nipype.interfaces.semtools.utilities.brains module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
BRAINSAlignMSP¶
Bases: SEMLikeCommandLine
Wrapped executable:
BRAINSAlignMSP.title: Align Mid Sagittal Brain (BRAINS)
category: Utilities.BRAINS
description: Resample an image into ACPC alignment ACPCDetect
- Optional Inputs:
BackgroundFillValue (a 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.OutputresampleMSP (a boolean or a pathlike object or string representing a file) – , The image to be output., . Maps to a command-line argument:
--OutputresampleMSP %s.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputVolume (a 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.mspQualityLevel (an integer) – , Flag controls how aggressive 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.rescaleIntensities (a boolean) – , Flag to turn on rescaling image intensities on input., . Maps to a command-line argument:
--rescaleIntensities.rescaleIntensitiesOutputRange (a list of items which are an integer) – , 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.resultsDir (a 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.trimRescaledIntensities (a 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.verbose (a boolean) – , Show more verbose output, . Maps to a command-line argument:
--verbose.writedebuggingImagesLevel (an integer) – , 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.- Outputs:
OutputresampleMSP (a pathlike object or string representing an existing file) – , The image to be output., .
resultsDir (a pathlike object or string representing an existing directory) – , The directory for the results to be written., .
BRAINSClipInferior¶
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
- Optional Inputs:
BackgroundFillValue (a 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.acLowerBound (a 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.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputVolume (a 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a 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.- Outputs:
outputVolume (a 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¶
Bases: SEMLikeCommandLine
Wrapped executable:
BRAINSConstellationModeler.title: Generate Landmarks Model (BRAINS)
category: Utilities.BRAINS
description: Train up a model for BRAINSConstellationDetector
- Optional Inputs:
BackgroundFillValue (a 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.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputTrainingList (a 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.mspQualityLevel (an integer) – , Flag controls how aggressive 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.optimizedLandmarksFilenameExtender (a 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.outputModel (a 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.rescaleIntensities (a boolean) – , Flag to turn on rescaling image intensities on input., . Maps to a command-line argument:
--rescaleIntensities.rescaleIntensitiesOutputRange (a list of items which are an integer) – , 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.resultsDir (a 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.saveOptimizedLandmarks (a 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.trimRescaledIntensities (a 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.verbose (a boolean) – , Show more verbose output, . Maps to a command-line argument:
--verbose.writedebuggingImagesLevel (an integer) – , 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.- Outputs:
outputModel (a pathlike object or string representing an existing file) – , The full filename of the output model file., .
resultsDir (a pathlike object or string representing an existing directory) – , The directory for the results to be written., .
BRAINSEyeDetector¶
Bases: SEMLikeCommandLine
Wrapped executable:
BRAINSEyeDetector.title: Eye Detector (BRAINS)
category: Utilities.BRAINS
version: 1.0
documentation-url: http://www.nitrc.org/projects/brainscdetector/
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.debugDir (a string) – A place for debug information. Maps to a command-line argument:
--debugDir %s.environ (a 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:
{})inputVolume (a pathlike object or string representing an existing file) – The input volume. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – The output volume. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – The output volume.
BRAINSInitializedControlPoints¶
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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputVolume (a pathlike object or string representing an existing file) – Input Volume. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputLandmarksFile (a string) – Output filename. Maps to a command-line argument:
--outputLandmarksFile %s.outputVolume (a boolean or a pathlike object or string representing a file) – Output Volume. Maps to a command-line argument:
--outputVolume %s.permuteOrder (a list of items which are an integer) – The permutation order for the images. The default is 0,1,2 (i.e. no permutation). Maps to a command-line argument:
--permuteOrder %s.splineGridSize (a list of items which are an integer) – 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.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Output Volume.
BRAINSLandmarkInitializer¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputFixedLandmarkFilename (a pathlike object or string representing an existing file) – Input fixed landmark. *.fcsv. Maps to a command-line argument:
--inputFixedLandmarkFilename %s.inputMovingLandmarkFilename (a pathlike object or string representing an existing file) – Input moving landmark. *.fcsv. Maps to a command-line argument:
--inputMovingLandmarkFilename %s.inputWeightFilename (a pathlike object or string representing an existing file) – Input weight file name for landmarks. Higher weighted landmark will be considered more heavily. Weights are proportional, that is the magnitude of weights will be normalized by its minimum and maximum value. . Maps to a command-line argument:
--inputWeightFilename %s.outputTransformFilename (a 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.- Outputs:
outputTransformFilename (a pathlike object or string representing an existing file) – Output transform file name (ex: ./outputTransform.mat) .
BRAINSLinearModelerEPCA¶
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/
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputTrainingList (a pathlike object or string representing an existing file) – Input Training Landmark List Filename, . Maps to a command-line argument:
--inputTrainingList %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.
BRAINSLmkTransform¶
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/
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputFixedLandmarks (a pathlike object or string representing an existing file) – Input Fixed Landmark list file in fcsv, . Maps to a command-line argument:
--inputFixedLandmarks %s.inputMovingLandmarks (a pathlike object or string representing an existing file) – Input Moving Landmark list file in fcsv, . Maps to a command-line argument:
--inputMovingLandmarks %s.inputMovingVolume (a pathlike object or string representing an existing file) – The filename of input moving volume. Maps to a command-line argument:
--inputMovingVolume %s.inputReferenceVolume (a pathlike object or string representing an existing file) – The filename of the reference volume. Maps to a command-line argument:
--inputReferenceVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputAffineTransform (a 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.outputResampledVolume (a 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.- Outputs:
outputAffineTransform (a pathlike object or string representing an existing file) – The filename for the estimated affine transform, .
outputResampledVolume (a pathlike object or string representing an existing file) – The filename of the output resampled volume.
BRAINSMush¶
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.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.boundingBoxSize (a list of items which are an integer) – Size of the cubic bounding box mask used when no brain mask is present. Maps to a command-line argument:
--boundingBoxSize %s.boundingBoxStart (a list of items which are an integer) – 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.desiredMean (a float) – Desired mean within the mask for weighted sum of both images. Maps to a command-line argument:
--desiredMean %f.desiredVariance (a float) – Desired variance within the mask for weighted sum of both images. Maps to a command-line argument:
--desiredVariance %f.environ (a 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:
{})inputFirstVolume (a pathlike object or string representing an existing file) – Input image (1) for mixture optimization. Maps to a command-line argument:
--inputFirstVolume %s.inputMaskVolume (a pathlike object or string representing an existing file) – Input label image for mixture optimization. Maps to a command-line argument:
--inputMaskVolume %s.inputSecondVolume (a pathlike object or string representing an existing file) – Input image (2) for mixture optimization. Maps to a command-line argument:
--inputSecondVolume %s.lowerThresholdFactor (a float) – Lower threshold factor for defining the brain mask. Maps to a command-line argument:
--lowerThresholdFactor %f.lowerThresholdFactorPre (a float) – Lower threshold factor for finding an initial brain mask. Maps to a command-line argument:
--lowerThresholdFactorPre %f.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputMask (a 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.outputVolume (a 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.outputWeightsFile (a boolean or a pathlike object or string representing a file) – Output Weights File. Maps to a command-line argument:
--outputWeightsFile %s.seed (a list of items which are an integer) – Seed Point for Brain Region Filling. Maps to a command-line argument:
--seed %s.upperThresholdFactor (a float) – Upper threshold factor for defining the brain mask. Maps to a command-line argument:
--upperThresholdFactor %f.upperThresholdFactorPre (a float) – Upper threshold factor for finding an initial brain mask. Maps to a command-line argument:
--upperThresholdFactorPre %f.- Outputs:
outputMask (a pathlike object or string representing an existing file) – The brain volume mask generated from the MUSH image.
outputVolume (a pathlike object or string representing an existing file) – The MUSH image produced from the T1 and T2 weighted images.
outputWeightsFile (a pathlike object or string representing an existing file) – Output Weights File.
BRAINSSnapShotWriter¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputBinaryVolumes (a 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....inputPlaneDirection (a list of items which are an integer) – Plane to display. In general, 0=sagittal, 1=coronal, and 2=axial plane. Maps to a command-line argument:
--inputPlaneDirection %s.inputSliceToExtractInIndex (a list of items which are an integer) – 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.inputSliceToExtractInPercent (a list of items which are an integer) – 2D slice number of input images. Percentage input from 0%-100%. (ex. –inputSliceToExtractInPercent 50,50,50. Maps to a command-line argument:
--inputSliceToExtractInPercent %s.inputSliceToExtractInPhysicalPoint (a 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.inputVolumes (a 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....outputFilename (a 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.- Outputs:
outputFilename (a pathlike object or string representing an existing file) – 2D file name of input images. Required.
BRAINSTransformConvert¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.displacementVolume (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--displacementVolume %s.environ (a 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:
{})inputTransform (a 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.outputTransform (a 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.referenceVolume (a pathlike object or string representing an existing file) – Maps to a command-line argument:
--referenceVolume %s.- Outputs:
displacementVolume (a pathlike object or string representing an existing file)
outputTransform (a pathlike object or string representing an existing file)
BRAINSTrimForegroundInDirection¶
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/
- Optional Inputs:
BackgroundFillValue (a 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.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.closingSize (an integer) – , This is a parameter to FindLargestForegroundFilledMask, . Maps to a command-line argument:
--closingSize %d.directionCode (an integer) – , This flag chooses which dimension to compare. The sign lets you flip direction., . Maps to a command-line argument:
--directionCode %d.environ (a 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:
{})headSizeLimit (a 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.inputVolume (a 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.otsuPercentileThreshold (a float) – , This is a parameter to FindLargestForegroundFilledMask, which is employed to trim off air-filling noise., . Maps to a command-line argument:
--otsuPercentileThreshold %f.outputVolume (a 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.- Outputs:
outputVolume (a 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¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputBinaryVolumes (a 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....outputBinaryVolumes (a 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....- Outputs:
outputBinaryVolumes (a 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¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.axis (an integer) – Maps to a command-line argument:
--axis %d.backgroundValue (an integer) – Maps to a command-line argument:
--backgroundValue %d.clippedImageMask (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--clippedImageMask %s.closingSize (an integer) – Maps to a command-line argument:
--closingSize %d.debugAfterGridComputationsForegroundImage (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--debugAfterGridComputationsForegroundImage %s.debugClippedImageMask (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--debugClippedImageMask %s.debugDistanceImage (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--debugDistanceImage %s.debugGridImage (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--debugGridImage %s.debugTrimmedImage (a boolean or a pathlike object or string representing a file) – Maps to a command-line argument:
--debugTrimmedImage %s.environ (a 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:
{})generateDebugImages (a boolean) – Maps to a command-line argument:
--generateDebugImages.headSizeEstimate (a float) – Maps to a command-line argument:
--headSizeEstimate %f.headSizeLimit (a float) – Maps to a command-line argument:
--headSizeLimit %f.imageMask (a pathlike object or string representing an existing file) – Maps to a command-line argument:
--imageMask %s.inputVolume (a pathlike object or string representing an existing file) – The image in which to find the center. Maps to a command-line argument:
--inputVolume %s.maximize (a boolean) – Maps to a command-line argument:
--maximize.otsuPercentileThreshold (a float) – Maps to a command-line argument:
--otsuPercentileThreshold %f.- Outputs:
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¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputVolumes (a list of items which are a pathlike object or string representing an existing file) – The Input probaiblity images to be computed for label maps. Maps to a command-line argument:
--inputVolumes %s....numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputLabelVolume (a 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.- Outputs:
outputLabelVolume (a pathlike object or string representing an existing file) – The Input binary image for region of interest.
ImageRegionPlotter¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputBinaryROIVolume (a pathlike object or string representing an existing file) – The Input binary image for region of interest. Maps to a command-line argument:
--inputBinaryROIVolume %s.inputLabelVolume (a pathlike object or string representing an existing file) – The Label Image. Maps to a command-line argument:
--inputLabelVolume %s.inputVolume1 (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--inputVolume1 %s.inputVolume2 (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--inputVolume2 %s.numberOfHistogramBins (an integer) – the number of histogram levels. Maps to a command-line argument:
--numberOfHistogramBins %d.outputJointHistogramData (a string) – output data file name. Maps to a command-line argument:
--outputJointHistogramData %s.useIntensityForHistogram (a boolean) – Create Intensity Joint Histogram instead of Quantile Joint Histogram. Maps to a command-line argument:
--useIntensityForHistogram.useROIAUTO (a boolean) – Use ROIAUTO to compute region of interest. This cannot be used with inputLabelVolume. Maps to a command-line argument:
--useROIAUTO.verbose (a boolean) – print debugging information, . Maps to a command-line argument:
--verbose.
JointHistogram¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputMaskVolumeInXAxis (a 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.inputMaskVolumeInYAxis (a 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.inputVolumeInXAxis (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--inputVolumeInXAxis %s.inputVolumeInYAxis (a pathlike object or string representing an existing file) – The Input image to be computed for statistics. Maps to a command-line argument:
--inputVolumeInYAxis %s.outputJointHistogramImage (a string) – output joint histogram image file name. Histogram is usually 2D image. . Maps to a command-line argument:
--outputJointHistogramImage %s.verbose (a boolean) – print debugging information, . Maps to a command-line argument:
--verbose.
ShuffleVectorsModule¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputVectorFileBaseName (a 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.outputVectorFileBaseName (a 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.resampleProportion (a 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.- Outputs:
outputVectorFileBaseName (a 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¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})landmarkGlobPattern (a string) – Glob pattern to select fcsv files. Maps to a command-line argument:
--landmarkGlobPattern %s.landmarkTypesList (a pathlike object or string representing an existing file) – , file containing list of landmark types, . Maps to a command-line argument:
--landmarkTypesList %s.landmarksInformationFile (a 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.modelFile (a 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.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.versionID (a 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.- Outputs:
landmarksInformationFile (a pathlike object or string representing an existing file) – , name of HDF5 file to write matrices into, .
modelFile (a pathlike object or string representing an existing file) – , name of HDF5 file containing BRAINSConstellationDetector Model file (LLSMatrices, LLSMeans and LLSSearchRadii), .
insertMidACPCpoint¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputLandmarkFile (a pathlike object or string representing an existing file) – Input landmark file (.fcsv). Maps to a command-line argument:
--inputLandmarkFile %s.outputLandmarkFile (a boolean or a pathlike object or string representing a file) – Output landmark file (.fcsv). Maps to a command-line argument:
--outputLandmarkFile %s.- Outputs:
outputLandmarkFile (a pathlike object or string representing an existing file) – Output landmark file (.fcsv).
landmarksConstellationAligner¶
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
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputLandmarksPaired (a pathlike object or string representing an existing file) – Input landmark file (.fcsv). Maps to a command-line argument:
--inputLandmarksPaired %s.outputLandmarksPaired (a boolean or a pathlike object or string representing a file) – Output landmark file (.fcsv). Maps to a command-line argument:
--outputLandmarksPaired %s.- Outputs:
outputLandmarksPaired (a pathlike object or string representing an existing file) – Output landmark file (.fcsv).
landmarksConstellationWeights¶
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
- Optional Inputs:
LLSModel (a pathlike object or string representing an existing file) – Linear least squares model filename in HD5 format. Maps to a command-line argument:
--LLSModel %s.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})inputTemplateModel (a pathlike object or string representing an existing file) – User-specified template model., . Maps to a command-line argument:
--inputTemplateModel %s.inputTrainingList (a 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.outputWeightsList (a 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.- Outputs:
outputWeightsList (a pathlike object or string representing an existing file) – , The filename of a csv file which is a list of landmarks and their corresponding weights., .