This function wraps probtrackx2 from FSL
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, ...)Basename for samples files - e.g. 'merged'
Bet binary mask file in diffusion space
Seed volume or list (ascii text file) of volumes and/or surfaces
Verbose level, [0-2]
Output file (default='fdt_paths')
Directory to put the final volumes in - code makes this directory - default='logdir'
Use the actual directory name given - i.e. don't add + to make a new directory
Track from a list of voxels (seed must be a ASCII list of coordinates)
Activate network mode - only keep paths going through at least one of the other seed masks
Output path distribution
Correct path distribution for the length of the pathways
Other mask for binning tract distribution
Output seeds to targets
Output seed-to-target counts as a text file (default in simple mode)
File containing a list of target masks - for seeds_to_targets classification
Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks
Waypoint condition. Either 'AND' (default) or 'OR'
Reject streamlines that do not hit waypoints in given order. Only valid if waycond=AND
Apply waypoint conditions to each half tract separately
Reject pathways passing through locations given by this mask
Stop tracking at locations given by this mask file
Output matrix1 - SeedToSeed Connectivity
Discards samples (in matrix1) shorter than this threshold (in mm - default=0)
Output matrix2 - SeedToLowResMask
Low resolution binary brain mask for storing connectivity distribution in matrix2 mode
Output matrix3 (NxN connectivity matrix)
Mask used for NxN connectivity matrix (or Nxn if lrtarget3 is set)
Column-space mask used for Nxn connectivity matrix
Discards samples (in matrix3) shorter than this threshold (in mm - default=0)
Transform taking seed space to DTI space (either FLIRT matrix or FNIRT warpfield) - default is identity
Transform taking DTI space to seed space (compulsory when using a warpfield for seeds_to_dti)
Reference vol to define seed space in simple mode - diffusion space assumed if absent
Mesh reference space - either 'caret' (default) or 'freesurfer' or 'first' or 'vox'
Number of samples - default=5000
Number of steps per sample - default=2000
Steplength in mm - default=0.5
Discards samples shorter than this threshold (in mm - default=0)
Curvature threshold - default=0.2
Volume fraction before subsidiary fibre orientations are considered - default=0.01
Perform loopchecks on paths - slower, but allows lower curvature threshold
Use anisotropy to constrain tracking
Use modified euler streamlining
Sample random points within x mm sphere seed voxels (e.g. --sampvox=5). Default=0
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)
Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0
Random seed
Additional arguments