line argument: `--outputWeightsFile %s`.

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

>   Seed Point for Brain Region Filling. Maps to a command-line argument: `--seed %s`.

> upperThresholdFactora float

>   Upper threshold factor for defining the brain mask. Maps to a command-line argument: `--upperThresholdFactor %f`.

> upperThresholdFactorPrea float

>   Upper threshold factor for finding an initial brain mask. Maps to a command-line argument: `--upperThresholdFactorPre %f`.

> outputMaska pathlike object or string representing an existing file

>   The brain volume mask generated from the MUSH image.

> outputVolumea pathlike object or string representing an existing file

>   The MUSH image produced from the T1 and T2 weighted images.

> outputWeightsFilea pathlike object or string representing an existing file

>   Output Weights File.

## BRAINSSnapShotWriter

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSSnapShotWriter`.

> title: BRAINSSnapShotWriter

> category: Utilities.BRAINS

> description: Create 2D snapshot of input images. Mask images are color-coded

> version: 1.0

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

> contributor: Eunyoung Regina Kim

> 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: `{}`)

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

>   Input mask (binary) volume list to be extracted as 2D image. Multiple input is possible. Maps to a command-line argument: `--inputBinaryVolumes %s...`.

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

>   Plane to display. In general, 0=saggital, 1=coronal, and 2=axial plane. Maps to a command-line argument: `--inputPlaneDirection %s`.

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

>   2D slice number of input images. For size of 256*256*256 image, 128 is usually used. Maps to a command-line argument: `--inputSliceToExtractInIndex %s`.

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

>   2D slice number of input images. Percentage input from 0%-100%. (ex. –inputSliceToExtractInPercent 50,50,50. Maps to a command-line argument: `--inputSliceToExtractInPercent %s`.

> inputSliceToExtractInPhysicalPointa list of items which are a float

>   2D slice number of input images. For autoWorkUp output, which AC-PC aligned, 0,0,0 will be the center. Maps to a command-line argument: `--inputSliceToExtractInPhysicalPoint %s`.

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

>   Input image volume list to be extracted as 2D image. Multiple input is possible. At least one input is required. Maps to a command-line argument: `--inputVolumes %s...`.

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

>   2D file name of input images. Required. Maps to a command-line argument: `--outputFilename %s`.

> outputFilenamea pathlike object or string representing an existing file

>   2D file name of input images. Required.

## BRAINSTransformConvert

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSTransformConvert`.

> title: BRAINS Transform Convert

> category: Utilities.BRAINS

> description: Convert ITK transforms to higher order transforms

> version: 1.0

> documentation-url: A utility to convert between transform file formats.

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

> contributor: Hans J. Johnson,Kent Williams, Ali Ghayoor

> argsa unicode string

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

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

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

> inputTransforma pathlike object or string representing an existing file

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

> outputPrecisionType‘double’ or ‘float’

>   Precision type of the output transform. It can be either single precision or double precision. Maps to a command-line argument: `--outputPrecisionType %s`.

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

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

> outputTransformType‘Affine’ or ‘VersorRigid’ or ‘ScaleVersor’ or ‘ScaleSkewVersor’ or ‘DisplacementField’ or ‘Same’

>   The target transformation type. Must be conversion-compatible with the input transform type. Maps to a command-line argument: `--outputTransformType %s`.

> referenceVolumea pathlike object or string representing an existing file

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

> displacementVolume : a pathlike object or string representing an existing file outputTransform : a pathlike object or string representing an existing file

## BRAINSTrimForegroundInDirection

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `BRAINSTrimForegroundInDirection`.

> title: Trim Foreground In Direction (BRAINS)

> category: Utilities.BRAINS

> description: This program will trim off the neck and also air-filling noise from the inputImage.

> version: 0.1

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

> 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`.

> argsa unicode string

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

> closingSizean integer (int or long)

>   , This is a parameter to FindLargestForegroundFilledMask, . Maps to a command-line argument: `--closingSize %d`.

> directionCodean integer (int or long)

>   , This flag chooses which dimension to compare. The sign lets you flip direction., . Maps to a command-line argument: `--directionCode %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: `{}`)

> headSizeLimita float

>   , Use this to vary from the command line our search for how much upper tissue is head for the center-of-mass calculation. Units are CCs, not cubic millimeters., . Maps to a command-line argument: `--headSizeLimit %f`.

> inputVolumea pathlike object or string representing an existing file

>   Input image to trim off the neck (and also air-filling noise.). Maps to a command-line argument: `--inputVolume %s`.

> 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 to trim off air-filling noise., . Maps to a command-line argument: `--otsuPercentileThreshold %f`.

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

>   Output image with neck and air-filling noise trimmed isotropic image with AC at center of image. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Output image with neck and air-filling noise trimmed isotropic image with AC at center of image.

## CleanUpOverlapLabels

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `CleanUpOverlapLabels`.

> title: Clean Up Overla Labels

> category: Utilities.BRAINS

> description: Take a series of input binary images and clean up for those overlapped area. Binary volumes given first always wins out

> version: 0.1.0

> contributor: Eun Young Kim

> 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: `{}`)

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

>   The list of binary images to be checked and cleaned up. Order is important. Binary volume given first always wins out. . Maps to a command-line argument: `--inputBinaryVolumes %s...`.

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

>   The output label map images, with integer values in it. Each label value specified in the inputLabels is combined into this output label map volume. Maps to a command-line argument: `--outputBinaryVolumes %s...`.

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

>   The output label map images, with integer values in it. Each label value specified in the inputLabels is combined into this output label map volume.

## FindCenterOfBrain

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `FindCenterOfBrain`.

> title: Center Of Brain (BRAINS)

> category: Utilities.BRAINS

> description: Finds the center point of a brain

> version: 3.0.0

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

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

> acknowledgements: Hans Johnson(1,3,4); Kent Williams(1); (1=University of Iowa Department of Psychiatry, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering

> argsa unicode string

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

> axisan integer (int or long)

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

> backgroundValuean integer (int or long)

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

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

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

> closingSizean integer (int or long)

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

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

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

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

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

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

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

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

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

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

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

> generateDebugImagesa boolean

>   Maps to a command-line argument: `--generateDebugImages`.

> headSizeEstimatea float

>   Maps to a command-line argument: `--headSizeEstimate %f`.

> headSizeLimita float

>   Maps to a command-line argument: `--headSizeLimit %f`.

> imageMaska pathlike object or string representing an existing file

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

> inputVolumea pathlike object or string representing an existing file

>   The image in which to find the center. Maps to a command-line argument: `--inputVolume %s`.

> maximizea boolean

>   Maps to a command-line argument: `--maximize`.

> otsuPercentileThresholda float

>   Maps to a command-line argument: `--otsuPercentileThreshold %f`.

> clippedImageMask : a pathlike object or string representing an existing file debugAfterGridComputationsForegroundImage : a pathlike object or string representing an existing file debugClippedImageMask : a pathlike object or string representing an existing file debugDistanceImage : a pathlike object or string representing an existing file debugGridImage : a pathlike object or string representing an existing file debugTrimmedImage : a pathlike object or string representing an existing file

## GenerateLabelMapFromProbabilityMap

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `GenerateLabelMapFromProbabilityMap`.

> title: Label Map from Probability Images

> category: Utilities.BRAINS

> description: Given a list of probability maps for labels, create a discrete label map where only the highest probability region is used for the labeling.

> 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: `{}`)

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

>   The Input probaiblity images to be computed for lable maps. Maps to a command-line argument: `--inputVolumes %s...`.

> numberOfThreadsan integer (int or long)

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

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

>   The Input binary image for region of interest. Maps to a command-line argument: `--outputLabelVolume %s`.

> outputLabelVolumea pathlike object or string representing an existing file

>   The Input binary image for region of interest.

## ImageRegionPlotter

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `ImageRegionPlotter`.

> title: Write Out Image Intensities

> category: Utilities.BRAINS

> 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: `{}`)

> inputBinaryROIVolumea pathlike object or string representing an existing file

>   The Input binary image for region of interest. Maps to a command-line argument: `--inputBinaryROIVolume %s`.

> inputLabelVolumea pathlike object or string representing an existing file

>   The Label Image. Maps to a command-line argument: `--inputLabelVolume %s`.

> inputVolume1a pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--inputVolume1 %s`.

> inputVolume2a pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--inputVolume2 %s`.

> numberOfHistogramBinsan integer (int or long)

>   > the number of histogram levels.

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

> outputJointHistogramDataa unicode string

>   > output data file name.

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

> useIntensityForHistograma boolean

>   > Create Intensity Joint Histogram instead of Quantile Joint Histogram.

>   Maps to a command-line argument: `--useIntensityForHistogram`.

> useROIAUTOa boolean

>   > Use ROIAUTO to compute region of interest. This cannot be used with inputLabelVolume.

>   Maps to a command-line argument: `--useROIAUTO`.

> verbosea boolean

>   > print debugging information, .

>   Maps to a command-line argument: `--verbose`.

## JointHistogram

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `JointHistogram`.

> title: Write Out Image Intensities

> category: Utilities.BRAINS

> 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: `{}`)

> inputMaskVolumeInXAxisa pathlike object or string representing an existing file

>   Input mask volume for inputVolumeInXAxis. Histogram will be computed just for the masked region. Maps to a command-line argument: `--inputMaskVolumeInXAxis %s`.

> inputMaskVolumeInYAxisa pathlike object or string representing an existing file

>   Input mask volume for inputVolumeInYAxis. Histogram will be computed just for the masked region. Maps to a command-line argument: `--inputMaskVolumeInYAxis %s`.

> inputVolumeInXAxisa pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--inputVolumeInXAxis %s`.

> inputVolumeInYAxisa pathlike object or string representing an existing file

>   The Input image to be computed for statistics. Maps to a command-line argument: `--inputVolumeInYAxis %s`.

> outputJointHistogramImagea unicode string

>   > output joint histogram image file name. Histogram is usually 2D image. .

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

> verbosea boolean

>   > print debugging information, .

>   Maps to a command-line argument: `--verbose`.

## ShuffleVectorsModule

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `ShuffleVectorsModule`.

> title: ShuffleVectors

> category: Utilities.BRAINS

> description: Automatic Segmentation using neural networks

> version: 1.0

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

> contributor: Hans Johnson

> 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: `{}`)

> inputVectorFileBaseNamea pathlike object or string representing an existing file

>   Input vector file name prefix. Usually end with .txt and header file has prost fix of .txt.hdr. Maps to a command-line argument: `--inputVectorFileBaseName %s`.

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

>   Output vector file name prefix. Usually end with .txt and header file has prost fix of .txt.hdr. Maps to a command-line argument: `--outputVectorFileBaseName %s`.

> resampleProportiona float

>   Downsample size of 1 will be the same size as the input images, downsample size of 3 will throw 2/3 the vectors away. Maps to a command-line argument: `--resampleProportion %f`.

> outputVectorFileBaseNamea pathlike object or string representing an existing file

>   Output vector file name prefix. Usually end with .txt and header file has prost fix of .txt.hdr.

## fcsv_to_hdf5

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `fcsv_to_hdf5`.

> title: fcsv_to_hdf5 (BRAINS)

> category: Utilities.BRAINS

> description: Convert a collection of fcsv files to a HDF5 format file

> 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: `{}`)

> landmarkGlobPatterna unicode string

>   Glob pattern to select fcsv files. Maps to a command-line argument: `--landmarkGlobPattern %s`.

> landmarkTypesLista pathlike object or string representing an existing file

>   , file containing list of landmark types, . Maps to a command-line argument: `--landmarkTypesList %s`.

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

>   , name of HDF5 file to write matrices into, . Maps to a command-line argument: `--landmarksInformationFile %s`.

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

>   , name of HDF5 file containing BRAINSConstellationDetector Model file (LLSMatrices, LLSMeans and LLSSearchRadii), . Maps to a command-line argument: `--modelFile %s`.

> numberOfThreadsan integer (int or long)

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

> versionIDa unicode string

>   , Current version ID. It should be match with the version of BCD that will be using the output model file, . Maps to a command-line argument: `--versionID %s`.

> landmarksInformationFilea pathlike object or string representing an existing file

>   , name of HDF5 file to write matrices into, .

> modelFilea pathlike object or string representing an existing file

>   , name of HDF5 file containing BRAINSConstellationDetector Model file (LLSMatrices, LLSMeans and LLSSearchRadii), .

## insertMidACPCpoint

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `insertMidACPCpoint`.

> title: MidACPC Landmark Insertion

> category: Utilities.BRAINS

> description: This program gets a landmark fcsv file and adds a new landmark as the midpoint between AC and PC points to the output landmark fcsv file

> 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: `{}`)

> inputLandmarkFilea pathlike object or string representing an existing file

>   Input landmark file (.fcsv). Maps to a command-line argument: `--inputLandmarkFile %s`.

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

>   Output landmark file (.fcsv). Maps to a command-line argument: `--outputLandmarkFile %s`.

> outputLandmarkFilea pathlike object or string representing an existing file

>   Output landmark file (.fcsv).

## landmarksConstellationAligner

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `landmarksConstellationAligner`.

> title: MidACPC Landmark Insertion

> category: Utilities.BRAINS

> description: This program converts the original landmark files to the acpc-aligned landmark files

> 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: `{}`)

> inputLandmarksPaireda pathlike object or string representing an existing file

>   Input landmark file (.fcsv). Maps to a command-line argument: `--inputLandmarksPaired %s`.

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

>   Output landmark file (.fcsv). Maps to a command-line argument: `--outputLandmarksPaired %s`.

> outputLandmarksPaireda pathlike object or string representing an existing file

>   Output landmark file (.fcsv).

## landmarksConstellationWeights

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `landmarksConstellationWeights`.

> title: Generate Landmarks Weights (BRAINS)

> category: Utilities.BRAINS

> description: Train up a list of Weights for the Landmarks in BRAINSConstellationDetector

> 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`.

> 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: `{}`)

> inputTemplateModela pathlike object or string representing an existing file

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

> inputTrainingLista pathlike object or string representing an existing file

>   , Setup file, giving all parameters for training up a Weight list for landmark., . Maps to a command-line argument: `--inputTrainingList %s`.

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

>   , The filename of a csv file which is a list of landmarks and their corresponding weights., . Maps to a command-line argument: `--outputWeightsList %s`.

> outputWeightsLista pathlike object or string representing an existing file

>   , The filename of a csv file which is a list of landmarks and their corresponding weights., .