Probabilistic diffusion tractography with multiple fibre orientations
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, ...)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 subsidiary 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<fibthresh) |
fibst |
Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0 |
rseed |
Random seed |
... |
Additional arguments |
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