interfaces.semtools.diffusion.tractography.ukftractography¶
UKFTractography¶
Wraps 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:
[Mandatory]
[Optional]
Ql: (a float)
Process noise for eigenvalues
flag: --Ql %f
Qm: (a float)
Process noise for angles/direction
flag: --Qm %f
Qw: (a float)
Process noise for free water weights, ignored if no free water
estimation
flag: --Qw %f
Rs: (a float)
Measurement noise
flag: --Rs %f
args: (a string)
Additional parameters to the command
flag: %s
dwiFile: (an existing file name)
Input DWI volume
flag: --dwiFile %s
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
freeWater: (a boolean)
Adds a term for free water difusion to the model. (Note for experts:
if checked, the 1T simple model is forced)
flag: --freeWater
fullTensorModel: (a boolean)
Whether to use the full tensor model. If unchecked, use the default
simple tensor model
flag: --fullTensorModel
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
labels: (a list of items which are an integer (int or long))
A vector of the ROI labels to be used
flag: --labels %s
maskFile: (an existing file name)
Mask for diffusion tractography
flag: --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 supressed when this maxBranchingAngle is set to 0.0
flag: --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
flag: --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)
flag: --minBranchingAngle %f
minFA: (a float)
Abort the tractography when the Fractional Anisotropy is less than
this value
flag: --minFA %f
minGA: (a float)
Abort the tractography when the Generalized Anisotropy is less than
this value
flag: --minGA %f
numTensor: ('1' or '2')
Number of tensors used
flag: --numTensor %s
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.
flag: --numThreads %d
recordCovariance: (a boolean)
Whether to store the covariance. Will generate field 'covariance' in
fiber.
flag: --recordCovariance
recordFA: (a boolean)
Whether to store FA. Attaches field 'FA', and 'FA2' for 2-tensor
case to fiber.
flag: --recordFA
recordFreeWater: (a boolean)
Whether to store the fraction of free water. Attaches field
'FreeWater' to fiber.
flag: --recordFreeWater
recordLength: (a float)
Record length of tractography, in millimeters
flag: --recordLength %f
recordNMSE: (a boolean)
Whether to store NMSE. Attaches field 'NMSE' to fiber.
flag: --recordNMSE
recordState: (a boolean)
Whether to attach the states to the fiber. Will generate field
'state'.
flag: --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.
flag: --recordTensors
recordTrace: (a boolean)
Whether to store Trace. Attaches field 'Trace', and 'Trace2' for
2-tensor case to fiber.
flag: --recordTrace
seedFALimit: (a float)
Seed points whose FA are below this value are excluded
flag: --seedFALimit %f
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
flag: --seedsFile %s
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).,
flag: --seedsPerVoxel %d
stepLength: (a float)
Step length of tractography, in millimeters
flag: --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
flag: --storeGlyphs
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
tracts: (a boolean or a file name)
Tracts generated, with first tensor output
flag: --tracts %s
tractsWithSecondTensor: (a boolean or a file name)
Tracts generated, with second tensor output (if there is one)
flag: --tractsWithSecondTensor %s
writeAsciiTracts: (a boolean)
Write tract file as a VTK binary data file
flag: --writeAsciiTracts
writeUncompressedTracts: (a boolean)
Write tract file as a VTK uncompressed data file
flag: --writeUncompressedTracts
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)