This function wraps probtrackx
from FSL
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 = ""
)
A filename of the output file
(nifti/character) Basename for samples files
(nifti/character) Bet binary mask file in diffusion space
(nifti/character) Seed volume, or voxel, or ascii file with multiple volumes, or freesurfer label file
(character) Output file (default='fdt_paths')
(logical/numeric) Verbose level, [0-2]
(character) Use --mode=simple for single seed voxel
(character) File containing a list of target masks - required for seeds_to_targets classification
(nifti/character) Second mask in twomask_symm mode.
(nifti/character) Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks
(logical) Activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks)
(character) Freesurfer-type surface descriptor (in ascii format)
(nifti/character) Reference vol to define seed space in simple mode - diffusion space assumed if absent
(logical) Directory to put the final volumes in - code makes this directory - default='logdir'
(logical) Use the actual directory name given - i.e. don't add + to make a new directory
(logical) Output path distribution
(logical) Correct path distribution for the length of the pathways
(logical) Output seeds to targets
(nifti/character) Reject pathways passing through locations given by this mask
(nifti/character) Stop tracking at locations given by this mask file
(character) Transform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity
(character) Transform taking DTI space to seed space (compulsory when using a warpfield for seeds_to_dti)
(numeric) Number of samples - default=5000
(numeric) Number of steps per sample - default=2000
(numeric) Discards samples shorter than this threshold (in mm - default=0)
(numeric) Curvature threshold - default=0.2
(numeric) Volume fraction before subsidiary fibre orientations are considered - default=0.01
(logical) Sample random points within seed voxels
(numeric) Steplength in mm - default=0.5
(logical) Perform loopchecks on paths - slower, but allows lower curvature threshold
(logical) Use anisotropy to constrain tracking
(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)
(numeric) Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0
(logical) Use modified euler streamlining
(numeric) Random seed
(logical) Output seed-to-target counts as a text file (useful when seeding from a mesh)
Additional options or way to specify things instead of command line arguments