interfaces.semtools.diffusion.tractography.ukftractography

UKFTractography

Link to code

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 unicode 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 newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, 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: (u'stream' or u'allatonce' or u'file' or u'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)