Usage
probtrackx(samples = "merged", mask, seed, verbose = TRUE, out = NULL, dir = NULL, forcedir = FALSE, simple = NULL, network = FALSE, opd = NULL, pd = FALSE, fopd = NULL, os2t = FALSE, s2tastext = NULL, targetmasks = NULL, waypoints = NULL, waycond = c("AND", "OR"), wayorder = NULL, onewaycondition = FALSE, avoid = NULL, stop = NULL, omatrix1 = NULL, distthresh1 = NULL, omatrix2 = NULL, target2 = NULL, omatrix3 = NULL, target3 = NULL, lrtarget3 = NULL, distthresh3 = 0, xfm = NULL, invxfm = NULL, seedref = NULL, meshspace = c("caret", "freesurfer", "first", "vox"), nsamples = 5000, nsteps = 2000, steplength = 0.5, distthresh = 0, cthr = 0.2, fibthresh = 0.01, loopcheck = FALSE, usef = FALSE, modeuler = FALSE, sampvox = 0, randfib = 0, fibst = 1, rseed = NULL, ...)
Arguments
samples
Basename for samples files - e.g. 'merged'
mask
Bet binary mask file in diffusion space
seed
Seed volume or list (ascii text file) of volumes and/or surfaces
verbose
Verbose level, [0-2]
out
Output file (default='fdt_paths')
dir
Directory to put the final volumes in - code makes this directory - default='logdir'
forcedir
Use the actual directory name given - i.e. don't add + to make a new directory
simple
Track from a list of voxels (seed must be a ASCII list of coordinates)
network
Activate network mode - only keep paths going through at least one of the other seed masks
opd
Output path distribution
pd
Correct path distribution for the length of the pathways
fopd
Other mask for binning tract distribution
os2t
Output seeds to targets
s2tastext
Output seed-to-target counts as a text file (default in simple mode)
targetmasks
File containing a list of target masks - for seeds_to_targets classification
waypoints
Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks
waycond
Waypoint condition. Either 'AND' (default) or 'OR'
wayorder
Reject streamlines that do not hit waypoints in given order. Only valid if waycond=AND
onewaycondition
Apply waypoint conditions to each half tract separately
avoid
Reject pathways passing through locations given by this mask
stop
Stop tracking at locations given by this mask file
omatrix1
Output matrix1 - SeedToSeed Connectivity
distthresh1
Discards samples (in matrix1) shorter than this threshold (in mm - default=0)
omatrix2
Output matrix2 - SeedToLowResMask
target2
Low resolution binary brain mask for storing connectivity distribution in matrix2 mode
omatrix3
Output matrix3 (NxN connectivity matrix)
target3
Mask used for NxN connectivity matrix (or Nxn if lrtarget3 is set)
lrtarget3
Column-space mask used for Nxn connectivity matrix
distthresh3
Discards samples (in matrix3) shorter than this threshold (in mm - default=0)
xfm
Transform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity
invxfm
Transform taking DTI space to seed space (compulsory when using a warpfield for seeds_to_dti)
seedref
Reference vol to define seed space in simple mode - diffusion space assumed if absent
meshspace
Mesh reference space - either 'caret' (default) or 'freesurfer' or 'first' or 'vox'
nsamples
Number of samples - default=5000
nsteps
Number of steps per sample - default=2000
steplength
Steplength in mm - default=0.5
distthresh
Discards samples shorter than this threshold (in mm - default=0)
cthr
Curvature threshold - default=0.2
fibthresh
Volume fraction before subsidary fibre orientations are considered - default=0.01
loopcheck
Perform loopchecks on paths - slower, but allows lower curvature threshold
usef
Use anisotropy to constrain tracking
modeuler
Use modified euler streamlining
sampvox
Sample random points within x mm sphere seed voxels (e.g. --sampvox=5). Default=0
randfib
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
fibst
Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0