probtrackx: Probabilistic diffusion tractography with multiple fibre...

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Probabilistic diffusion tractography with multiple fibre orientations

Description

This function wraps probtrackx from FSL

Usage

probtrackx(
  samples = "merged",
  mask,
  seed,
  outdir = "fdt_paths",
  verbose = TRUE,
  mode = NULL,
  targetmasks = NULL,
  mask2 = NULL,
  waypoints = NULL,
  network = FALSE,
  mesh = NULL,
  seedref = NULL,
  dir = FALSE,
  forcedir = FALSE,
  opd = FALSE,
  pd = FALSE,
  os2t = FALSE,
  avoid = NULL,
  stop = NULL,
  xfm = NULL,
  invxfm = NULL,
  nsamples = 5000,
  nsteps = 2000,
  distthresh = 0,
  cthr = 0.2,
  fibthresh = 0.01,
  sampvox = FALSE,
  steplength = 0.5,
  loopcheck = FALSE,
  usef = FALSE,
  randfib = c(0, 1, 2, 3),
  fibst = 1,
  modeuler = FALSE,
  rseed = NULL,
  s2tastext = FALSE,
  opts = ""
)

Arguments

samples	(nifti/character) Basename for samples files
mask	(nifti/character) Bet binary mask file in diffusion space
seed	(nifti/character) Seed volume, or voxel, or ascii file with multiple volumes, or freesurfer label file
outdir	(character) Output file (default='fdt_paths')
verbose	(logical/numeric) Verbose level, [0-2]
mode	(character) Use –mode=simple for single seed voxel
targetmasks	(character) File containing a list of target masks - required for seeds_to_targets classification
mask2	(nifti/character) Second mask in twomask_symm mode.
waypoints	(nifti/character) Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks
network	(logical) Activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks)
mesh	(character) Freesurfer-type surface descriptor (in ascii format)
seedref	(nifti/character) Reference vol to define seed space in simple mode - diffusion space assumed if absent
dir	(logical) Directory to put the final volumes in - code makes this directory - default='logdir'
forcedir	(logical) Use the actual directory name given - i.e. don't add + to make a new directory
opd	(logical) Output path distribution
pd	(logical) Correct path distribution for the length of the pathways
os2t	(logical) Output seeds to targets
avoid	(nifti/character) Reject pathways passing through locations given by this mask
stop	(nifti/character) Stop tracking at locations given by this mask file
xfm	(character) Transform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity
invxfm	(character) Transform taking DTI space to seed space (compulsory when using a warpfield for seeds_to_dti)
nsamples	(numeric) Number of samples - default=5000
nsteps	(numeric) Number of steps per sample - default=2000
distthresh	(numeric) Discards samples shorter than this threshold (in mm - default=0)
cthr	(numeric) Curvature threshold - default=0.2
fibthresh	(numeric) Volume fraction before subsidiary fibre orientations are considered - default=0.01
sampvox	(logical) Sample random points within seed voxels
steplength	(numeric) Steplength in mm - default=0.5
loopcheck	(logical) Perform loopchecks on paths - slower, but allows lower curvature threshold
usef	(logical) Use anisotropy to constrain tracking
randfib	(numeric) Default 0. Set to 1 to randomly sample initial fibres (with f > fibthresh). Set to 2 to sample in proportion fibres (with f>fibthresh) to f. Set to 3 to sample ALL populations at random (even if f<fibthresh)
fibst	(numeric) Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0
modeuler	(logical) Use modified euler streamlining
rseed	(numeric) Random seed
s2tastext	(logical) Output seed-to-target counts as a text file (useful when seeding from a mesh)
opts	Additional options or way to specify things instead of command line arguments

Value

A filename of the output file

muschellij2/fslr documentation built on Aug. 31, 2022, 8:47 p.m.