nipype.interfaces.semtools.diffusion.tractography.ukftractography module¶
Autogenerated file - DO NOT EDIT If you spot a bug, please report it on the mailing list and/or change the generator.
UKFTractography¶
Bases: SEMLikeCommandLine
Wrapped executable:
UKFTractography.title: UKF Tractography
category: Diffusion.Tractography
description: This module traces fibers in a DWI Volume using the multiple tensor unscented Kalman Filter methology. For more information check the documentation.
version: 1.0
documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/ukftractography:MainPage
contributor: Yogesh Rathi, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner, Kent Williams, Hans Johnson, Peter Savadjiev, Carl-Fredrik Westin.
acknowledgements: The development of this module was supported by NIH grants R01 MH097979 (PI Rathi), R01 MH092862 (PIs Westin and Verma), U01 NS083223 (PI Westin), R01 MH074794 (PI Westin) and P41 EB015902 (PI Kikinis).
- Optional Inputs:
Ql (a float) – Process noise for eigenvalues. Maps to a command-line argument:
--Ql %f.Qm (a float) – Process noise for angles/direction. Maps to a command-line argument:
--Qm %f.Qw (a float) – Process noise for free water weights, ignored if no free water estimation. Maps to a command-line argument:
--Qw %f.Rs (a float) – Measurement noise. Maps to a command-line argument:
--Rs %f.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.dwiFile (a pathlike object or string representing an existing file) – Input DWI volume. Maps to a command-line argument:
--dwiFile %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:
{})freeWater (a boolean) – Adds a term for free water difusion to the model. (Note for experts: if checked, the 1T simple model is forced) . Maps to a command-line argument:
--freeWater.fullTensorModel (a boolean) – Whether to use the full tensor model. If unchecked, use the default simple tensor model. Maps to a command-line argument:
--fullTensorModel.labels (a list of items which are an integer) – A vector of the ROI labels to be used. Maps to a command-line argument:
--labels %s.maskFile (a pathlike object or string representing an existing file) – Mask for diffusion tractography. Maps to a command-line argument:
--maskFile %s.maxBranchingAngle (a float) – Maximum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors’ major directions form an angle between (minBranchingAngle, maxBranchingAngle). Branching is suppressed when this maxBranchingAngle is set to 0.0. Maps to a command-line argument:
--maxBranchingAngle %f.maxHalfFiberLength (a float) – The max length limit of the half fibers generated during tractography. Here the fiber is ‘half’ because the tractography goes in only one direction from one seed point at a time. Maps to a command-line argument:
--maxHalfFiberLength %f.minBranchingAngle (a float) – Minimum branching angle, in degrees. When using multiple tensors, a new branch will be created when the tensors’ major directions form an angle between (minBranchingAngle, maxBranchingAngle). Maps to a command-line argument:
--minBranchingAngle %f.minFA (a float) – Abort the tractography when the Fractional Anisotropy is less than this value. Maps to a command-line argument:
--minFA %f.minGA (a float) – Abort the tractography when the Generalized Anisotropy is less than this value. Maps to a command-line argument:
--minGA %f.numTensor (‘1’ or ‘2’) – Number of tensors used. Maps to a command-line argument:
--numTensor %s.numThreads (an integer) – Number of threads used during computation. Set to the number of cores on your workstation for optimal speed. If left undefined the number of cores detected will be used. . Maps to a command-line argument:
--numThreads %d.recordCovariance (a boolean) – Whether to store the covariance. Will generate field ‘covariance’ in fiber. Maps to a command-line argument:
--recordCovariance.recordFA (a boolean) – Whether to store FA. Attaches field ‘FA’, and ‘FA2’ for 2-tensor case to fiber. . Maps to a command-line argument:
--recordFA.recordFreeWater (a boolean) – Whether to store the fraction of free water. Attaches field ‘FreeWater’ to fiber. Maps to a command-line argument:
--recordFreeWater.recordLength (a float) – Record length of tractography, in millimeters. Maps to a command-line argument:
--recordLength %f.recordNMSE (a boolean) – Whether to store NMSE. Attaches field ‘NMSE’ to fiber. . Maps to a command-line argument:
--recordNMSE.recordState (a boolean) – Whether to attach the states to the fiber. Will generate field ‘state’. Maps to a command-line argument:
--recordState.recordTensors (a boolean) – Recording the tensors enables Slicer to color the fiber bundles by FA, orientation, and so on. The fields will be called ‘TensorN’, where N is the tensor number. . Maps to a command-line argument:
--recordTensors.recordTrace (a boolean) – Whether to store Trace. Attaches field ‘Trace’, and ‘Trace2’ for 2-tensor case to fiber. Maps to a command-line argument:
--recordTrace.seedFALimit (a float) – Seed points whose FA are below this value are excluded. Maps to a command-line argument:
--seedFALimit %f.seedsFile (a pathlike object or string representing an existing file) – Seeds for diffusion. If not specified, full brain tractography will be performed, and the algorithm will start from every voxel in the brain mask where the Generalized Anisotropy is bigger than 0.18. Maps to a command-line argument:
--seedsFile %s.seedsPerVoxel (an integer) – Each seed generates a fiber, thus using more seeds generates more fibers. In general use 1 or 2 seeds, and for a more thorough result use 5 or 10 (depending on your machine this may take up to 2 days to run)., . Maps to a command-line argument:
--seedsPerVoxel %d.stepLength (a float) – Step length of tractography, in millimeters. Maps to a command-line argument:
--stepLength %f.storeGlyphs (a boolean) – Store tensors’ main directions as two-point lines in a separate file named glyphs_{tracts}. When using multiple tensors, only the major tensors’ main directions are stored. Maps to a command-line argument:
--storeGlyphs.tracts (a boolean or a pathlike object or string representing a file) – Tracts generated, with first tensor output. Maps to a command-line argument:
--tracts %s.tractsWithSecondTensor (a boolean or a pathlike object or string representing a file) – Tracts generated, with second tensor output (if there is one). Maps to a command-line argument:
--tractsWithSecondTensor %s.writeAsciiTracts (a boolean) – Write tract file as a VTK binary data file. Maps to a command-line argument:
--writeAsciiTracts.writeUncompressedTracts (a boolean) – Write tract file as a VTK uncompressed data file. Maps to a command-line argument:
--writeUncompressedTracts.- Outputs:
tracts (a pathlike object or string representing an existing file) – Tracts generated, with first tensor output.
tractsWithSecondTensor (a pathlike object or string representing an existing file) – Tracts generated, with second tensor output (if there is one).