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# interfaces.semtools.diffusion.gtract

## compareTractInclusion

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    closeness: (a 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
            flag: --closeness %f
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    numberOfPoints: (an integer (int or long))
            Number of points in comparison fiber pairs
            flag: --numberOfPoints %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    standardFiber: (an existing file name)
            Required: standard fiber tract file name
            flag: --standardFiber %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    testFiber: (an existing file name)
            Required: test fiber tract file name
            flag: --testFiber %s
    testForBijection: (a boolean)
            Flag to apply the closeness criterion both ways
            flag: --testForBijection
    testForFiberCardinality: (a boolean)
            Flag to require the same number of fibers in both tracts
            flag: --testForFiberCardinality
    writeXMLPolyDataFile: (a boolean)
            Flag to make use of XML files when reading and writing vtkPolyData.
            flag: --writeXMLPolyDataFile

Outputs:

    None

## extractNrrdVectorIndex

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputVolume: (an existing file name)
            Required: input file containing the vector that will be extracted
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the vector image at
            the given index
            flag: --outputVolume %s
    setImageOrientation: ('AsAcquired' or 'Axial' or 'Coronal' or
             'Sagittal')
            Sets the image orientation of the extracted vector (Axial, Coronal,
            Sagittal)
            flag: --setImageOrientation %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    vectorIndex: (an integer (int or long))
            Index in the vector image to extract
            flag: --vectorIndex %d

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the vector image at
            the given index

## gtractAnisotropyMap

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    anisotropyType: ('ADC' or 'FA' or 'RA' or 'VR' or 'AD' or 'RD' or
             'LI')
            Anisotropy Mapping Type: ADC, FA, RA, VR, AD, RD, LI
            flag: --anisotropyType %s
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputTensorVolume: (an existing file name)
            Required: input file containing the diffusion tensor image
            flag: --inputTensorVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the selected kind of
            anisotropy scalar.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the selected kind of
            anisotropy scalar.

## gtractAverageBvalues

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    averageB0only: (a boolean)
            Average only baseline gradients. All other gradient directions are
            not averaged, but retained in the outputVolume
            flag: --averageB0only
    directionsTolerance: (a float)
            Tolerance for matching identical gradient direction pairs
            flag: --directionsTolerance %f
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputVolume: (an existing file name)
            Required: input image file name containing multiple baseline
            gradients to average
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing directly averaged
            baseline images
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing directly averaged
            baseline images

## gtractClipAnisotropy

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    clipFirstSlice: (a boolean)
            Clip the first slice of the anisotropy image
            flag: --clipFirstSlice
    clipLastSlice: (a boolean)
            Clip the last slice of the anisotropy image
            flag: --clipLastSlice
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputVolume: (an existing file name)
            Required: input image file name
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the clipped anisotropy
            image
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the clipped anisotropy
            image

## gtractCoRegAnatomy

Link to code

Wraps command ** 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 shoud 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    borderSize: (an integer (int or long))
            Size of border
            flag: --borderSize %d
    convergence: (a float)
            Convergence Factor
            flag: --convergence %f
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    gradientTolerance: (a float)
            Gradient Tolerance
            flag: --gradientTolerance %f
    gridSize: (a list of items which are an integer (int or long))
            Number of grid subdivisions in all 3 directions
            flag: --gridSize %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnatomicalVolume: (an existing file name)
            Required: input anatomical image file name. It is recommended that
            that the input anatomical image has been skull stripped and has the
            same orientation as the DWI scan.
            flag: --inputAnatomicalVolume %s
    inputRigidTransform: (an existing file name)
            Required (for B-Spline type co-registration): input rigid transform
            file name. Used as a starting point for the anatomical B-Spline
            registration.
            flag: --inputRigidTransform %s
    inputVolume: (an existing file name)
            Required: input vector image file name. It is recommended that the
            input volume is the skull stripped baseline image of the DWI scan.
            flag: --inputVolume %s
    maxBSplineDisplacement: (a 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.,
            flag: --maxBSplineDisplacement %f
    maximumStepSize: (a float)
            Maximum permitted step size to move in the selected 3D fit
            flag: --maximumStepSize %f
    minimumStepSize: (a float)
            Minimum required step size to move in the selected 3D fit without
            converging -- decrease this to make the fit more exacting
            flag: --minimumStepSize %f
    numberOfHistogramBins: (an integer (int or long))
            Number of histogram bins
            flag: --numberOfHistogramBins %d
    numberOfIterations: (an integer (int or long))
            Number of iterations in the selected 3D fit
            flag: --numberOfIterations %d
    numberOfSamples: (an integer (int or long))
            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.
            flag: --numberOfSamples %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTransformName: (a boolean or a file name)
            Required: filename for the fit transform.
            flag: --outputTransformName %s
    relaxationFactor: (a float)
            Fraction of gradient from Jacobian to attempt to move in the
            selected 3D fit
            flag: --relaxationFactor %f
    samplingPercentage: (a 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.
            flag: --samplingPercentage %f
    spatialScale: (an integer (int or long))
            Scales the number of voxels in the image by this value to specify
            the number of voxels used in the registration
            flag: --spatialScale %d
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformType: ('Rigid' or 'Bspline')
            Transform Type: Rigid|Bspline
            flag: --transformType %s
    translationScale: (a 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
            flag: --translationScale %f
    useCenterOfHeadAlign: (a 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 superceeds the use of transformType if any of
            them are set.
            flag: --useCenterOfHeadAlign
    useGeometryAlign: (a 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 superceeds the use of transformType if any of them
            are set.
            flag: --useGeometryAlign
    useMomentsAlign: (a 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 superceeds the use of
            transformType if any of them are set.
            flag: --useMomentsAlign
    vectorIndex: (an integer (int or long))
            Vector image index in the moving image (within the DWI) to be used
            for registration.
            flag: --vectorIndex %d

Outputs:

    outputTransformName: (an existing file name)
            Required: filename for the fit transform.

## gtractConcatDwi

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignoreOrigins: (a boolean)
            If image origins are different force all images to origin of first
            image
            flag: --ignoreOrigins
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputVolume: (a list of items which are an existing file name)
            Required: input file containing the first diffusion weighted image
            flag: --inputVolume %s...
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the combined diffusion
            weighted images.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the combined diffusion
            weighted images.

## gtractCopyImageOrientation

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputReferenceVolume: (an existing file name)
            Required: input file containing orietation that will be cloned.
            flag: --inputReferenceVolume %s
    inputVolume: (an existing file name)
            Required: input file containing the signed short image to reorient
            without resampling.
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD or Nifti file containing the
            reoriented image in reference image space.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD or Nifti file containing the
            reoriented image in reference image space.

## gtractCoregBvalues

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    debugLevel: (an integer (int or long))
            Display debug messages, and produce debug intermediate results.
            0=OFF, 1=Minimal, 10=Maximum debugging.
            flag: --debugLevel %d
    eddyCurrentCorrection: (a boolean)
            Flag to perform eddy current corection in addition to motion
            correction (recommended)
            flag: --eddyCurrentCorrection
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    fixedVolume: (an existing file name)
            Required: input fixed image file name. It is recommended that this
            image should either contain or be a b0 image.
            flag: --fixedVolume %s
    fixedVolumeIndex: (an integer (int or long))
            Index in the fixed image for registration. It is recommended that
            this image should be a b0 image.
            flag: --fixedVolumeIndex %d
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    maximumStepSize: (a float)
            Maximum permitted step size to move in each 3D fit step (adjust when
            eddyCurrentCorrection is enabled; suggested value = 0.1)
            flag: --maximumStepSize %f
    minimumStepSize: (a float)
            Minimum required step size to move in each 3D fit step without
            converging -- decrease this to make the fit more exacting
            flag: --minimumStepSize %f
    movingVolume: (an existing file name)
            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.
            flag: --movingVolume %s
    numberOfIterations: (an integer (int or long))
            Number of iterations in each 3D fit
            flag: --numberOfIterations %d
    numberOfSpatialSamples: (an integer (int or long))
            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.
            flag: --numberOfSpatialSamples %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTransform: (a boolean or a file name)
            Registration 3D transforms concatenated in a single output file.
            There are no tools that can use this, but can be used for debugging
            purposes.
            flag: --outputTransform %s
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing moving images
            individually resampled and fit to the specified fixed image index.
            flag: --outputVolume %s
    registerB0Only: (a boolean)
            Register the B0 images only
            flag: --registerB0Only
    relaxationFactor: (a float)
            Fraction of gradient from Jacobian to attempt to move in each 3D fit
            step (adjust when eddyCurrentCorrection is enabled; suggested value
            = 0.25)
            flag: --relaxationFactor %f
    samplingPercentage: (a 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.
            flag: --samplingPercentage %f
    spatialScale: (a 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
            flag: --spatialScale %f
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputTransform: (an existing file name)
            Registration 3D transforms concatenated in a single output file.
            There are no tools that can use this, but can be used for debugging
            purposes.
    outputVolume: (an existing file name)
            Required: name of output NRRD file containing moving images
            individually resampled and fit to the specified fixed image index.

## gtractCostFastMarching

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    anisotropyWeight: (a float)
            Anisotropy weight used for vcl_cost function calculations
            flag: --anisotropyWeight %f
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnisotropyVolume: (an existing file name)
            Required: input anisotropy image file name
            flag: --inputAnisotropyVolume %s
    inputStartingSeedsLabelMapVolume: (an existing file name)
            Required: input starting seeds LabelMap image file name
            flag: --inputStartingSeedsLabelMapVolume %s
    inputTensorVolume: (an existing file name)
            Required: input tensor image file name
            flag: --inputTensorVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputCostVolume: (a boolean or a file name)
            Output vcl_cost image
            flag: --outputCostVolume %s
    outputSpeedVolume: (a boolean or a file name)
            Output speed image
            flag: --outputSpeedVolume %s
    seedThreshold: (a float)
            Anisotropy threshold used for seed selection
            flag: --seedThreshold %f
    startingSeedsLabel: (an integer (int or long))
            Label value for Starting Seeds
            flag: --startingSeedsLabel %d
    stoppingValue: (a float)
            Terminiating value for vcl_cost function estimation
            flag: --stoppingValue %f
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputCostVolume: (an existing file name)
            Output vcl_cost image
    outputSpeedVolume: (an existing file name)
            Output speed image

## gtractCreateGuideFiber

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputFiber: (an existing file name)
            Required: input fiber tract file name
            flag: --inputFiber %s
    numberOfPoints: (an integer (int or long))
            Number of points in output guide fiber
            flag: --numberOfPoints %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputFiber: (a boolean or a file name)
            Required: output guide fiber file name
            flag: --outputFiber %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    writeXMLPolyDataFile: (a boolean)
            Flag to make use of XML files when reading and writing vtkPolyData.
            flag: --writeXMLPolyDataFile

Outputs:

    outputFiber: (an existing file name)
            Required: output guide fiber file name

## gtractFastMarchingTracking

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    costStepSize: (a float)
            Cost image sub-voxel sampling
            flag: --costStepSize %f
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnisotropyVolume: (an existing file name)
            Required: input anisotropy image file name
            flag: --inputAnisotropyVolume %s
    inputCostVolume: (an existing file name)
            Required: input vcl_cost image file name
            flag: --inputCostVolume %s
    inputStartingSeedsLabelMapVolume: (an existing file name)
            Required: input starting seeds LabelMap image file name
            flag: --inputStartingSeedsLabelMapVolume %s
    inputTensorVolume: (an existing file name)
            Required: input tensor image file name
            flag: --inputTensorVolume %s
    maximumStepSize: (a float)
            Maximum step size to move when tracking
            flag: --maximumStepSize %f
    minimumStepSize: (a float)
            Minimum step size to move when tracking
            flag: --minimumStepSize %f
    numberOfIterations: (an integer (int or long))
            Number of iterations used for the optimization
            flag: --numberOfIterations %d
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTract: (a boolean or a file name)
            Required: name of output vtkPolydata file containing tract lines and
            the point data collected along them.
            flag: --outputTract %s
    seedThreshold: (a float)
            Anisotropy threshold used for seed selection
            flag: --seedThreshold %f
    startingSeedsLabel: (an integer (int or long))
            Label value for Starting Seeds
            flag: --startingSeedsLabel %d
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    trackingThreshold: (a float)
            Anisotropy threshold used for fiber tracking
            flag: --trackingThreshold %f
    writeXMLPolyDataFile: (a boolean)
            Flag to make use of the XML format for vtkPolyData fiber tracts.
            flag: --writeXMLPolyDataFile

Outputs:

    outputTract: (an existing file name)
            Required: name of output vtkPolydata file containing tract lines and
            the point data collected along them.

## gtractFiberTracking

Link to code

Wraps command ** 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 ther 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 severeal 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-ambigous regions and utilizes branching and a graph search algorithm in ambigous 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 alogrithm 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    branchingAngle: (a float)
            Branching angle in degrees (recommended for GraphSearch fiber
            tracking method)
            flag: --branchingAngle %f
    branchingThreshold: (a float)
            Anisotropy Branching threshold (recommended for GraphSearch fiber
            tracking method)
            flag: --branchingThreshold %f
    curvatureThreshold: (a float)
            Curvature threshold in degrees (recommended for Free fiber tracking)
            flag: --curvatureThreshold %f
    endingSeedsLabel: (an integer (int or long))
            Label value for Ending Seeds (required if Label number used to
            create seed point in Slicer was not 1)
            flag: --endingSeedsLabel %d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    guidedCurvatureThreshold: (a float)
            Guided Curvature Threshold (Degrees)
            flag: --guidedCurvatureThreshold %f
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnisotropyVolume: (an existing file name)
            Required (for Free, Streamline, GraphSearch, and Guided fiber
            tracking methods): input anisotropy image file name
            flag: --inputAnisotropyVolume %s
    inputEndingSeedsLabelMapVolume: (an existing file name)
            Required (for Streamline, GraphSearch, and Guided fiber tracking
            methods): input ending seeds LabelMap image file name
            flag: --inputEndingSeedsLabelMapVolume %s
    inputStartingSeedsLabelMapVolume: (an existing file name)
            Required (for Free, Streamline, GraphSearch, and Guided fiber
            tracking methods): input starting seeds LabelMap image file name
            flag: --inputStartingSeedsLabelMapVolume %s
    inputTensorVolume: (an existing file name)
            Required (for Free, Streamline, GraphSearch, and Guided fiber
            tracking methods): input tensor image file name
            flag: --inputTensorVolume %s
    inputTract: (an existing file name)
            Required (for Guided fiber tracking method): guide fiber in
            vtkPolydata file containing one tract line.
            flag: --inputTract %s
    maximumBranchPoints: (an integer (int or long))
            Maximum branch points (recommended for GraphSearch fiber tracking
            method)
            flag: --maximumBranchPoints %d
    maximumGuideDistance: (a float)
            Maximum distance for using the guide fiber direction
            flag: --maximumGuideDistance %f
    maximumLength: (a float)
            Maximum fiber length (voxels)
            flag: --maximumLength %f
    minimumLength: (a float)
            Minimum fiber length. Helpful for filtering invalid tracts.
            flag: --minimumLength %f
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTract: (a boolean or a file name)
            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.
            flag: --outputTract %s
    randomSeed: (an integer (int or long))
            Random number generator seed
            flag: --randomSeed %d
    seedThreshold: (a float)
            Anisotropy threshold for seed selection (recommended for Free fiber
            tracking)
            flag: --seedThreshold %f
    startingSeedsLabel: (an integer (int or long))
            Label value for Starting Seeds (required if Label number used to
            create seed point in Slicer was not 1)
            flag: --startingSeedsLabel %d
    stepSize: (a float)
            Fiber tracking step size
            flag: --stepSize %f
    tendF: (a float)
            Tend F parameter
            flag: --tendF %f
    tendG: (a float)
            Tend G parameter
            flag: --tendG %f
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    trackingMethod: ('Guided' or 'Free' or 'Streamline' or 'GraphSearch')
            Fiber tracking Filter Type: Guided|Free|Streamline|GraphSearch
            flag: --trackingMethod %s
    trackingThreshold: (a float)
            Anisotropy threshold for fiber tracking (anisotropy values of the
            next point along the path)
            flag: --trackingThreshold %f
    useLoopDetection: (a boolean)
            Flag to make use of loop detection.
            flag: --useLoopDetection
    useRandomWalk: (a boolean)
            Flag to use random walk.
            flag: --useRandomWalk
    useTend: (a boolean)
            Flag to make use of Tend F and Tend G parameters.
            flag: --useTend
    writeXMLPolyDataFile: (a boolean)
            Flag to make use of the XML format for vtkPolyData fiber tracts.
            flag: --writeXMLPolyDataFile

Outputs:

    outputTract: (an existing file name)
            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

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputReferenceVolume: (an existing file name)
            Required: input file containing the standard image to clone the
            characteristics of.
            flag: --inputReferenceVolume %s
    inputVolume: (an existing file name)
            Required: input file containing the signed short image to reorient
            without resampling.
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output Nrrd or Nifti file containing the
            reoriented image in reference image space.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output Nrrd or Nifti file containing the
            reoriented image in reference image space.

## gtractInvertBSplineTransform

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputReferenceVolume: (an existing file name)
            Required: input image file name to exemplify the anatomical space to
            interpolate over.
            flag: --inputReferenceVolume %s
    inputTransform: (an existing file name)
            Required: input B-Spline transform file name
            flag: --inputTransform %s
    landmarkDensity: (a list of items which are an integer (int or long))
            Number of landmark subdivisions in all 3 directions
            flag: --landmarkDensity %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTransform: (a boolean or a file name)
            Required: output transform file name
            flag: --outputTransform %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputTransform: (an existing file name)
            Required: output transform file name

## gtractInvertDisplacementField

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    baseImage: (an existing file name)
            Required: base image used to define the size of the inverse field
            flag: --baseImage %s
    deformationImage: (an existing file name)
            Required: Displacement field image
            flag: --deformationImage %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: Output deformation field
            flag: --outputVolume %s
    subsamplingFactor: (an integer (int or long))
            Subsampling factor for the deformation field
            flag: --subsamplingFactor %d
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: Output deformation field

## gtractInvertRigidTransform

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputTransform: (an existing file name)
            Required: input rigid transform file name
            flag: --inputTransform %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTransform: (a boolean or a file name)
            Required: output transform file name
            flag: --outputTransform %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputTransform: (an existing file name)
            Required: output transform file name

## gtractResampleAnisotropy

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnatomicalVolume: (an existing file name)
            Required: input file containing the anatomical image whose
            characteristics will be cloned.
            flag: --inputAnatomicalVolume %s
    inputAnisotropyVolume: (an existing file name)
            Required: input file containing the anisotropy image
            flag: --inputAnisotropyVolume %s
    inputTransform: (an existing file name)
            Required: input Rigid OR Bspline transform file name
            flag: --inputTransform %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the resampled
            transformed anisotropy image.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformType: ('Rigid' or 'B-Spline')
            Transform type: Rigid, B-Spline
            flag: --transformType %s

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the resampled
            transformed anisotropy image.

## gtractResampleB0

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputAnatomicalVolume: (an existing file name)
            Required: input file containing the anatomical image defining the
            origin, spacing and size of the resampled image (template)
            flag: --inputAnatomicalVolume %s
    inputTransform: (an existing file name)
            Required: input Rigid OR Bspline transform file name
            flag: --inputTransform %s
    inputVolume: (an existing file name)
            Required: input file containing the 4D image
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the resampled input
            image.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformType: ('Rigid' or 'B-Spline')
            Transform type: Rigid, B-Spline
            flag: --transformType %s
    vectorIndex: (an integer (int or long))
            Index in the diffusion weighted image set for the B0 image
            flag: --vectorIndex %d

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the resampled input
            image.

## gtractResampleCodeImage

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputCodeVolume: (an existing file name)
            Required: input file containing the code image
            flag: --inputCodeVolume %s
    inputReferenceVolume: (an existing file name)
            Required: input file containing the standard image to clone the
            characteristics of.
            flag: --inputReferenceVolume %s
    inputTransform: (an existing file name)
            Required: input Rigid or Inverse-B-Spline transform file name
            flag: --inputTransform %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the resampled code
            image in acquisition space.
            flag: --outputVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    transformType: ('Rigid' or 'Affine' or 'B-Spline' or
             'Inverse-B-Spline' or 'None')
            Transform type: Rigid or Inverse-B-Spline
            flag: --transformType %s

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the resampled code
            image in acquisition space.

## gtractResampleDWIInPlace

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    debugLevel: (an integer (int or long))
            Display debug messages, and produce debug intermediate results.
            0=OFF, 1=Minimal, 10=Maximum debugging.
            flag: --debugLevel %d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    imageOutputSize: (a list of items which are an integer (int or long))
            The voxel lattice for the output image, padding is added if
            necessary. NOTE: if 0,0,0, then the inputVolume size is used.
            flag: --imageOutputSize %s
    inputTransform: (an existing file name)
            Required: transform file derived from rigid registration of b0 image
            to reference structural image.
            flag: --inputTransform %s
    inputVolume: (an existing file name)
            Required: input image is a 4D NRRD image.
            flag: --inputVolume %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputResampledB0: (a boolean or a file name)
            Convenience function for extracting the first index location
            (assumed to be the B0)
            flag: --outputResampledB0 %s
    outputVolume: (a boolean or a file name)
            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.
            flag: --outputVolume %s
    referenceVolume: (an existing file name)
            If provided, resample to the final space of the referenceVolume 3D
            data set.
            flag: --referenceVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    warpDWITransform: (an existing file name)
            Optional: transform file to warp gradient volumes.
            flag: --warpDWITransform %s

Outputs:

    outputResampledB0: (an existing file name)
            Convenience function for extracting the first index location
            (assumed to be the B0)
    outputVolume: (an existing file name)
            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

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputForwardDeformationFieldVolume: (an existing file name)
            Required: input forward deformation field image file name
            flag: --inputForwardDeformationFieldVolume %s
    inputReverseDeformationFieldVolume: (an existing file name)
            Required: input reverse deformation field image file name
            flag: --inputReverseDeformationFieldVolume %s
    inputTract: (an existing file name)
            Required: name of input vtkPolydata file containing tract lines.
            flag: --inputTract %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputTract: (a boolean or a file name)
            Required: name of output vtkPolydata file containing tract lines and
            the point data collected along them.
            flag: --outputTract %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    writeXMLPolyDataFile: (a boolean)
            Flag to make use of the XML format for vtkPolyData fiber tracts.
            flag: --writeXMLPolyDataFile

Outputs:

    outputTract: (an existing file name)
            Required: name of output vtkPolydata file containing tract lines and
            the point data collected along them.

## gtractTensor

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    applyMeasurementFrame: (a boolean)
            Flag to apply the measurement frame to the gradient directions
            flag: --applyMeasurementFrame
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    b0Index: (an integer (int or long))
            Index in input vector index to extract
            flag: --b0Index %d
    backgroundSuppressingThreshold: (an integer (int or long))
            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.
            flag: --backgroundSuppressingThreshold %d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignoreIndex: (a list of items which are an integer (int or long))
            Ignore diffusion gradient index. Used to remove specific gradient
            directions with artifacts.
            flag: --ignoreIndex %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputVolume: (an existing file name)
            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.
            flag: --inputVolume %s
    maskProcessingMode: ('NOMASK' or 'ROIAUTO' or 'ROI')
            ROIAUTO: mask is implicitly defined using a otsu forground 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
            flag: --maskProcessingMode %s
    maskVolume: (an existing file name)
            Mask Image, if maskProcessingMode is ROI
            flag: --maskVolume %s
    medianFilterSize: (a list of items which are an integer (int or
             long))
            Median filter radius in all 3 directions
            flag: --medianFilterSize %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputVolume: (a boolean or a file name)
            Required: name of output NRRD file containing the Tensor vector
            image
            flag: --outputVolume %s
    resampleIsotropic: (a boolean)
            Flag to resample to isotropic voxels. Enabling this feature is
            recommended if fiber tracking will be performed.
            flag: --resampleIsotropic
    size: (a float)
            Isotropic voxel size to resample to
            flag: --size %f
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputVolume: (an existing file name)
            Required: name of output NRRD file containing the Tensor vector
            image

## gtractTransformToDisplacementField

Link to code

Wraps command ** 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

Inputs:

    [Mandatory]

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    inputReferenceVolume: (an existing file name)
            Required: input image file name to exemplify the anatomical space
            over which to vcl_express the transform as a displacement field.
            flag: --inputReferenceVolume %s
    inputTransform: (an existing file name)
            Input Transform File Name
            flag: --inputTransform %s
    numberOfThreads: (an integer (int or long))
            Explicitly specify the maximum number of threads to use.
            flag: --numberOfThreads %d
    outputDeformationFieldVolume: (a boolean or a file name)
            Output deformation field
            flag: --outputDeformationFieldVolume %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    outputDeformationFieldVolume: (an existing file name)
            Output deformation field