[Mandatory]
in_file: (an existing file name)
input file to be processed
argument: ``%s``, position: -2
out_file: (a file name, nipype default value: tracked.tck)
output file containing tracks
argument: ``%s``, position: -1
[Optional]
sph_trait: (a tuple of the form: (a float, a float, a float, a
float))
argument: ``%f,%f,%f,%f``
algorithm: ('iFOD2' or 'FACT' or 'iFOD1' or 'Nulldist' or 'SD_Stream'
or 'Tensor_Det' or 'Tensor_Prob', nipype default value: iFOD2)
tractography algorithm to be used
argument: ``-algorithm %s``
roi_incl: (an existing file name or a tuple of the form: (a float, a
float, a float, a float))
specify an inclusion region of interest, streamlines must traverse
ALL inclusion regions to be accepted
argument: ``-include %s``
roi_excl: (an existing file name or a tuple of the form: (a float, a
float, a float, a float))
specify an exclusion region of interest, streamlines that enter ANY
exclude region will be discarded
argument: ``-exclude %s``
roi_mask: (an existing file name or a tuple of the form: (a float, a
float, a float, a float))
specify a masking region of interest. If defined,streamlines exiting
the mask will be truncated
argument: ``-mask %s``
step_size: (a float)
set the step size of the algorithm in mm (default is 0.1 x
voxelsize; for iFOD2: 0.5 x voxelsize)
argument: ``-step %f``
angle: (a float)
set the maximum angle between successive steps (default is 90deg x
stepsize / voxelsize)
argument: ``-angle %f``
n_tracks: (an integer (int or long))
set the desired number of tracks. The program will continue to
generate tracks until this number of tracks have been selected and
written to the output file
argument: ``-number %d``
select: (an integer (int or long))
set the desired number of tracks. The program will continue to
generate tracks until this number of tracks have been selected and
written to the output file
argument: ``-select %d``
max_tracks: (an integer (int or long))
set the maximum number of tracks to generate. The program will not
generate more tracks than this number, even if the desired number of
tracks hasn't yet been reached (default is 100 x number)
argument: ``-maxnum %d``
max_length: (a float)
set the maximum length of any track in mm (default is 100 x
voxelsize)
argument: ``-maxlength %f``
min_length: (a float)
set the minimum length of any track in mm (default is 5 x voxelsize)
argument: ``-minlength %f``
cutoff: (a float)
set the FA or FOD amplitude cutoff for terminating tracks (default
is 0.1)
argument: ``-cutoff %f``
cutoff_init: (a float)
set the minimum FA or FOD amplitude for initiating tracks (default
is the same as the normal cutoff)
argument: ``-initcutoff %f``
n_trials: (an integer (int or long))
set the maximum number of sampling trials at each point (only used
for probabilistic tracking)
argument: ``-trials %d``
unidirectional: (a boolean)
track from the seed point in one direction only (default is to track
in both directions)
argument: ``-unidirectional``
init_dir: (a tuple of the form: (a float, a float, a float))
specify an initial direction for the tracking (this should be
supplied as a vector of 3 comma-separated values
argument: ``-initdirection %f,%f,%f``
noprecompt: (a boolean)
do NOT pre-compute legendre polynomial values. Warning: this will
slow down the algorithm by a factor of approximately 4
argument: ``-noprecomputed``
power: (an integer (int or long))
raise the FOD to the power specified (default is 1/nsamples)
argument: ``-power %d``
n_samples: (an integer (int or long), nipype default value: 4)
set the number of FOD samples to take per step for the 2nd order
(iFOD2) method
argument: ``-samples %d``
use_rk4: (a boolean)
use 4th-order Runge-Kutta integration (slower, but eliminates
curvature overshoot in 1st-order deterministic methods)
argument: ``-rk4``
stop: (a boolean)
stop propagating a streamline once it has traversed all include
regions
argument: ``-stop``
downsample: (a float)
downsample the generated streamlines to reduce output file size
argument: ``-downsample %f``
act_file: (an existing file name)
use the Anatomically-Constrained Tractography framework during
tracking; provided image must be in the 5TT (five - tissue - type)
format
argument: ``-act %s``
backtrack: (a boolean)
allow tracks to be truncated
argument: ``-backtrack``
crop_at_gmwmi: (a boolean)
crop streamline endpoints more precisely as they cross the GM-WM
interface
argument: ``-crop_at_gmwmi``
seed_sphere: (a tuple of the form: (a float, a float, a float, a
float))
spherical seed
argument: ``-seed_sphere %f,%f,%f,%f``
seed_image: (an existing file name)
seed streamlines entirely at random within mask
argument: ``-seed_image %s``
seed_rnd_voxel: (a tuple of the form: (an existing file name, an
integer (int or long)))
seed a fixed number of streamlines per voxel in a mask image; random
placement of seeds in each voxel
argument: ``-seed_random_per_voxel %s %d``
mutually_exclusive: seed_image, seed_grid_voxel
seed_grid_voxel: (a tuple of the form: (an existing file name, an
integer (int or long)))
seed a fixed number of streamlines per voxel in a mask image; place
seeds on a 3D mesh grid (grid_size argument is per axis; so a
grid_size of 3 results in 27 seeds per voxel)
argument: ``-seed_grid_per_voxel %s %d``
mutually_exclusive: seed_image, seed_rnd_voxel
seed_rejection: (an existing file name)
seed from an image using rejection sampling (higher values = more
probable to seed from
argument: ``-seed_rejection %s``
seed_gmwmi: (an existing file name)
seed from the grey matter - white matter interface (only valid if
using ACT framework)
argument: ``-seed_gmwmi %s``
requires: act_file
seed_dynamic: (an existing file name)
determine seed points dynamically using the SIFT model (must not
provide any other seeding mechanism). Note that while this seeding
mechanism improves the distribution of reconstructed streamlines
density, it should NOT be used as a substitute for the SIFT method
itself.
argument: ``-seed_dynamic %s``
max_seed_attempts: (an integer (int or long))
set the maximum number of times that the tracking algorithm should
attempt to find an appropriate tracking direction from a given seed
point
argument: ``-max_seed_attempts %d``
out_seeds: (a file name, nipype default value: out_seeds.nii.gz)
output the seed location of all successful streamlines to a file
argument: ``-output_seeds %s``
nthreads: (an integer (int or long))
number of threads. if zero, the number of available cpus will be
used
argument: ``-nthreads %d``
grad_file: (an existing file name)
dw gradient scheme (MRTrix format
argument: ``-grad %s``
grad_fsl: (a tuple of the form: (an existing file name, an existing
file name))
(bvecs, bvals) dw gradient scheme (FSL format
argument: ``-fslgrad %s %s``
bval_scale: ('yes' or 'no')
specifies whether the b - values should be scaled by the square of
the corresponding DW gradient norm, as often required for multishell
or DSI DW acquisition schemes. The default action can also be set in
the MRtrix config file, under the BValueScaling entry. Valid choices
are yes / no, true / false, 0 / 1 (default: true).
argument: ``-bvalue_scaling %s``
in_bvec: (an existing file name)
bvecs file in FSL format
argument: ``-fslgrad %s %s``
in_bval: (an existing file name)
bvals file in FSL format
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
