interfaces.semtools.diffusion.tractography.ukftractography¶
UKFTractography¶
Wraps the executable command `` 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 informations 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).
Inputs:
[Optional]
dwiFile: (an existing file name)
Input DWI volume
argument: ``--dwiFile %s``
seedsFile: (an existing file name)
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
argument: ``--seedsFile %s``
labels: (a list of items which are an integer (int or long))
A vector of the ROI labels to be used
argument: ``--labels %s``
maskFile: (an existing file name)
Mask for diffusion tractography
argument: ``--maskFile %s``
tracts: (a boolean or a file name)
Tracts generated, with first tensor output
argument: ``--tracts %s``
writeAsciiTracts: (a boolean)
Write tract file as a VTK binary data file
argument: ``--writeAsciiTracts ``
writeUncompressedTracts: (a boolean)
Write tract file as a VTK uncompressed data file
argument: ``--writeUncompressedTracts ``
seedsPerVoxel: (an integer (int or long))
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).,
argument: ``--seedsPerVoxel %d``
numTensor: ('1' or '2')
Number of tensors used
argument: ``--numTensor %s``
freeWater: (a boolean)
Adds a term for free water difusion to the model. (Note for experts:
if checked, the 1T simple model is forced)
argument: ``--freeWater ``
recordFA: (a boolean)
Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor
case to fiber.
argument: ``--recordFA ``
recordFreeWater: (a boolean)
Whether to store the fraction of free water. Attaches field
'FreeWater' to fiber.
argument: ``--recordFreeWater ``
recordTrace: (a boolean)
Whether to store Trace. Attaches field 'Trace', and 'Trace2' for
2-tensor case to fiber.
argument: ``--recordTrace ``
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.
argument: ``--recordTensors ``
recordNMSE: (a boolean)
Whether to store NMSE. Attaches field 'NMSE' to fiber.
argument: ``--recordNMSE ``
recordState: (a boolean)
Whether to attach the states to the fiber. Will generate field
'state'.
argument: ``--recordState ``
recordCovariance: (a boolean)
Whether to store the covariance. Will generate field 'covariance' in
fiber.
argument: ``--recordCovariance ``
recordLength: (a float)
Record length of tractography, in millimeters
argument: ``--recordLength %f``
minFA: (a float)
Abort the tractography when the Fractional Anisotropy is less than
this value
argument: ``--minFA %f``
minGA: (a float)
Abort the tractography when the Generalized Anisotropy is less than
this value
argument: ``--minGA %f``
fullTensorModel: (a boolean)
Whether to use the full tensor model. If unchecked, use the default
simple tensor model
argument: ``--fullTensorModel ``
numThreads: (an integer (int or long))
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.
argument: ``--numThreads %d``
stepLength: (a float)
Step length of tractography, in millimeters
argument: ``--stepLength %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
argument: ``--maxHalfFiberLength %f``
seedFALimit: (a float)
Seed points whose FA are below this value are excluded
argument: ``--seedFALimit %f``
Qm: (a float)
Process noise for angles/direction
argument: ``--Qm %f``
Ql: (a float)
Process noise for eigenvalues
argument: ``--Ql %f``
Qw: (a float)
Process noise for free water weights, ignored if no free water
estimation
argument: ``--Qw %f``
Rs: (a float)
Measurement noise
argument: ``--Rs %f``
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 supressed when this maxBranchingAngle is set to 0.0
argument: ``--maxBranchingAngle %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)
argument: ``--minBranchingAngle %f``
tractsWithSecondTensor: (a boolean or a file name)
Tracts generated, with second tensor output (if there is one)
argument: ``--tractsWithSecondTensor %s``
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
argument: ``--storeGlyphs ``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
tracts: (an existing file name)
Tracts generated, with first tensor output
tractsWithSecondTensor: (an existing file name)
Tracts generated, with second tensor output (if there is one)