nipype.interfaces.semtools.diffusion.gtract module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
compareTractInclusion¶
Bases: SEMLikeCommandLine
Wrapped executable:
compareTractInclusion.title: Compare Tracts
category: Diffusion.GTRACT
description: This program will halt with a status code indicating whether a test tract is nearly enough included in a standard tract in the sense that every fiber in the test tract has a low enough sum of squares distance to some fiber in the standard tract modulo spline resampling of every fiber to a fixed number of points.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%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. Maps to a command-line argument:
--closeness %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})numberOfPoints (an integer) – Number of points in comparison fiber pairs. Maps to a command-line argument:
--numberOfPoints %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.standardFiber (a pathlike object or string representing an existing file) – Required: standard fiber tract file name. Maps to a command-line argument:
--standardFiber %s.testFiber (a pathlike object or string representing an existing file) – Required: test fiber tract file name. Maps to a command-line argument:
--testFiber %s.testForBijection (a boolean) – Flag to apply the closeness criterion both ways. Maps to a command-line argument:
--testForBijection.testForFiberCardinality (a boolean) – Flag to require the same number of fibers in both tracts. Maps to a command-line argument:
--testForFiberCardinality.writeXMLPolyDataFile (a boolean) – Flag to make use of XML files when reading and writing vtkPolyData. Maps to a command-line argument:
--writeXMLPolyDataFile.
extractNrrdVectorIndex¶
Bases: SEMLikeCommandLine
Wrapped executable:
extractNrrdVectorIndex.title: Extract Nrrd Index
category: Diffusion.GTRACT
description: This program will extract a 3D image (single vector) from a vector 3D image at a given vector index.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputVolume (a pathlike object or string representing an existing file) – Required: input file containing the vector that will be extracted. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the vector image at the given index. Maps to a command-line argument:
--outputVolume %s.setImageOrientation (‘AsAcquired’ or ‘Axial’ or ‘Coronal’ or ‘Sagittal’) – Sets the image orientation of the extracted vector (Axial, Coronal, Sagittal). Maps to a command-line argument:
--setImageOrientation %s.vectorIndex (an integer) – Index in the vector image to extract. Maps to a command-line argument:
--vectorIndex %d.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the vector image at the given index.
gtractAnisotropyMap¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractAnisotropyMap.title: Anisotropy Map
category: Diffusion.GTRACT
description: This program will generate a scalar map of anisotropy, given a tensor representation. Anisotropy images are used for fiber tracking, but the anisotropy scalars are not defined along the path. Instead, the tensor representation is included as point data allowing all of these metrics to be computed using only the fiber tract point data. The images can be saved in any ITK supported format, but it is suggested that you use an image format that supports the definition of the image origin. This includes NRRD, NifTI, and Meta formats. These images can also be used for scalar analysis including regional anisotropy measures or VBM style analysis.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
anisotropyType (‘ADC’ or ‘FA’ or ‘RA’ or ‘VR’ or ‘AD’ or ‘RD’ or ‘LI’) – Anisotropy Mapping Type: ADC, FA, RA, VR, AD, RD, LI. Maps to a command-line argument:
--anisotropyType %s.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputTensorVolume (a pathlike object or string representing an existing file) – Required: input file containing the diffusion tensor image. Maps to a command-line argument:
--inputTensorVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the selected kind of anisotropy scalar. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the selected kind of anisotropy scalar.
gtractAverageBvalues¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractAverageBvalues.title: Average B-Values
category: Diffusion.GTRACT
description: This program will directly average together the baseline gradients (b value equals 0) within a DWI scan. This is usually used after gtractCoregBvalues.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.averageB0only (a boolean) – Average only baseline gradients. All other gradient directions are not averaged, but retained in the outputVolume. Maps to a command-line argument:
--averageB0only.directionsTolerance (a float) – Tolerance for matching identical gradient direction pairs. Maps to a command-line argument:
--directionsTolerance %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputVolume (a pathlike object or string representing an existing file) – Required: input image file name containing multiple baseline gradients to average. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing directly averaged baseline images. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing directly averaged baseline images.
gtractClipAnisotropy¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractClipAnisotropy.title: Clip Anisotropy
category: Diffusion.GTRACT
description: This program will zero the first and/or last slice of an anisotropy image, creating a clipped anisotropy image.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.clipFirstSlice (a boolean) – Clip the first slice of the anisotropy image. Maps to a command-line argument:
--clipFirstSlice.clipLastSlice (a boolean) – Clip the last slice of the anisotropy image. Maps to a command-line argument:
--clipLastSlice.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputVolume (a pathlike object or string representing an existing file) – Required: input image file name. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the clipped anisotropy image. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the clipped anisotropy image.
gtractCoRegAnatomy¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractCoRegAnatomy.title: Coregister B0 to Anatomy B-Spline
category: Diffusion.GTRACT
description: This program will register a Nrrd diffusion weighted 4D vector image to a fixed anatomical image. Two registration methods are supported for alignment with anatomical images: Rigid and B-Spline. The rigid registration performs a rigid body registration with the anatomical images and should be done as well to initialize the B-Spline transform. The B-SPline transform is the deformable transform, where the user can control the amount of deformation based on the number of control points as well as the maximum distance that these points can move. The B-Spline registration places a low dimensional grid in the image, which is deformed. This allows for some susceptibility related distortions to be removed from the diffusion weighted images. In general the amount of motion in the slice selection and read-out directions direction should be kept low. The distortion is in the phase encoding direction in the images. It is recommended that skull stripped (i.e. image containing only brain with skull removed) images should be used for image co-registration with the B-Spline transform.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.borderSize (an integer) – Size of border. Maps to a command-line argument:
--borderSize %d.convergence (a float) – Convergence Factor. Maps to a command-line argument:
--convergence %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})gradientTolerance (a float) – Gradient Tolerance. Maps to a command-line argument:
--gradientTolerance %f.gridSize (a list of items which are an integer) – Number of grid subdivisions in all 3 directions. Maps to a command-line argument:
--gridSize %s.inputAnatomicalVolume (a pathlike object or string representing an existing file) – Required: input anatomical image file name. It is recommended that the input anatomical image has been skull stripped and has the same orientation as the DWI scan. Maps to a command-line argument:
--inputAnatomicalVolume %s.inputRigidTransform (a pathlike object or string representing an existing file) – Required (for B-Spline type co-registration): input rigid transform file name. Used as a starting point for the anatomical B-Spline registration. Maps to a command-line argument:
--inputRigidTransform %s.inputVolume (a pathlike object or string representing an existing file) – Required: input vector image file name. It is recommended that the input volume is the skull stripped baseline image of the DWI scan. Maps to a command-line argument:
--inputVolume %s.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., . Maps to a command-line argument:
--maxBSplineDisplacement %f.maximumStepSize (a float) – Maximum permitted step size to move in the selected 3D fit. Maps to a command-line argument:
--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. Maps to a command-line argument:
--minimumStepSize %f.numberOfHistogramBins (an integer) – Number of histogram bins. Maps to a command-line argument:
--numberOfHistogramBins %d.numberOfIterations (an integer) – Number of iterations in the selected 3D fit. Maps to a command-line argument:
--numberOfIterations %d.numberOfSamples (an integer) – The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. NOTE that it is suggested to use samplingPercentage instead of this option. However, if set, it overwrites the samplingPercentage option. . Maps to a command-line argument:
--numberOfSamples %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTransformName (a boolean or a pathlike object or string representing a file) – Required: filename for the fit transform. Maps to a command-line argument:
--outputTransformName %s.relaxationFactor (a float) – Fraction of gradient from Jacobian to attempt to move in the selected 3D fit. Maps to a command-line argument:
--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. Maps to a command-line argument:
--samplingPercentage %f.spatialScale (an integer) – Scales the number of voxels in the image by this value to specify the number of voxels used in the registration. Maps to a command-line argument:
--spatialScale %d.transformType (‘Rigid’ or ‘Bspline’) – Transform Type: Rigid|Bspline. Maps to a command-line argument:
--transformType %s.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. Maps to a command-line argument:
--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 supersedes the use of transformType if any of them are set. Maps to a command-line argument:
--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 supersedes the use of transformType if any of them are set. Maps to a command-line argument:
--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 supersedes the use of transformType if any of them are set. Maps to a command-line argument:
--useMomentsAlign.vectorIndex (an integer) – Vector image index in the moving image (within the DWI) to be used for registration. Maps to a command-line argument:
--vectorIndex %d.- Outputs:
outputTransformName (a pathlike object or string representing an existing file) – Required: filename for the fit transform.
gtractConcatDwi¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractConcatDwi.title: Concat DWI Images
category: Diffusion.GTRACT
description: This program will concatenate two DTI runs together.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})ignoreOrigins (a boolean) – If image origins are different force all images to origin of first image. Maps to a command-line argument:
--ignoreOrigins.inputVolume (a list of items which are a pathlike object or string representing an existing file) – Required: input file containing the first diffusion weighted image. Maps to a command-line argument:
--inputVolume %s....numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the combined diffusion weighted images. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the combined diffusion weighted images.
gtractCopyImageOrientation¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractCopyImageOrientation.title: Copy Image Orientation
category: Diffusion.GTRACT
description: This program will copy the orientation from the reference image into the moving image. Currently, the registration process requires that the diffusion weighted images and the anatomical images have the same image orientation (i.e. Axial, Coronal, Sagittal). It is suggested that you copy the image orientation from the diffusion weighted images and apply this to the anatomical image. This image can be subsequently removed after the registration step is complete. We anticipate that this limitation will be removed in future versions of the registration programs.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputReferenceVolume (a pathlike object or string representing an existing file) – Required: input file containing orientation that will be cloned. Maps to a command-line argument:
--inputReferenceVolume %s.inputVolume (a pathlike object or string representing an existing file) – Required: input file containing the signed short image to reorient without resampling. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD or Nifti file containing the reoriented image in reference image space. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD or Nifti file containing the reoriented image in reference image space.
gtractCoregBvalues¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractCoregBvalues.title: Coregister B-Values
category: Diffusion.GTRACT
description: This step should be performed after converting DWI scans from DICOM to NRRD format. This program will register all gradients in a NRRD diffusion weighted 4D vector image (moving image) to a specified index in a fixed image. It also supports co-registration with a T2 weighted image or field map in the same plane as the DWI data. The fixed image for the registration should be a b0 image. A mutual information metric cost function is used for the registration because of the differences in signal intensity as a result of the diffusion gradients. The full affine allows the registration procedure to correct for eddy current distortions that may exist in the data. If the eddyCurrentCorrection is enabled, relaxationFactor (0.25) and maximumStepSize (0.1) should be adjusted.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.debugLevel (an integer) – Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. Maps to a command-line argument:
--debugLevel %d.eddyCurrentCorrection (a boolean) – Flag to perform eddy current correction in addition to motion correction (recommended). Maps to a command-line argument:
--eddyCurrentCorrection.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})fixedVolume (a pathlike object or string representing an existing file) – Required: input fixed image file name. It is recommended that this image should either contain or be a b0 image. Maps to a command-line argument:
--fixedVolume %s.fixedVolumeIndex (an integer) – Index in the fixed image for registration. It is recommended that this image should be a b0 image. Maps to a command-line argument:
--fixedVolumeIndex %d.maximumStepSize (a float) – Maximum permitted step size to move in each 3D fit step (adjust when eddyCurrentCorrection is enabled; suggested value = 0.1). Maps to a command-line argument:
--maximumStepSize %f.minimumStepSize (a float) – Minimum required step size to move in each 3D fit step without converging – decrease this to make the fit more exacting. Maps to a command-line argument:
--minimumStepSize %f.movingVolume (a pathlike object or string representing an existing file) – Required: input moving image file name. In order to register gradients within a scan to its first gradient, set the movingVolume and fixedVolume as the same image. Maps to a command-line argument:
--movingVolume %s.numberOfIterations (an integer) – Number of iterations in each 3D fit. Maps to a command-line argument:
--numberOfIterations %d.numberOfSpatialSamples (an integer) – The number of voxels sampled for mutual information computation. Increase this for a slower, more careful fit. NOTE that it is suggested to use samplingPercentage instead of this option. However, if set, it overwrites the samplingPercentage option. . Maps to a command-line argument:
--numberOfSpatialSamples %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTransform (a boolean or a pathlike object or string representing a file) – Registration 3D transforms concatenated in a single output file. There are no tools that can use this, but can be used for debugging purposes. Maps to a command-line argument:
--outputTransform %s.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing moving images individually resampled and fit to the specified fixed image index. Maps to a command-line argument:
--outputVolume %s.registerB0Only (a boolean) – Register the B0 images only. Maps to a command-line argument:
--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). Maps to a command-line argument:
--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. Maps to a command-line argument:
--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. Maps to a command-line argument:
--spatialScale %f.- Outputs:
outputTransform (a pathlike object or string representing an existing file) – Registration 3D transforms concatenated in a single output file. There are no tools that can use this, but can be used for debugging purposes.
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing moving images individually resampled and fit to the specified fixed image index.
gtractCostFastMarching¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractCostFastMarching.title: Cost Fast Marching
category: Diffusion.GTRACT
description: This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the first portion of the algorithm. The user must first run gtractFastMarchingTracking to generate the actual fiber tracts. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
anisotropyWeight (a float) – Anisotropy weight used for vcl_cost function calculations. Maps to a command-line argument:
--anisotropyWeight %f.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputAnisotropyVolume (a pathlike object or string representing an existing file) – Required: input anisotropy image file name. Maps to a command-line argument:
--inputAnisotropyVolume %s.inputStartingSeedsLabelMapVolume (a pathlike object or string representing an existing file) – Required: input starting seeds LabelMap image file name. Maps to a command-line argument:
--inputStartingSeedsLabelMapVolume %s.inputTensorVolume (a pathlike object or string representing an existing file) – Required: input tensor image file name. Maps to a command-line argument:
--inputTensorVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputCostVolume (a boolean or a pathlike object or string representing a file) – Output vcl_cost image. Maps to a command-line argument:
--outputCostVolume %s.outputSpeedVolume (a boolean or a pathlike object or string representing a file) – Output speed image. Maps to a command-line argument:
--outputSpeedVolume %s.seedThreshold (a float) – Anisotropy threshold used for seed selection. Maps to a command-line argument:
--seedThreshold %f.startingSeedsLabel (an integer) – Label value for Starting Seeds. Maps to a command-line argument:
--startingSeedsLabel %d.stoppingValue (a float) – Terminating value for vcl_cost function estimation. Maps to a command-line argument:
--stoppingValue %f.- Outputs:
outputCostVolume (a pathlike object or string representing an existing file) – Output vcl_cost image.
outputSpeedVolume (a pathlike object or string representing an existing file) – Output speed image.
gtractCreateGuideFiber¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractCreateGuideFiber.title: Create Guide Fiber
category: Diffusion.GTRACT
description: This program will create a guide fiber by averaging fibers from a previously generated tract.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputFiber (a pathlike object or string representing an existing file) – Required: input fiber tract file name. Maps to a command-line argument:
--inputFiber %s.numberOfPoints (an integer) – Number of points in output guide fiber. Maps to a command-line argument:
--numberOfPoints %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputFiber (a boolean or a pathlike object or string representing a file) – Required: output guide fiber file name. Maps to a command-line argument:
--outputFiber %s.writeXMLPolyDataFile (a boolean) – Flag to make use of XML files when reading and writing vtkPolyData. Maps to a command-line argument:
--writeXMLPolyDataFile.- Outputs:
outputFiber (a pathlike object or string representing an existing file) – Required: output guide fiber file name.
gtractFastMarchingTracking¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractFastMarchingTracking.title: Fast Marching Tracking
category: Diffusion.GTRACT
description: This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the second portion of the algorithm. The user must first run gtractCostFastMarching to generate the vcl_cost image. The second step of the algorithm implemented here is a gradient descent soplution from the defined ending region back to the seed points specified in gtractCostFastMarching. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.costStepSize (a float) – Cost image sub-voxel sampling. Maps to a command-line argument:
--costStepSize %f.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputAnisotropyVolume (a pathlike object or string representing an existing file) – Required: input anisotropy image file name. Maps to a command-line argument:
--inputAnisotropyVolume %s.inputCostVolume (a pathlike object or string representing an existing file) – Required: input vcl_cost image file name. Maps to a command-line argument:
--inputCostVolume %s.inputStartingSeedsLabelMapVolume (a pathlike object or string representing an existing file) – Required: input starting seeds LabelMap image file name. Maps to a command-line argument:
--inputStartingSeedsLabelMapVolume %s.inputTensorVolume (a pathlike object or string representing an existing file) – Required: input tensor image file name. Maps to a command-line argument:
--inputTensorVolume %s.maximumStepSize (a float) – Maximum step size to move when tracking. Maps to a command-line argument:
--maximumStepSize %f.minimumStepSize (a float) – Minimum step size to move when tracking. Maps to a command-line argument:
--minimumStepSize %f.numberOfIterations (an integer) – Number of iterations used for the optimization. Maps to a command-line argument:
--numberOfIterations %d.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTract (a boolean or a pathlike object or string representing a file) – Required: name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument:
--outputTract %s.seedThreshold (a float) – Anisotropy threshold used for seed selection. Maps to a command-line argument:
--seedThreshold %f.startingSeedsLabel (an integer) – Label value for Starting Seeds. Maps to a command-line argument:
--startingSeedsLabel %d.trackingThreshold (a float) – Anisotropy threshold used for fiber tracking. Maps to a command-line argument:
--trackingThreshold %f.writeXMLPolyDataFile (a boolean) – Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument:
--writeXMLPolyDataFile.- Outputs:
outputTract (a pathlike object or string representing an existing file) – Required: name of output vtkPolydata file containing tract lines and the point data collected along them.
gtractFiberTracking¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractFiberTracking.title: Fiber Tracking
category: Diffusion.GTRACT
description: This program implements four fiber tracking methods (Free, Streamline, GraphSearch, Guided). The output of the fiber tracking is vtkPolyData (i.e. Polylines) that can be loaded into Slicer3 for visualization. The poly data can be saved in either old VTK format files (.vtk) or in the new VTK XML format (.xml). The polylines contain point data that defines the Tensor at each point along the fiber tract. This can then be used to rendered as glyphs in Slicer3 and can be used to define several scalar measures without referencing back to the anisotropy images. (1) Free tracking is a basic streamlines algorithm. This is a direct implementation of the method original proposed by Basser et al. The tracking follows the primarty eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either as a result of maximum fiber length, low ansiotropy, or large curvature. This is a great way to explore your data. (2) The streamlines algorithm is a direct implementation of the method originally proposed by Basser et al. The tracking follows the primary eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either by reaching the ending region or reaching some stopping criteria. Stopping criteria are specified using the following parameters: tracking threshold, curvature threshold, and max length. Only paths terminating in the ending region are kept in this method. The TEND algorithm proposed by Lazar et al. (Human Brain Mapping 18:306-321, 2003) has been instrumented. This can be enabled using the –useTend option while performing Streamlines tracking. This utilizes the entire diffusion tensor to deflect the incoming vector instead of simply following the primary eigenvector. The TEND parameters are set using the –tendF and –tendG options. (3) Graph Search tracking is the first step in the full GTRACT algorithm developed by Cheng et al. (NeuroImage 31(3): 1075-1085, 2006) for finding the tracks in a tensor image. This method was developed to generate fibers in a Tensor representation where crossing fibers occur. The graph search algorithm follows the primary eigenvector in non-ambiguous regions and utilizes branching and a graph search algorithm in ambiguous regions. Ambiguous tracking regions are defined based on two criteria: Branching Al Threshold (anisotropy values below this value and above the traching threshold) and Curvature Major Eigen (angles of the primary eigenvector direction and the current tracking direction). In regions that meet this criteria, two or three tracking paths are considered. The first is the standard primary eigenvector direction. The second is the seconadary eigenvector direction. This is based on the assumption that these regions may be prolate regions. If the Random Walk option is selected then a third direction is also considered. This direction is defined by a cone pointing from the current position to the centroid of the ending region. The interior angle of the cone is specified by the user with the Branch/Guide Angle parameter. A vector contained inside of the cone is selected at random and used as the third direction. This method can also utilize the TEND option where the primary tracking direction is that specified by the TEND method instead of the primary eigenvector. The parameter ‘–maximumBranchPoints’ allows the tracking to have this number of branches being considered at a time. If this number of branch points is exceeded at any time, then the algorithm will revert back to a streamline algorithm until the number of branches is reduced. This allows the user to constrain the computational complexity of the algorithm. (4) The second phase of the GTRACT algorithm is Guided Tracking. This method incorporates anatomical information about the track orientation using an initial guess of the fiber track. In the originally proposed GTRACT method, this would be created from the fibers resulting from the Graph Search tracking. However, in practice this can be created using any method and could be defined manually. To create the guide fiber the program gtractCreateGuideFiber can be used. This program will load a fiber tract that has been generated and create a centerline representation of the fiber tract (i.e. a single fiber). In this method, the fiber tracking follows the primary eigenvector direction unless it deviates from the guide fiber track by a angle greater than that specified by the ‘–guidedCurvatureThreshold’ parameter. The user must specify the guide fiber when running this program.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta, Greg Harris and Yongqiang Zhao.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.branchingAngle (a float) – Branching angle in degrees (recommended for GraphSearch fiber tracking method). Maps to a command-line argument:
--branchingAngle %f.branchingThreshold (a float) – Anisotropy Branching threshold (recommended for GraphSearch fiber tracking method). Maps to a command-line argument:
--branchingThreshold %f.curvatureThreshold (a float) – Curvature threshold in degrees (recommended for Free fiber tracking). Maps to a command-line argument:
--curvatureThreshold %f.endingSeedsLabel (an integer) – Label value for Ending Seeds (required if Label number used to create seed point in Slicer was not 1). Maps to a command-line argument:
--endingSeedsLabel %d.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})guidedCurvatureThreshold (a float) – Guided Curvature Threshold (Degrees). Maps to a command-line argument:
--guidedCurvatureThreshold %f.inputAnisotropyVolume (a pathlike object or string representing an existing file) – Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input anisotropy image file name. Maps to a command-line argument:
--inputAnisotropyVolume %s.inputEndingSeedsLabelMapVolume (a pathlike object or string representing an existing file) – Required (for Streamline, GraphSearch, and Guided fiber tracking methods): input ending seeds LabelMap image file name. Maps to a command-line argument:
--inputEndingSeedsLabelMapVolume %s.inputStartingSeedsLabelMapVolume (a pathlike object or string representing an existing file) – Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input starting seeds LabelMap image file name. Maps to a command-line argument:
--inputStartingSeedsLabelMapVolume %s.inputTensorVolume (a pathlike object or string representing an existing file) – Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): input tensor image file name. Maps to a command-line argument:
--inputTensorVolume %s.inputTract (a pathlike object or string representing an existing file) – Required (for Guided fiber tracking method): guide fiber in vtkPolydata file containing one tract line. Maps to a command-line argument:
--inputTract %s.maximumBranchPoints (an integer) – Maximum branch points (recommended for GraphSearch fiber tracking method). Maps to a command-line argument:
--maximumBranchPoints %d.maximumGuideDistance (a float) – Maximum distance for using the guide fiber direction. Maps to a command-line argument:
--maximumGuideDistance %f.maximumLength (a float) – Maximum fiber length (voxels). Maps to a command-line argument:
--maximumLength %f.minimumLength (a float) – Minimum fiber length. Helpful for filtering invalid tracts. Maps to a command-line argument:
--minimumLength %f.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTract (a boolean or a pathlike object or string representing a file) – Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument:
--outputTract %s.randomSeed (an integer) – Random number generator seed. Maps to a command-line argument:
--randomSeed %d.seedThreshold (a float) – Anisotropy threshold for seed selection (recommended for Free fiber tracking). Maps to a command-line argument:
--seedThreshold %f.startingSeedsLabel (an integer) – Label value for Starting Seeds (required if Label number used to create seed point in Slicer was not 1). Maps to a command-line argument:
--startingSeedsLabel %d.stepSize (a float) – Fiber tracking step size. Maps to a command-line argument:
--stepSize %f.tendF (a float) – Tend F parameter. Maps to a command-line argument:
--tendF %f.tendG (a float) – Tend G parameter. Maps to a command-line argument:
--tendG %f.trackingMethod (‘Guided’ or ‘Free’ or ‘Streamline’ or ‘GraphSearch’) – Fiber tracking Filter Type: Guided|Free|Streamline|GraphSearch. Maps to a command-line argument:
--trackingMethod %s.trackingThreshold (a float) – Anisotropy threshold for fiber tracking (anisotropy values of the next point along the path). Maps to a command-line argument:
--trackingThreshold %f.useLoopDetection (a boolean) – Flag to make use of loop detection. Maps to a command-line argument:
--useLoopDetection.useRandomWalk (a boolean) – Flag to use random walk. Maps to a command-line argument:
--useRandomWalk.useTend (a boolean) – Flag to make use of Tend F and Tend G parameters. Maps to a command-line argument:
--useTend.writeXMLPolyDataFile (a boolean) – Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument:
--writeXMLPolyDataFile.- Outputs:
outputTract (a pathlike object or string representing an existing file) – Required (for Free, Streamline, GraphSearch, and Guided fiber tracking methods): name of output vtkPolydata file containing tract lines and the point data collected along them.
gtractImageConformity¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractImageConformity.title: Image Conformity
category: Diffusion.GTRACT
description: This program will straighten out the Direction and Origin to match the Reference Image.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputReferenceVolume (a pathlike object or string representing an existing file) – Required: input file containing the standard image to clone the characteristics of. Maps to a command-line argument:
--inputReferenceVolume %s.inputVolume (a pathlike object or string representing an existing file) – Required: input file containing the signed short image to reorient without resampling. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output Nrrd or Nifti file containing the reoriented image in reference image space. Maps to a command-line argument:
--outputVolume %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output Nrrd or Nifti file containing the reoriented image in reference image space.
gtractInvertBSplineTransform¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractInvertBSplineTransform.title: B-Spline Transform Inversion
category: Diffusion.GTRACT
description: This program will invert a B-Spline transform using a thin-plate spline approximation.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputReferenceVolume (a pathlike object or string representing an existing file) – Required: input image file name to exemplify the anatomical space to interpolate over. Maps to a command-line argument:
--inputReferenceVolume %s.inputTransform (a pathlike object or string representing an existing file) – Required: input B-Spline transform file name. Maps to a command-line argument:
--inputTransform %s.landmarkDensity (a list of items which are an integer) – Number of landmark subdivisions in all 3 directions. Maps to a command-line argument:
--landmarkDensity %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTransform (a boolean or a pathlike object or string representing a file) – Required: output transform file name. Maps to a command-line argument:
--outputTransform %s.- Outputs:
outputTransform (a pathlike object or string representing an existing file) – Required: output transform file name.
gtractInvertDisplacementField¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractInvertDisplacementField.title: Invert Displacement Field
category: Diffusion.GTRACT
description: This program will invert a deformatrion field. The size of the deformation field is defined by an example image provided by the user
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.baseImage (a pathlike object or string representing an existing file) – Required: base image used to define the size of the inverse field. Maps to a command-line argument:
--baseImage %s.deformationImage (a pathlike object or string representing an existing file) – Required: Displacement field image. Maps to a command-line argument:
--deformationImage %s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: Output deformation field. Maps to a command-line argument:
--outputVolume %s.subsamplingFactor (an integer) – Subsampling factor for the deformation field. Maps to a command-line argument:
--subsamplingFactor %d.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: Output deformation field.
gtractInvertRigidTransform¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractInvertRigidTransform.title: Rigid Transform Inversion
category: Diffusion.GTRACT
description: This program will invert a Rigid transform.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputTransform (a pathlike object or string representing an existing file) – Required: input rigid transform file name. Maps to a command-line argument:
--inputTransform %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTransform (a boolean or a pathlike object or string representing a file) – Required: output transform file name. Maps to a command-line argument:
--outputTransform %s.- Outputs:
outputTransform (a pathlike object or string representing an existing file) – Required: output transform file name.
gtractResampleAnisotropy¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractResampleAnisotropy.title: Resample Anisotropy
category: Diffusion.GTRACT
description: This program will resample a floating point image using either the Rigid or B-Spline transform. You may want to save the aligned B0 image after each of the anisotropy map co-registration steps with the anatomical image to check the registration quality with another tool.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputAnatomicalVolume (a pathlike object or string representing an existing file) – Required: input file containing the anatomical image whose characteristics will be cloned. Maps to a command-line argument:
--inputAnatomicalVolume %s.inputAnisotropyVolume (a pathlike object or string representing an existing file) – Required: input file containing the anisotropy image. Maps to a command-line argument:
--inputAnisotropyVolume %s.inputTransform (a pathlike object or string representing an existing file) – Required: input Rigid OR Bspline transform file name. Maps to a command-line argument:
--inputTransform %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the resampled transformed anisotropy image. Maps to a command-line argument:
--outputVolume %s.transformType (‘Rigid’ or ‘B-Spline’) – Transform type: Rigid, B-Spline. Maps to a command-line argument:
--transformType %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the resampled transformed anisotropy image.
gtractResampleB0¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractResampleB0.title: Resample B0
category: Diffusion.GTRACT
description: This program will resample a signed short image using either a Rigid or B-Spline transform. The user must specify a template image that will be used to define the origin, orientation, spacing, and size of the resampled image.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputAnatomicalVolume (a pathlike object or string representing an existing file) – Required: input file containing the anatomical image defining the origin, spacing and size of the resampled image (template). Maps to a command-line argument:
--inputAnatomicalVolume %s.inputTransform (a pathlike object or string representing an existing file) – Required: input Rigid OR Bspline transform file name. Maps to a command-line argument:
--inputTransform %s.inputVolume (a pathlike object or string representing an existing file) – Required: input file containing the 4D image. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the resampled input image. Maps to a command-line argument:
--outputVolume %s.transformType (‘Rigid’ or ‘B-Spline’) – Transform type: Rigid, B-Spline. Maps to a command-line argument:
--transformType %s.vectorIndex (an integer) – Index in the diffusion weighted image set for the B0 image. Maps to a command-line argument:
--vectorIndex %d.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the resampled input image.
gtractResampleCodeImage¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractResampleCodeImage.title: Resample Code Image
category: Diffusion.GTRACT
description: This program will resample a short integer code image using either the Rigid or Inverse-B-Spline transform. The reference image is the DTI tensor anisotropy image space, and the input code image is in anatomical space.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputCodeVolume (a pathlike object or string representing an existing file) – Required: input file containing the code image. Maps to a command-line argument:
--inputCodeVolume %s.inputReferenceVolume (a pathlike object or string representing an existing file) – Required: input file containing the standard image to clone the characteristics of. Maps to a command-line argument:
--inputReferenceVolume %s.inputTransform (a pathlike object or string representing an existing file) – Required: input Rigid or Inverse-B-Spline transform file name. Maps to a command-line argument:
--inputTransform %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the resampled code image in acquisition space. Maps to a command-line argument:
--outputVolume %s.transformType (‘Rigid’ or ‘Affine’ or ‘B-Spline’ or ‘Inverse-B-Spline’ or ‘None’) – Transform type: Rigid or Inverse-B-Spline. Maps to a command-line argument:
--transformType %s.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the resampled code image in acquisition space.
gtractResampleDWIInPlace¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractResampleDWIInPlace.title: Resample DWI In Place
category: Diffusion.GTRACT
description: Resamples DWI image to structural image.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta, Greg Harris, Hans Johnson, and Joy Matsui.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.debugLevel (an integer) – Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. Maps to a command-line argument:
--debugLevel %d.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})imageOutputSize (a list of items which are an integer) – The voxel lattice for the output image, padding is added if necessary. NOTE: if 0,0,0, then the inputVolume size is used. Maps to a command-line argument:
--imageOutputSize %s.inputTransform (a pathlike object or string representing an existing file) – Required: transform file derived from rigid registration of b0 image to reference structural image. Maps to a command-line argument:
--inputTransform %s.inputVolume (a pathlike object or string representing an existing file) – Required: input image is a 4D NRRD image. Maps to a command-line argument:
--inputVolume %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputResampledB0 (a boolean or a pathlike object or string representing a file) – Convenience function for extracting the first index location (assumed to be the B0). Maps to a command-line argument:
--outputResampledB0 %s.outputVolume (a boolean or a pathlike object or string representing a file) – Required: output image (NRRD file) that has been rigidly transformed into the space of the structural image and padded if image padding was changed from 0,0,0 default. Maps to a command-line argument:
--outputVolume %s.referenceVolume (a pathlike object or string representing an existing file) – If provided, resample to the final space of the referenceVolume 3D data set. Maps to a command-line argument:
--referenceVolume %s.warpDWITransform (a pathlike object or string representing an existing file) – Optional: transform file to warp gradient volumes. Maps to a command-line argument:
--warpDWITransform %s.- Outputs:
outputResampledB0 (a pathlike object or string representing an existing file) – Convenience function for extracting the first index location (assumed to be the B0).
outputVolume (a pathlike object or string representing an existing file) – Required: output image (NRRD file) that has been rigidly transformed into the space of the structural image and padded if image padding was changed from 0,0,0 default.
gtractResampleFibers¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractResampleFibers.title: Resample Fibers
category: Diffusion.GTRACT
description: This program will resample a fiber tract with respect to a pair of deformation fields that represent the forward and reverse deformation fields.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputForwardDeformationFieldVolume (a pathlike object or string representing an existing file) – Required: input forward deformation field image file name. Maps to a command-line argument:
--inputForwardDeformationFieldVolume %s.inputReverseDeformationFieldVolume (a pathlike object or string representing an existing file) – Required: input reverse deformation field image file name. Maps to a command-line argument:
--inputReverseDeformationFieldVolume %s.inputTract (a pathlike object or string representing an existing file) – Required: name of input vtkPolydata file containing tract lines. Maps to a command-line argument:
--inputTract %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputTract (a boolean or a pathlike object or string representing a file) – Required: name of output vtkPolydata file containing tract lines and the point data collected along them. Maps to a command-line argument:
--outputTract %s.writeXMLPolyDataFile (a boolean) – Flag to make use of the XML format for vtkPolyData fiber tracts. Maps to a command-line argument:
--writeXMLPolyDataFile.- Outputs:
outputTract (a pathlike object or string representing an existing file) – Required: name of output vtkPolydata file containing tract lines and the point data collected along them.
gtractTensor¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractTensor.title: Tensor Estimation
category: Diffusion.GTRACT
description: This step will convert a b-value averaged diffusion tensor image to a 3x3 tensor voxel image. This step takes the diffusion tensor image data and generates a tensor representation of the data based on the signal intensity decay, b values applied, and the diffusion difrections. The apparent diffusion coefficient for a given orientation is computed on a pixel-by-pixel basis by fitting the image data (voxel intensities) to the Stejskal-Tanner equation. If at least 6 diffusion directions are used, then the diffusion tensor can be computed. This program uses itk::DiffusionTensor3DReconstructionImageFilter. The user can adjust background threshold, median filter, and isotropic resampling.
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta and Greg Harris.
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
applyMeasurementFrame (a boolean) – Flag to apply the measurement frame to the gradient directions. Maps to a command-line argument:
--applyMeasurementFrame.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.b0Index (an integer) – Index in input vector index to extract. Maps to a command-line argument:
--b0Index %d.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. Maps to a command-line argument:
--backgroundSuppressingThreshold %d.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})ignoreIndex (a list of items which are an integer) – Ignore diffusion gradient index. Used to remove specific gradient directions with artifacts. Maps to a command-line argument:
--ignoreIndex %s.inputVolume (a pathlike object or string representing an existing file) – Required: input image 4D NRRD image. Must contain data based on at least 6 distinct diffusion directions. The inputVolume is allowed to have multiple b0 and gradient direction images. Averaging of the b0 image is done internally in this step. Prior averaging of the DWIs is not required. Maps to a command-line argument:
--inputVolume %s.maskProcessingMode (‘NOMASK’ or ‘ROIAUTO’ or ‘ROI’) – ROIAUTO: mask is implicitly defined using a otsu foreground and hole filling algorithm. ROI: Uses the masks to define what parts of the image should be used for computing the transform. NOMASK: no mask used. Maps to a command-line argument:
--maskProcessingMode %s.maskVolume (a pathlike object or string representing an existing file) – Mask Image, if maskProcessingMode is ROI. Maps to a command-line argument:
--maskVolume %s.medianFilterSize (a list of items which are an integer) – Median filter radius in all 3 directions. Maps to a command-line argument:
--medianFilterSize %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputVolume (a boolean or a pathlike object or string representing a file) – Required: name of output NRRD file containing the Tensor vector image. Maps to a command-line argument:
--outputVolume %s.resampleIsotropic (a boolean) – Flag to resample to isotropic voxels. Enabling this feature is recommended if fiber tracking will be performed. Maps to a command-line argument:
--resampleIsotropic.size (a float) – Isotropic voxel size to resample to. Maps to a command-line argument:
--size %f.- Outputs:
outputVolume (a pathlike object or string representing an existing file) – Required: name of output NRRD file containing the Tensor vector image.
gtractTransformToDisplacementField¶
Bases: SEMLikeCommandLine
Wrapped executable:
gtractTransformToDisplacementField.title: Create Displacement Field
category: Diffusion.GTRACT
description: This program will compute forward deformation from the given Transform. The size of the DF is equal to MNI space
version: 4.0.0
documentation-url: http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT
license: http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt
contributor: This tool was developed by Vincent Magnotta, Madhura Ingalhalikar, and Greg Harris
acknowledgements: Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})inputReferenceVolume (a pathlike object or string representing an existing file) – Required: input image file name to exemplify the anatomical space over which to vcl_express the transform as a displacement field. Maps to a command-line argument:
--inputReferenceVolume %s.inputTransform (a pathlike object or string representing an existing file) – Input Transform File Name. Maps to a command-line argument:
--inputTransform %s.numberOfThreads (an integer) – Explicitly specify the maximum number of threads to use. Maps to a command-line argument:
--numberOfThreads %d.outputDeformationFieldVolume (a boolean or a pathlike object or string representing a file) – Output deformation field. Maps to a command-line argument:
--outputDeformationFieldVolume %s.- Outputs:
outputDeformationFieldVolume (a pathlike object or string representing an existing file) – Output deformation field.