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tend-fiber - Man Page

fiber tractography, from one or more seeds

Synopsis

tend fiber [-i <nin>] [-dwi] [-s <seed point>] [-ns <seed nrrd>] [-wsp] [-t <type>] [-n <intg>] [-k <kernel>] [-wp <which>] [-ap] [-wspo] [-step <step size>] -stop <stop1 ...> [-v <verbose>] [-nmat <transform>] [-o <nout>]

Description

Fiber tractography, from one or more seeds. A fairly complete command-line interface to the tenFiber API.

Options

-i <nin>

input volume; default: “-

-dwi

input volume is a DWI volume, not a single tensor volume

-s <seed point>

seed point for fiber; it will propogate in two opposite directions starting from here (3 doubles); default: “0 0 0

-ns <seed nrrd>

3-by-N nrrd of seedpoints; default: “”

-wsp

define seedpoint and output path in worldspace. Otherwise, (without using this option) everything is in index space

-t <type>

fiber type; defaults to something (string)

-n <intg>

integration method for fiber tracking; default: “rk4

-k <kernel>

kernel for reconstructing tensor field; default: “tent

-wp <which>

when doing multi-tensor tracking, index of path to follow (made moot by “-ap”) (unsigned int); default: “0

-ap

follow all paths from (all) seedpoint(s), output will be polydata, rather than a single 3-by-N nrrd, even if only a single path is generated

-wspo

output should be in worldspace, even if input is not (this feature is unstable and/or confusing)

-s <step size>

stepsize along fiber, in world space (double); default: “0.01

-stop <stop1 ...>

the conditions that should signify the end of a fiber, or when to discard a fiber that is done propagating. Multiple stopping criteria are logically OR-ed and tested at every point along the fiber. Possibilities include:

  • aniso:<type>,<thresh>”: require anisotropy to be above the given threshold. Which anisotropy type is given as with tend-anvol(1)
  • len:<length>”: limits the length, in world space, of each fiber half
  • steps:<N>”: the number of steps in each fiber half is capped at N
  • conf:<thresh>”: requires the tensor confidence value to be above the given thresh
  • radius:<thresh>”: requires that the radius of curvature of the fiber stay above given thresh
  • frac:<F>”: in multi-tensor tracking, the fraction of the tracked component must stay above F
  • minlen:<len>”: discard fiber if its final whole length is below len (not really a termination criterion)
  • minsteps:<N>”: discard fiber if its final number of steps is below N (not really a termination criterion) (1 or more fiber stops)
-v <verbose>

verbosity level (int) default: “0

-nmat <transform>

a 4x4 homogenous transform matrix (as a nrrd, or just a text file) given with this option will be applied to the output tractography vertices just prior to output; default: “”

-o <nout>

output fiber(s) (string) default: “-

See Also

tend(1), tend-anvol(1)

Referenced By

tend(1).

April 2021