R/probtrackx.R
probtrackx.RdThis 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 = ""
)| 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 |
A filename of the output file