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# nipype.interfaces.semtools.diffusion.gtract module

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## compareTractInclusion

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `compareTractInclusion`.

> title: Compare Tracts

> category: Diffusion.GTRACT

> description: This program will halt with a status code indicating whether a test tract is nearly enough included in a standard tract in the sense that every fiber in the test tract has a low enough sum of squares distance to some fiber in the standard tract modulo spline resampling of every fiber to a fixed number of points.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> closenessa float

>   Closeness of every test fiber to some fiber in the standard tract, computed as a sum of squares of spatial differences of standard points. Maps to a command-line argument: `--closeness %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: `{}`)

> numberOfPointsan integer

>   Number of points in comparison fiber pairs. Maps to a command-line argument: `--numberOfPoints %d`.

> numberOfThreadsan integer

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

> standardFibera pathlike object or string representing an existing file

>   Required: standard fiber tract file name. Maps to a command-line argument: `--standardFiber %s`.

> testFibera pathlike object or string representing an existing file

>   Required: test fiber tract file name. Maps to a command-line argument: `--testFiber %s`.

> testForBijectiona boolean

>   Flag to apply the closeness criterion both ways. Maps to a command-line argument: `--testForBijection`.

> testForFiberCardinalitya boolean

>   Flag to require the same number of fibers in both tracts. Maps to a command-line argument: `--testForFiberCardinality`.

> writeXMLPolyDataFilea boolean

>   Flag to make use of XML files when reading and writing vtkPolyData. Maps to a command-line argument: `--writeXMLPolyDataFile`.

## extractNrrdVectorIndex

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `extractNrrdVectorIndex`.

> title: Extract Nrrd Index

> category: Diffusion.GTRACT

> description: This program will extract a 3D image (single vector) from a vector 3D image at a given vector index.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   Required: input file containing the vector that will be extracted. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the vector image at the given index. Maps to a command-line argument: `--outputVolume %s`.

> setImageOrientation‘AsAcquired’ or ‘Axial’ or ‘Coronal’ or ‘Sagittal’

>   Sets the image orientation of the extracted vector (Axial, Coronal, Sagittal). Maps to a command-line argument: `--setImageOrientation %s`.

> vectorIndexan integer

>   Index in the vector image to extract. Maps to a command-line argument: `--vectorIndex %d`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the vector image at the given index.

## gtractAnisotropyMap

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractAnisotropyMap`.

> title: Anisotropy Map

> category: Diffusion.GTRACT

> description: This program will generate a scalar map of anisotropy, given a tensor representation. Anisotropy images are used for fiber tracking, but the anisotropy scalars are not defined along the path. Instead, the tensor representation is included as point data allowing all of these metrics to be computed using only the fiber tract point data. The images can be saved in any ITK supported format, but it is suggested that you use an image format that supports the definition of the image origin. This includes NRRD, NifTI, and Meta formats. These images can also be used for scalar analysis including regional anisotropy measures or VBM style analysis.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> anisotropyType‘ADC’ or ‘FA’ or ‘RA’ or ‘VR’ or ‘AD’ or ‘RD’ or ‘LI’

>   Anisotropy Mapping Type: ADC, FA, RA, VR, AD, RD, LI. Maps to a command-line argument: `--anisotropyType %s`.

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputTensorVolumea pathlike object or string representing an existing file

>   Required: input file containing the diffusion tensor image. Maps to a command-line argument: `--inputTensorVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the selected kind of anisotropy scalar. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the selected kind of anisotropy scalar.

## gtractAverageBvalues

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractAverageBvalues`.

> title: Average B-Values

> category: Diffusion.GTRACT

> description: This program will directly average together the baseline gradients (b value equals 0) within a DWI scan. This is usually used after gtractCoregBvalues.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> averageB0onlya boolean

>   Average only baseline gradients. All other gradient directions are not averaged, but retained in the outputVolume. Maps to a command-line argument: `--averageB0only`.

> directionsTolerancea float

>   Tolerance for matching identical gradient direction pairs. Maps to a command-line argument: `--directionsTolerance %f`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   Required: input image file name containing multiple baseline gradients to average. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing directly averaged baseline images. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing directly averaged baseline images.

## gtractClipAnisotropy

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractClipAnisotropy`.

> title: Clip Anisotropy

> category: Diffusion.GTRACT

> description: This program will zero the first and/or last slice of an anisotropy image, creating a clipped anisotropy image.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> clipFirstSlicea boolean

>   Clip the first slice of the anisotropy image. Maps to a command-line argument: `--clipFirstSlice`.

> clipLastSlicea boolean

>   Clip the last slice of the anisotropy image. Maps to a command-line argument: `--clipLastSlice`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputVolumea pathlike object or string representing an existing file

>   Required: input image file name. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the clipped anisotropy image. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the clipped anisotropy image.

## gtractCoRegAnatomy

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractCoRegAnatomy`.

> title: Coregister B0 to Anatomy B-Spline

> category: Diffusion.GTRACT

> description: This program will register a Nrrd diffusion weighted 4D vector image to a fixed anatomical image. Two registration methods are supported for alignment with anatomical images: Rigid and B-Spline. The rigid registration performs a rigid body registration with the anatomical images and should be done as well to initialize the B-Spline transform. The B-SPline transform is the deformable transform, where the user can control the amount of deformation based on the number of control points as well as the maximum distance that these points can move. The B-Spline registration places a low dimensional grid in the image, which is deformed. This allows for some susceptibility related distortions to be removed from the diffusion weighted images. In general the amount of motion in the slice selection and read-out directions direction should be kept low. The distortion is in the phase encoding direction in the images. It is recommended that skull stripped (i.e. image containing only brain with skull removed) images should be used for image co-registration with the B-Spline transform.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> borderSizean integer

>   Size of border. Maps to a command-line argument: `--borderSize %d`.

> convergencea float

>   Convergence Factor. Maps to a command-line argument: `--convergence %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: `{}`)

> gradientTolerancea float

>   Gradient Tolerance. Maps to a command-line argument: `--gradientTolerance %f`.

> gridSizea list of items which are an integer

>   Number of grid subdivisions in all 3 directions. Maps to a command-line argument: `--gridSize %s`.

> inputAnatomicalVolumea pathlike object or string representing an existing file

>   Required: input anatomical image file name. It is recommended that the input anatomical image has been skull stripped and has the same orientation as the DWI scan. Maps to a command-line argument: `--inputAnatomicalVolume %s`.

> inputRigidTransforma pathlike object or string representing an existing file

>   Required (for B-Spline type co-registration): input rigid transform file name. Used as a starting point for the anatomical B-Spline registration. Maps to a command-line argument: `--inputRigidTransform %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input vector image file name. It is recommended that the input volume is the skull stripped baseline image of the DWI scan. Maps to a command-line argument: `--inputVolume %s`.

> maxBSplineDisplacementa float

>   > Sets the maximum allowed displacements in image physical coordinates for BSpline control grid along each axis. A value of 0.0 indicates that the problem should be unbounded. NOTE: This only constrains the BSpline portion, and does not limit the displacement from the associated bulk transform. This can lead to a substantial reduction in computation time in the BSpline optimizer., .

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

> maximumStepSizea float

>   Maximum permitted step size to move in the selected 3D fit. Maps to a command-line argument: `--maximumStepSize %f`.

> minimumStepSizea float

>   Minimum required step size to move in the selected 3D fit without converging – decrease this to make the fit more exacting. Maps to a command-line argument: `--minimumStepSize %f`.

> numberOfHistogramBinsan integer

>   Number of histogram bins. Maps to a command-line argument: `--numberOfHistogramBins %d`.

> numberOfIterationsan integer

>   Number of iterations in the selected 3D fit. Maps to a command-line argument: `--numberOfIterations %d`.

> numberOfSamplesan integer

>   The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. NOTE that it is suggested to use samplingPercentage instead of this option. However, if set, it overwrites the samplingPercentage option. . Maps to a command-line argument: `--numberOfSamples %d`.

> numberOfThreadsan integer

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

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

>   Required: filename for the fit transform. Maps to a command-line argument: `--outputTransformName %s`.

> relaxationFactora float

>   Fraction of gradient from Jacobian to attempt to move in the selected 3D fit. Maps to a command-line argument: `--relaxationFactor %f`.

> samplingPercentagea float

>   This is a number in (0.0,1.0] interval that shows the percentage of the input fixed image voxels that are sampled for mutual information computation. Increase this for a slower, more careful fit. You can also limit the sampling focus with ROI masks and ROIAUTO mask generation. The default is to use approximately 5% of voxels (for backwards compatibility 5% ~= 500000/(256*256*256)). Typical values range from 1% for low detail images to 20% for high detail images. Maps to a command-line argument: `--samplingPercentage %f`.

> spatialScalean integer

>   Scales the number of voxels in the image by this value to specify the number of voxels used in the registration. Maps to a command-line argument: `--spatialScale %d`.

> transformType‘Rigid’ or ‘Bspline’

>   Transform Type: Rigid|Bspline. Maps to a command-line argument: `--transformType %s`.

> translationScalea float

>   How much to scale up changes in position compared to unit rotational changes in radians – decrease this to put more translation in the fit. Maps to a command-line argument: `--translationScale %f`.

> useCenterOfHeadAligna boolean

>   CenterOfHeadAlign attempts to find a hemisphere full of foreground voxels from the superior direction as an estimate of where the center of a head shape would be to drive a center of mass estimate. Perform a CenterOfHeadAlign registration as part of the sequential registration steps. This option MUST come first, and CAN NOT be used with either MomentsAlign, GeometryAlign, or initialTransform file. This family of options supersedes the use of transformType if any of them are set. Maps to a command-line argument: `--useCenterOfHeadAlign`.

> useGeometryAligna boolean

>   GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures. Perform a GeometryCenterAlign registration as part of the sequential registration steps. This option MUST come first, and CAN NOT be used with either MomentsAlign, CenterOfHeadAlign, or initialTransform file. This family of options supersedes the use of transformType if any of them are set. Maps to a command-line argument: `--useGeometryAlign`.

> useMomentsAligna boolean

>   MomentsAlign assumes that the center of mass of the images represent similar structures. Perform a MomentsAlign registration as part of the sequential registration steps. This option MUST come first, and CAN NOT be used with either CenterOfHeadLAlign, GeometryAlign, or initialTransform file. This family of options supersedes the use of transformType if any of them are set. Maps to a command-line argument: `--useMomentsAlign`.

> vectorIndexan integer

>   Vector image index in the moving image (within the DWI) to be used for registration. Maps to a command-line argument: `--vectorIndex %d`.

> outputTransformNamea pathlike object or string representing an existing file

>   Required: filename for the fit transform.

## gtractConcatDwi

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractConcatDwi`.

> title: Concat DWI Images

> category: Diffusion.GTRACT

> description: This program will concatenate two DTI runs together.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> ignoreOriginsa boolean

>   If image origins are different force all images to origin of first image. Maps to a command-line argument: `--ignoreOrigins`.

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

>   Required: input file containing the first diffusion weighted image. Maps to a command-line argument: `--inputVolume %s...`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the combined diffusion weighted images. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the combined diffusion weighted images.

## gtractCopyImageOrientation

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractCopyImageOrientation`.

> title: Copy Image Orientation

> category: Diffusion.GTRACT

> description: This program will copy the orientation from the reference image into the moving image. Currently, the registration process requires that the diffusion weighted images and the anatomical images have the same image orientation (i.e. Axial, Coronal, Sagittal). It is suggested that you copy the image orientation from the diffusion weighted images and apply this to the anatomical image. This image can be subsequently removed after the registration step is complete. We anticipate that this limitation will be removed in future versions of the registration programs.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputReferenceVolumea pathlike object or string representing an existing file

>   Required: input file containing orientation that will be cloned. Maps to a command-line argument: `--inputReferenceVolume %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input file containing the signed short image to reorient without resampling. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD or Nifti file containing the reoriented image in reference image space. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD or Nifti file containing the reoriented image in reference image space.

## gtractCoregBvalues

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractCoregBvalues`.

> title: Coregister B-Values

> category: Diffusion.GTRACT

> description: This step should be performed after converting DWI scans from DICOM to NRRD format. This program will register all gradients in a NRRD diffusion weighted 4D vector image (moving image) to a specified index in a fixed image. It also supports co-registration with a T2 weighted image or field map in the same plane as the DWI data. The fixed image for the registration should be a b0 image. A mutual information metric cost function is used for the registration because of the differences in signal intensity as a result of the diffusion gradients. The full affine allows the registration procedure to correct for eddy current distortions that may exist in the data. If the eddyCurrentCorrection is enabled, relaxationFactor (0.25) and maximumStepSize (0.1) should be adjusted.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> debugLevelan integer

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

> eddyCurrentCorrectiona boolean

>   Flag to perform eddy current correction in addition to motion correction (recommended). Maps to a command-line argument: `--eddyCurrentCorrection`.

> 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: `{}`)

> fixedVolumea pathlike object or string representing an existing file

>   Required: input fixed image file name. It is recommended that this image should either contain or be a b0 image. Maps to a command-line argument: `--fixedVolume %s`.

> fixedVolumeIndexan integer

>   Index in the fixed image for registration. It is recommended that this image should be a b0 image. Maps to a command-line argument: `--fixedVolumeIndex %d`.

> maximumStepSizea float

>   Maximum permitted step size to move in each 3D fit step (adjust when eddyCurrentCorrection is enabled; suggested value = 0.1). Maps to a command-line argument: `--maximumStepSize %f`.

> minimumStepSizea float

>   Minimum required step size to move in each 3D fit step without converging – decrease this to make the fit more exacting. Maps to a command-line argument: `--minimumStepSize %f`.

> movingVolumea pathlike object or string representing an existing file

>   Required: input moving image file name. In order to register gradients within a scan to its first gradient, set the movingVolume and fixedVolume as the same image. Maps to a command-line argument: `--movingVolume %s`.

> numberOfIterationsan integer

>   Number of iterations in each 3D fit. Maps to a command-line argument: `--numberOfIterations %d`.

> numberOfSpatialSamplesan integer

>   The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. NOTE that it is suggested to use samplingPercentage instead of this option. However, if set, it overwrites the samplingPercentage option. . Maps to a command-line argument: `--numberOfSpatialSamples %d`.

> numberOfThreadsan integer

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

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

>   Registration 3D transforms concatenated in a single output file. There are no tools that can use this, but can be used for debugging purposes. Maps to a command-line argument: `--outputTransform %s`.

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

>   Required: name of output NRRD file containing moving images individually resampled and fit to the specified fixed image index. Maps to a command-line argument: `--outputVolume %s`.

> registerB0Onlya boolean

>   Register the B0 images only. Maps to a command-line argument: `--registerB0Only`.

> relaxationFactora float

>   Fraction of gradient from Jacobian to attempt to move in each 3D fit step (adjust when eddyCurrentCorrection is enabled; suggested value = 0.25). Maps to a command-line argument: `--relaxationFactor %f`.

> samplingPercentagea float

>   This is a number in (0.0,1.0] interval that shows the percentage of the input fixed image voxels that are sampled for mutual information computation. Increase this for a slower, more careful fit. You can also limit the sampling focus with ROI masks and ROIAUTO mask generation. The default is to use approximately 5% of voxels (for backwards compatibility 5% ~= 500000/(256*256*256)). Typical values range from 1% for low detail images to 20% for high detail images. Maps to a command-line argument: `--samplingPercentage %f`.

> spatialScalea float

>   How much to scale up changes in position compared to unit rotational changes in radians – decrease this to put more rotation in the fit. Maps to a command-line argument: `--spatialScale %f`.

> outputTransforma pathlike object or string representing an existing file

>   Registration 3D transforms concatenated in a single output file. There are no tools that can use this, but can be used for debugging purposes.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing moving images individually resampled and fit to the specified fixed image index.

## gtractCostFastMarching

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractCostFastMarching`.

> title: Cost Fast Marching

> category: Diffusion.GTRACT

> description: This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the first portion of the algorithm. The user must first run gtractFastMarchingTracking to generate the actual fiber tracts. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> anisotropyWeighta float

>   Anisotropy weight used for vcl_cost function calculations. Maps to a command-line argument: `--anisotropyWeight %f`.

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputAnisotropyVolumea pathlike object or string representing an existing file

>   Required: input anisotropy image file name. Maps to a command-line argument: `--inputAnisotropyVolume %s`.

> inputStartingSeedsLabelMapVolumea pathlike object or string representing an existing file

>   Required: input starting seeds LabelMap image file name. Maps to a command-line argument: `--inputStartingSeedsLabelMapVolume %s`.

> inputTensorVolumea pathlike object or string representing an existing file

>   Required: input tensor image file name. Maps to a command-line argument: `--inputTensorVolume %s`.

> numberOfThreadsan integer

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

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

>   Output vcl_cost image. Maps to a command-line argument: `--outputCostVolume %s`.

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

>   Output speed image. Maps to a command-line argument: `--outputSpeedVolume %s`.

> seedThresholda float

>   Anisotropy threshold used for seed selection. Maps to a command-line argument: `--seedThreshold %f`.

> startingSeedsLabelan integer

>   Label value for Starting Seeds. Maps to a command-line argument: `--startingSeedsLabel %d`.

> stoppingValuea float

>   Terminating value for vcl_cost function estimation. Maps to a command-line argument: `--stoppingValue %f`.

> outputCostVolumea pathlike object or string representing an existing file

>   Output vcl_cost image.

> outputSpeedVolumea pathlike object or string representing an existing file

>   Output speed image.

## gtractCreateGuideFiber

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractCreateGuideFiber`.

> title: Create Guide Fiber

> category: Diffusion.GTRACT

> description: This program will create a guide fiber by averaging fibers from a previously generated tract.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputFibera pathlike object or string representing an existing file

>   Required: input fiber tract file name. Maps to a command-line argument: `--inputFiber %s`.

> numberOfPointsan integer

>   Number of points in output guide fiber. Maps to a command-line argument: `--numberOfPoints %d`.

> numberOfThreadsan integer

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

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

>   Required: output guide fiber file name. Maps to a command-line argument: `--outputFiber %s`.

> writeXMLPolyDataFilea boolean

>   Flag to make use of XML files when reading and writing vtkPolyData. Maps to a command-line argument: `--writeXMLPolyDataFile`.

> outputFibera pathlike object or string representing an existing file

>   Required: output guide fiber file name.

## gtractFastMarchingTracking

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractFastMarchingTracking`.

> title: Fast Marching Tracking

> category: Diffusion.GTRACT

> description: This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the second portion of the algorithm. The user must first run gtractCostFastMarching to generate the vcl_cost image. The second step of the algorithm implemented here is a gradient descent soplution from the defined ending region back to the seed points specified in gtractCostFastMarching. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> costStepSizea float

>   Cost image sub-voxel sampling. Maps to a command-line argument: `--costStepSize %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: `{}`)

> inputAnisotropyVolumea pathlike object or string representing an existing file

>   Required: input anisotropy image file name. Maps to a command-line argument: `--inputAnisotropyVolume %s`.

> inputCostVolumea pathlike object or string representing an existing file

>   Required: input vcl_cost image file name. Maps to a command-line argument: `--inputCostVolume %s`.

> inputStartingSeedsLabelMapVolumea pathlike object or string representing an existing file

>   Required: input starting seeds LabelMap image file name. Maps to a command-line argument: `--inputStartingSeedsLabelMapVolume %s`.

> inputTensorVolumea pathlike object or string representing an existing file

>   Required: input tensor image file name. Maps to a command-line argument: `--inputTensorVolume %s`.

> maximumStepSizea float

>   Maximum step size to move when tracking. Maps to a command-line argument: `--maximumStepSize %f`.

> minimumStepSizea float

>   Minimum step size to move when tracking. Maps to a command-line argument: `--minimumStepSize %f`.

> numberOfIterationsan integer

>   Number of iterations used for the optimization. Maps to a command-line argument: `--numberOfIterations %d`.

> numberOfThreadsan integer

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

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

>   Required: name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument: `--outputTract %s`.

> seedThresholda float

>   Anisotropy threshold used for seed selection. Maps to a command-line argument: `--seedThreshold %f`.

> startingSeedsLabelan integer

>   Label value for Starting Seeds. Maps to a command-line argument: `--startingSeedsLabel %d`.

> trackingThresholda float

>   Anisotropy threshold used for fiber tracking. Maps to a command-line argument: `--trackingThreshold %f`.

> writeXMLPolyDataFilea boolean

>   Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument: `--writeXMLPolyDataFile`.

> outputTracta pathlike object or string representing an existing file

>   Required: name of output vtkPolydata file containing tract lines and the point data collected along them.

## gtractFiberTracking

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractFiberTracking`.

> title: Fiber Tracking

> category: Diffusion.GTRACT

> description: This program implements four fiber tracking methods (Free, Streamline, GraphSearch, Guided). The output of the fiber tracking is vtkPolyData (i.e. Polylines) that can be loaded into Slicer3 for visualization. The poly data can be saved in either old VTK format files (.vtk) or in the new VTK XML format (.xml). The polylines contain point data that defines the Tensor at each point along the fiber tract. This can then be used to rendered as glyphs in Slicer3 and can be used to define several scalar measures without referencing back to the anisotropy images. (1) Free tracking is a basic streamlines algorithm. This is a direct implementation of the method original proposed by Basser et al. The tracking follows the primarty eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either as a result of maximum fiber length, low ansiotropy, or large curvature. This is a great way to explore your data. (2) The streamlines algorithm is a direct implementation of the method originally proposed by Basser et al. The tracking follows the primary eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either by reaching the ending region or reaching some stopping criteria. Stopping criteria are specified using the following parameters: tracking threshold, curvature threshold, and max length. Only paths terminating in the ending region are kept in this method. The TEND algorithm proposed by Lazar et al. (Human Brain Mapping 18:306-321, 2003) has been instrumented. This can be enabled using the –useTend option while performing Streamlines tracking. This utilizes the entire diffusion tensor to deflect the incoming vector instead of simply following the primary eigenvector. The TEND parameters are set using the –tendF and –tendG options. (3) Graph Search tracking is the first step in the full GTRACT algorithm developed by Cheng et al. (NeuroImage 31(3): 1075-1085, 2006) for finding the tracks in a tensor image. This method was developed to generate fibers in a Tensor representation where crossing fibers occur. The graph search algorithm follows the primary eigenvector in non-ambiguous regions and utilizes branching and a graph search algorithm in ambiguous regions. Ambiguous tracking regions are defined based on two criteria: Branching Al Threshold (anisotropy values below this value and above the traching threshold) and Curvature Major Eigen (angles of the primary eigenvector direction and the current tracking direction). In regions that meet this criteria, two or three tracking paths are considered. The first is the standard primary eigenvector direction. The second is the seconadary eigenvector direction. This is based on the assumption that these regions may be prolate regions. If the Random Walk option is selected then a third direction is also considered. This direction is defined by a cone pointing from the current position to the centroid of the ending region. The interior angle of the cone is specified by the user with the Branch/Guide Angle parameter. A vector contained inside of the cone is selected at random and used as the third direction. This method can also utilize the TEND option where the primary tracking direction is that specified by the TEND method instead of the primary eigenvector. The parameter ‘–maximumBranchPoints’ allows the tracking to have this number of branches being considered at a time. If this number of branch points is exceeded at any time, then the algorithm will revert back to a streamline algorithm until the number of branches is reduced. This allows the user to constrain the computational complexity of the algorithm. (4) The second phase of the GTRACT algorithm is Guided Tracking. This method incorporates anatomical information about the track orientation using an initial guess of the fiber track. In the originally proposed GTRACT method, this would be created from the fibers resulting from the Graph Search tracking. However, in practice this can be created using any method and could be defined manually. To create the guide fiber the program gtractCreateGuideFiber can be used. This program will load a fiber tract that has been generated and create a centerline representation of the fiber tract (i.e. a single fiber). In this method, the fiber tracking follows the primary eigenvector direction unless it deviates from the guide fiber track by a angle greater than that specified by the ‘–guidedCurvatureThreshold’ parameter. The user must specify the guide fiber when running this program.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta, Greg Harris and Yongqiang Zhao.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> branchingAnglea float

>   Branching angle in degrees (recommended for GraphSearch fiber tracking method). Maps to a command-line argument: `--branchingAngle %f`.

> branchingThresholda float

>   Anisotropy Branching threshold (recommended for GraphSearch fiber tracking method). Maps to a command-line argument: `--branchingThreshold %f`.

> curvatureThresholda float

>   Curvature threshold in degrees (recommended for Free fiber tracking). Maps to a command-line argument: `--curvatureThreshold %f`.

> endingSeedsLabelan integer

>   Label value for Ending Seeds (required if Label number used to create seed point in Slicer was not 1). Maps to a command-line argument: `--endingSeedsLabel %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: `{}`)

> guidedCurvatureThresholda float

>   Guided Curvature Threshold (Degrees). Maps to a command-line argument: `--guidedCurvatureThreshold %f`.

> inputAnisotropyVolumea pathlike object or string representing an existing file

>   Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input anisotropy image file name. Maps to a command-line argument: `--inputAnisotropyVolume %s`.

> inputEndingSeedsLabelMapVolumea pathlike object or string representing an existing file

>   Required (for Streamline, GraphSearch, and Guided fiber tracking methods): input ending seeds LabelMap image file name. Maps to a command-line argument: `--inputEndingSeedsLabelMapVolume %s`.

> inputStartingSeedsLabelMapVolumea pathlike object or string representing an existing file

>   Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input starting seeds LabelMap image file name. Maps to a command-line argument: `--inputStartingSeedsLabelMapVolume %s`.

> inputTensorVolumea pathlike object or string representing an existing file

>   Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input tensor image file name. Maps to a command-line argument: `--inputTensorVolume %s`.

> inputTracta pathlike object or string representing an existing file

>   Required (for Guided fiber tracking method): guide fiber in vtkPolydata file containing one tract line. Maps to a command-line argument: `--inputTract %s`.

> maximumBranchPointsan integer

>   Maximum branch points (recommended for GraphSearch fiber tracking method). Maps to a command-line argument: `--maximumBranchPoints %d`.

> maximumGuideDistancea float

>   Maximum distance for using the guide fiber direction. Maps to a command-line argument: `--maximumGuideDistance %f`.

> maximumLengtha float

>   Maximum fiber length (voxels). Maps to a command-line argument: `--maximumLength %f`.

> minimumLengtha float

>   Minimum fiber length. Helpful for filtering invalid tracts. Maps to a command-line argument: `--minimumLength %f`.

> numberOfThreadsan integer

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

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

>   Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument: `--outputTract %s`.

> randomSeedan integer

>   Random number generator seed. Maps to a command-line argument: `--randomSeed %d`.

> seedThresholda float

>   Anisotropy threshold for seed selection (recommended for Free fiber tracking). Maps to a command-line argument: `--seedThreshold %f`.

> startingSeedsLabelan integer

>   Label value for Starting Seeds (required if Label number used to create seed point in Slicer was not 1). Maps to a command-line argument: `--startingSeedsLabel %d`.

> stepSizea float

>   Fiber tracking step size. Maps to a command-line argument: `--stepSize %f`.

> tendFa float

>   Tend F parameter. Maps to a command-line argument: `--tendF %f`.

> tendGa float

>   Tend G parameter. Maps to a command-line argument: `--tendG %f`.

> trackingMethod‘Guided’ or ‘Free’ or ‘Streamline’ or ‘GraphSearch’

>   Fiber tracking Filter Type: Guided|Free|Streamline|GraphSearch. Maps to a command-line argument: `--trackingMethod %s`.

> trackingThresholda float

>   Anisotropy threshold for fiber tracking (anisotropy values of the next point along the path). Maps to a command-line argument: `--trackingThreshold %f`.

> useLoopDetectiona boolean

>   Flag to make use of loop detection. Maps to a command-line argument: `--useLoopDetection`.

> useRandomWalka boolean

>   Flag to use random walk. Maps to a command-line argument: `--useRandomWalk`.

> useTenda boolean

>   Flag to make use of Tend F and Tend G parameters. Maps to a command-line argument: `--useTend`.

> writeXMLPolyDataFilea boolean

>   Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument: `--writeXMLPolyDataFile`.

> outputTracta pathlike object or string representing an existing file

>   Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): name of output vtkPolydata file containing tract lines and the point data collected along them.

## gtractImageConformity

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractImageConformity`.

> title: Image Conformity

> category: Diffusion.GTRACT

> description: This program will straighten out the Direction and Origin to match the Reference Image.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputReferenceVolumea pathlike object or string representing an existing file

>   Required: input file containing the standard image to clone the characteristics of. Maps to a command-line argument: `--inputReferenceVolume %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input file containing the signed short image to reorient without resampling. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output Nrrd or Nifti file containing the reoriented image in reference image space. Maps to a command-line argument: `--outputVolume %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output Nrrd or Nifti file containing the reoriented image in reference image space.

## gtractInvertBSplineTransform

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractInvertBSplineTransform`.

> title: B-Spline Transform Inversion

> category: Diffusion.GTRACT

> description: This program will invert a B-Spline transform using a thin-plate spline approximation.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputReferenceVolumea pathlike object or string representing an existing file

>   Required: input image file name to exemplify the anatomical space to interpolate over. Maps to a command-line argument: `--inputReferenceVolume %s`.

> inputTransforma pathlike object or string representing an existing file

>   Required: input B-Spline transform file name. Maps to a command-line argument: `--inputTransform %s`.

> landmarkDensitya list of items which are an integer

>   Number of landmark subdivisions in all 3 directions. Maps to a command-line argument: `--landmarkDensity %s`.

> numberOfThreadsan integer

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

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

>   Required: output transform file name. Maps to a command-line argument: `--outputTransform %s`.

> outputTransforma pathlike object or string representing an existing file

>   Required: output transform file name.

## gtractInvertDisplacementField

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractInvertDisplacementField`.

> title: Invert Displacement Field

> category: Diffusion.GTRACT

> description: This program will invert a deformatrion field. The size of the deformation field is defined by an example image provided by the user

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> baseImagea pathlike object or string representing an existing file

>   Required: base image used to define the size of the inverse field. Maps to a command-line argument: `--baseImage %s`.

> deformationImagea pathlike object or string representing an existing file

>   Required: Displacement field image. Maps to a command-line argument: `--deformationImage %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: `{}`)

> numberOfThreadsan integer

>   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

>   Required: Output deformation field. Maps to a command-line argument: `--outputVolume %s`.

> subsamplingFactoran integer

>   Subsampling factor for the deformation field. Maps to a command-line argument: `--subsamplingFactor %d`.

> outputVolumea pathlike object or string representing an existing file

>   Required: Output deformation field.

## gtractInvertRigidTransform

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractInvertRigidTransform`.

> title: Rigid Transform Inversion

> category: Diffusion.GTRACT

> description: This program will invert a Rigid transform.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputTransforma pathlike object or string representing an existing file

>   Required: input rigid transform file name. Maps to a command-line argument: `--inputTransform %s`.

> numberOfThreadsan integer

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

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

>   Required: output transform file name. Maps to a command-line argument: `--outputTransform %s`.

> outputTransforma pathlike object or string representing an existing file

>   Required: output transform file name.

## gtractResampleAnisotropy

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractResampleAnisotropy`.

> title: Resample Anisotropy

> category: Diffusion.GTRACT

> description: This program will resample a floating point image using either the Rigid or B-Spline transform. You may want to save the aligned B0 image after each of the anisotropy map co-registration steps with the anatomical image to check the registration quality with another tool.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputAnatomicalVolumea pathlike object or string representing an existing file

>   Required: input file containing the anatomical image whose characteristics will be cloned. Maps to a command-line argument: `--inputAnatomicalVolume %s`.

> inputAnisotropyVolumea pathlike object or string representing an existing file

>   Required: input file containing the anisotropy image. Maps to a command-line argument: `--inputAnisotropyVolume %s`.

> inputTransforma pathlike object or string representing an existing file

>   Required: input Rigid OR Bspline transform file name. Maps to a command-line argument: `--inputTransform %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the resampled transformed anisotropy image. Maps to a command-line argument: `--outputVolume %s`.

> transformType‘Rigid’ or ‘B-Spline’

>   Transform type: Rigid, B-Spline. Maps to a command-line argument: `--transformType %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the resampled transformed anisotropy image.

## gtractResampleB0

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractResampleB0`.

> title: Resample B0

> category: Diffusion.GTRACT

> description: This program will resample a signed short image using either a Rigid or B-Spline transform. The user must specify a template image that will be used to define the origin, orientation, spacing, and size of the resampled image.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputAnatomicalVolumea pathlike object or string representing an existing file

>   Required: input file containing the anatomical image defining the origin, spacing and size of the resampled image (template). Maps to a command-line argument: `--inputAnatomicalVolume %s`.

> inputTransforma pathlike object or string representing an existing file

>   Required: input Rigid OR Bspline transform file name. Maps to a command-line argument: `--inputTransform %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input file containing the 4D image. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the resampled input image. Maps to a command-line argument: `--outputVolume %s`.

> transformType‘Rigid’ or ‘B-Spline’

>   Transform type: Rigid, B-Spline. Maps to a command-line argument: `--transformType %s`.

> vectorIndexan integer

>   Index in the diffusion weighted image set for the B0 image. Maps to a command-line argument: `--vectorIndex %d`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the resampled input image.

## gtractResampleCodeImage

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractResampleCodeImage`.

> title: Resample Code Image

> category: Diffusion.GTRACT

> description: This program will resample a short integer code image using either the Rigid or Inverse-B-Spline transform. The reference image is the DTI tensor anisotropy image space, and the input code image is in anatomical space.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputCodeVolumea pathlike object or string representing an existing file

>   Required: input file containing the code image. Maps to a command-line argument: `--inputCodeVolume %s`.

> inputReferenceVolumea pathlike object or string representing an existing file

>   Required: input file containing the standard image to clone the characteristics of. Maps to a command-line argument: `--inputReferenceVolume %s`.

> inputTransforma pathlike object or string representing an existing file

>   Required: input Rigid or Inverse-B-Spline transform file name. Maps to a command-line argument: `--inputTransform %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the resampled code image in acquisition space. Maps to a command-line argument: `--outputVolume %s`.

> transformType‘Rigid’ or ‘Affine’ or ‘B-Spline’ or ‘Inverse-B-Spline’ or ‘None’

>   Transform type: Rigid or Inverse-B-Spline. Maps to a command-line argument: `--transformType %s`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the resampled code image in acquisition space.

## gtractResampleDWIInPlace

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractResampleDWIInPlace`.

> title: Resample DWI In Place

> category: Diffusion.GTRACT

> description: Resamples DWI image to structural image.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta, Greg Harris, Hans Johnson, and Joy Matsui.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> debugLevelan integer

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

> imageOutputSizea list of items which are an integer

>   The voxel lattice for the output image, padding is added if necessary. NOTE: if 0,0,0, then the inputVolume size is used. Maps to a command-line argument: `--imageOutputSize %s`.

> inputTransforma pathlike object or string representing an existing file

>   Required: transform file derived from rigid registration of b0 image to reference structural image. Maps to a command-line argument: `--inputTransform %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input image is a 4D NRRD image. Maps to a command-line argument: `--inputVolume %s`.

> numberOfThreadsan integer

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

> outputResampledB0a boolean or a pathlike object or string representing a file

>   Convenience function for extracting the first index location (assumed to be the B0). Maps to a command-line argument: `--outputResampledB0 %s`.

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

>   Required: output image (NRRD file) that has been rigidly transformed into the space of the structural image and padded if image padding was changed from 0,0,0 default. Maps to a command-line argument: `--outputVolume %s`.

> referenceVolumea pathlike object or string representing an existing file

>   If provided, resample to the final space of the referenceVolume 3D data set. Maps to a command-line argument: `--referenceVolume %s`.

> warpDWITransforma pathlike object or string representing an existing file

>   Optional: transform file to warp gradient volumes. Maps to a command-line argument: `--warpDWITransform %s`.

> outputResampledB0a pathlike object or string representing an existing file

>   Convenience function for extracting the first index location (assumed to be the B0).

> outputVolumea pathlike object or string representing an existing file

>   Required: output image (NRRD file) that has been rigidly transformed into the space of the structural image and padded if image padding was changed from 0,0,0 default.

## gtractResampleFibers

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractResampleFibers`.

> title: Resample Fibers

> category: Diffusion.GTRACT

> description: This program will resample a fiber tract with respect to a pair of deformation fields that represent the forward and reverse deformation fields.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputForwardDeformationFieldVolumea pathlike object or string representing an existing file

>   Required: input forward deformation field image file name. Maps to a command-line argument: `--inputForwardDeformationFieldVolume %s`.

> inputReverseDeformationFieldVolumea pathlike object or string representing an existing file

>   Required: input reverse deformation field image file name. Maps to a command-line argument: `--inputReverseDeformationFieldVolume %s`.

> inputTracta pathlike object or string representing an existing file

>   Required: name of input vtkPolydata file containing tract lines. Maps to a command-line argument: `--inputTract %s`.

> numberOfThreadsan integer

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

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

>   Required: name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument: `--outputTract %s`.

> writeXMLPolyDataFilea boolean

>   Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument: `--writeXMLPolyDataFile`.

> outputTracta pathlike object or string representing an existing file

>   Required: name of output vtkPolydata file containing tract lines and the point data collected along them.

## gtractTensor

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractTensor`.

> title: Tensor Estimation

> category: Diffusion.GTRACT

> description: This step will convert a b-value averaged diffusion tensor image to a 3x3 tensor voxel image. This step takes the diffusion tensor image data and generates a tensor representation of the data based on the signal intensity decay, b values applied, and the diffusion difrections. The apparent diffusion coefficient for a given orientation is computed on a pixel-by-pixel basis by fitting the image data (voxel intensities) to the Stejskal-Tanner equation. If at least 6 diffusion directions are used, then the diffusion tensor can be computed. This program uses itk::DiffusionTensor3DReconstructionImageFilter. The user can adjust background threshold, median filter, and isotropic resampling.

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta and Greg Harris.

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> applyMeasurementFramea boolean

>   Flag to apply the measurement frame to the gradient directions. Maps to a command-line argument: `--applyMeasurementFrame`.

> argsa string

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

> b0Indexan integer

>   Index in input vector index to extract. Maps to a command-line argument: `--b0Index %d`.

> backgroundSuppressingThresholdan integer

>   Image threshold to suppress background. This sets a threshold used on the b0 image to remove background voxels from processing. Typically, values of 100 and 500 work well for Siemens and GE DTI data, respectively. Check your data particularly in the globus pallidus to make sure the brain tissue is not being eliminated with this threshold. Maps to a command-line argument: `--backgroundSuppressingThreshold %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: `{}`)

> ignoreIndexa list of items which are an integer

>   Ignore diffusion gradient index. Used to remove specific gradient directions with artifacts. Maps to a command-line argument: `--ignoreIndex %s`.

> inputVolumea pathlike object or string representing an existing file

>   Required: input image 4D NRRD image. Must contain data based on at least 6 distinct diffusion directions. The inputVolume is allowed to have multiple b0 and gradient direction images. Averaging of the b0 image is done internally in this step. Prior averaging of the DWIs is not required. Maps to a command-line argument: `--inputVolume %s`.

> maskProcessingMode‘NOMASK’ or ‘ROIAUTO’ or ‘ROI’

>   ROIAUTO: mask is implicitly defined using a otsu foreground and hole filling algorithm. ROI: Uses the masks to define what parts of the image should be used for computing the transform. NOMASK: no mask used. Maps to a command-line argument: `--maskProcessingMode %s`.

> maskVolumea pathlike object or string representing an existing file

>   Mask Image, if maskProcessingMode is ROI. Maps to a command-line argument: `--maskVolume %s`.

> medianFilterSizea list of items which are an integer

>   Median filter radius in all 3 directions. Maps to a command-line argument: `--medianFilterSize %s`.

> numberOfThreadsan integer

>   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

>   Required: name of output NRRD file containing the Tensor vector image. Maps to a command-line argument: `--outputVolume %s`.

> resampleIsotropica boolean

>   Flag to resample to isotropic voxels. Enabling this feature is recommended if fiber tracking will be performed. Maps to a command-line argument: `--resampleIsotropic`.

> sizea float

>   Isotropic voxel size to resample to. Maps to a command-line argument: `--size %f`.

> outputVolumea pathlike object or string representing an existing file

>   Required: name of output NRRD file containing the Tensor vector image.

## gtractTransformToDisplacementField

Link to code

> Bases: SEMLikeCommandLine

> Wrapped executable: `gtractTransformToDisplacementField`.

> title: Create Displacement Field

> category: Diffusion.GTRACT

> description: This program will compute forward deformation from the given Transform. The size of the DF is equal to MNI space

> version: 4.0.0

> documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT

> license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt

> contributor: This tool was developed by Vincent Magnotta, Madhura Ingalhalikar, and Greg Harris

> acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1

> argsa string

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

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> inputReferenceVolumea pathlike object or string representing an existing file

>   Required: input image file name to exemplify the anatomical space over which to vcl_express the transform as a displacement field. Maps to a command-line argument: `--inputReferenceVolume %s`.

> inputTransforma pathlike object or string representing an existing file

>   Input Transform File Name. Maps to a command-line argument: `--inputTransform %s`.

> numberOfThreadsan integer

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

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

>   Output deformation field. Maps to a command-line argument: `--outputDeformationFieldVolume %s`.

> outputDeformationFieldVolumea pathlike object or string representing an existing file

>   Output deformation field.