probtrackx: Probabilistic diffusion tractography with multiple fibre...

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

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 subsidary 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

neuroconductor-devel-releases/fslr documentation built on May 6, 2020, 4:22 p.m.