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interfaces.slicer.diffusion.gtract

extractNrrdVectorIndex

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L272

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the vector image at the given index
setImageOrientation: ('AsAcquired' or 'Axial' or 'Coronal' or 'Sagittal')
        Sets the image orientation of the extracted vector (Axial, Coronal, Sagittal)
vectorIndex: (an integer)
        Index in the vector image to extract

Outputs:

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

gtractAnisotropyMap

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L529

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
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the selected kind of anisotropy scalar.

Outputs:

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

gtractAverageBvalues

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L418

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 string)
        Additional parameters to the command
averageB0only: (a boolean)
        Average only baseline gradients. All other gradient directions are not averaged, but
        retained in the outputVolume
directionsTolerance: (a float)
        Tolerance for matching identical gradient direction pairs
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing directly averaged baseline images

Outputs:

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

gtractClipAnisotropy

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L455

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 string)
        Additional parameters to the command
clipFirstSlice: (a boolean)
        Clip the first slice of the anisotropy image
clipLastSlice: (a boolean)
        Clip the last slice of the anisotropy image
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the clipped anisotropy image

Outputs:

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

gtractCoRegAnatomy

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L155

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 string)
        Additional parameters to the command
borderSize: (an integer)
        Size of border
convergence: (a float)
        Convergence Factor
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
gradientTolerance: (a float)
        Gradient Tolerance
gridSize: (an integer)
        Number of grid subdivisions in all 3 directions
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.
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.
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.
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.,
maximumStepSize: (a float)
        Maximum permitted step size to move in the selected 3D fit
minimumStepSize: (a float)
        Minimum required step size to move in the selected 3D fit without converging -- decrease
        this to make the fit more exacting
numberOfHistogramBins: (an integer)
        Number of histogram bins
numberOfIterations: (an integer)
        Number of iterations in the selected 3D fit
numberOfSamples: (an integer)
        Number of voxels sampled for mutual information computation in the selected 3D fit
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputTransformName: (a boolean or a file name)
        Required: filename for the  fit transform.
relaxationFactor: (a float)
        Fraction of gradient from Jacobian to attempt to move in the selected 3D fit
spatialScale: (an integer)
        Scales the number of voxels in the image by this value to specify the number of voxels
        used in the registration
transformType: ('Rigid' or 'Bspline')
        Transform Type: Rigid|Bspline
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
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.
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.
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.
vectorIndex: (an integer)
        Vector image index in the moving image (within the DWI) to be used for registration.

Outputs:

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

gtractConcatDwi

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L344

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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 first diffusion weighted image
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the combined diffusion weighted images.

Outputs:

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

gtractCopyImageOrientation

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L57

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
inputVolume: (an existing file name)
        Required: input file containing the signed short image to reorient without resampling.
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD or Nifti file containing the reoriented image in reference
        image space.

Outputs:

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

gtractCoregBvalues

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L725

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 string)
        Additional parameters to the command
debugLevel: (an integer)
        Display debug messages, and produce debug intermediate results.  0=OFF, 1=Minimal,
        10=Maximum debugging.
eddyCurrentCorrection: (a boolean)
        Flag to perform eddy current corection in addition to motion correction (recommended)
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
fixedVolumeIndex: (an integer)
        Index in the fixed image for registration. It is recommended that this image should be a
        b0 image.
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)
minimumStepSize: (a float)
        Minimum required step size to move in each 3D fit step without converging -- decrease
        this to make the fit more exacting
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.
numberOfIterations: (an integer)
        Number of iterations in each 3D fit
numberOfSpatialSamples: (an integer)
        Number of voxels sampled for mutual information computation in each 3D fit step
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
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.
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.
registerB0Only: (a boolean)
        Register the B0 images only
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)
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

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

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L100

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
args: (a string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
inputStartingSeedsLabelMapVolume: (an existing file name)
        Required: input starting seeds LabelMap image file name
inputTensorVolume: (an existing file name)
        Required: input tensor image file name
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputCostVolume: (a boolean or a file name)
        Output vcl_cost image
outputSpeedVolume: (a boolean or a file name)
        Output speed image
seedThreshold: (a float)
        Anisotropy threshold used for seed selection
startingSeedsLabel: (an integer)
        Label value for Starting Seeds
stoppingValue: (a float)
        Terminiating value for vcl_cost function estimation

Outputs:

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

gtractImageConformity

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L677

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
inputVolume: (an existing file name)
        Required: input file containing the signed short image to reorient without resampling.
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output Nrrd or Nifti file containing the reoriented image in reference
        image space.

Outputs:

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

gtractInvertBSplineTransform

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L309

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
inputTransform: (an existing file name)
        Required: input B-Spline transform file name
landmarkDensity: (an integer)
        Number of landmark subdivisions in all 3 directions
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputTransform: (a boolean or a file name)
        Required: output transform file name

Outputs:

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

gtractInvertDeformationField

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L381

Wraps command ** gtractInvertDeformationField **

title: Invert Deformation 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 string)
        Additional parameters to the command
baseImage: (an existing file name)
        Required: base image used to define the size of the inverse field
deformationImage: (an existing file name)
        Required: Deformation field image
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: Output deformation field
subsamplingFactor: (an integer)
        Subsampling factor for the deformation field

Outputs:

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

gtractInvertRigidTransform

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L564

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputTransform: (a boolean or a file name)
        Required: output transform file name

Outputs:

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

gtractResampleAnisotropy

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L493

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
inputAnisotropyVolume: (an existing file name)
        Required: input file containing the anisotropy image
inputTransform: (an existing file name)
        Required: input Rigid OR Bspline transform file name
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the resampled transformed anisotropy
        image.
transformType: ('Rigid' or 'B-Spline')
        Transform type: Rigid, B-Spline

Outputs:

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

gtractResampleB0

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L641

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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)
inputTransform: (an existing file name)
        Required: input Rigid OR Bspline transform file name
inputVolume: (an existing file name)
        Required: input file containing the 4D image
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the resampled input image.
transformType: ('Rigid' or 'B-Spline')
        Transform type: Rigid, B-Spline
vectorIndex: (an integer)
        Index in the diffusion weighted image set for the B0 image

Outputs:

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

gtractResampleCodeImage

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L602

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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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
inputReferenceVolume: (an existing file name)
        Required: input file containing the standard image to clone the characteristics of.
inputTransform: (an existing file name)
        Required: input Rigid or Inverse-B-Spline transform file name
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the resampled code image in acquisition
        space.
transformType: ('Rigid' or 'Affine' or 'B-Spline' or 'Inverse-B-Spline' or 'None')
        Transform type: Rigid or Inverse-B-Spline

Outputs:

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

gtractResampleDWIInPlace

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L21

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 and Greg Harris.

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

Inputs:

[Mandatory]

[Optional]
args: (a string)
        Additional parameters to the command
debugLevel: (an integer)
        Display debug messages, and produce debug intermediate results.  0=OFF, 1=Minimal,
        10=Maximum debugging.
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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: transform file derived from rigid registration of b0 image to reference
        structural image.
inputVolume: (an existing file name)
        Required: input image is a 4D NRRD image.
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: output image (NRRD file) that has been transformed into the space of the
        structural image.

Outputs:

outputVolume: (an existing file name)
        Required: output image (NRRD file) that has been transformed into the space of the
        structural image.

gtractTensor

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L235

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
args: (a string)
        Additional parameters to the command
b0Index: (an integer)
        Index in input vector index to extract
backgroundSuppressingThreshold: (an 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.
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', nipype default value: {})
        Environment variables
ignoreIndex: (an integer)
        Ignore diffusion gradient index. Used to remove specific gradient directions with
        artifacts.
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.
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
maskVolume: (an existing file name)
        Mask Image, if maskProcessingMode is ROI
medianFilterSize: (an integer)
        Median filter radius in all 3 directions
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputVolume: (a boolean or a file name)
        Required: name of output NRRD file containing the Tensor vector image
resampleIsotropic: (a boolean)
        Flag to resample to isotropic voxels. Enabling this feature is recommended if fiber
        tracking will be performed.
size: (a float)
        Isotropic voxel size to resample to

Outputs:

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

gtractTransformToDeformationField

Code: file:///build/buildd/nipype-0.6.0/nipype/interfaces/slicer/diffusion/gtract.py#L191

Wraps command ** gtractTransformToDeformationField **

title: Create Deformation 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 string)
        Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and with values which
         are a value of type 'str', 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.
inputTransform: (an existing file name)
        Input Transform File Name
numberOfThreads: (an integer)
        Explicitly specify the maximum number of threads to use.
outputDeformationFieldVolume: (a boolean or a file name)
        Output deformation field

Outputs:

outputDeformationFieldVolume: (an existing file name)
        Output deformation field