usage: __main__.py [-h] [--sphere SPHERE] [--mask MASK] [--sh_order SH_ORDER]
[--normalize_per_voxel] [--smooth_todi | --asymmetric]
[--n_steps N_STEPS] [--out_mask OUT_MASK]
[--out_tdi OUT_TDI] [--out_todi_sf OUT_TODI_SF]
[--out_todi_sh OUT_TODI_SH] [--reference REFERENCE]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_tractogram
Compute a Track Orientation Density Image (TODI).
Each segment of the streamlines is weighted by its length (to support
compressed streamlines).
This script can afterwards output a Track Density Image (TDI) or a TODI with SF
or SH representation, based on streamlines' segments.
Formerly: scil_compute_todi.py
positional arguments:
in_tractogram Input streamlines file.
options:
-h, --help show this help message and exit
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}
Spherical harmonics basis used for the SH coefficients.
Must be either descoteaux07', 'tournier07',
'descoteaux07_legacy' or 'tournier07_legacy' [['descoteaux07_legacy']]:
'descoteaux07' : SH basis from the Descoteaux et al.
MRM 2007 paper
'tournier07' : SH basis from the new Tournier et al.
NeuroImage 2019 paper, as in MRtrix 3.
'descoteaux07_legacy': SH basis from the legacy Dipy implementation
of the Descoteaux et al. MRM 2007 paper
'tournier07_legacy' : SH basis from the legacy Tournier et al.
NeuroImage 2007 paper.
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Computing options:
--sphere SPHERE Sphere used for the angular discretization. [repulsion724]
--mask MASK If set, use the given mask.
--sh_order SH_ORDER Order of the original SH. [8]
--normalize_per_voxel
If set, normalize each SF/SH at each voxel.
--smooth_todi If set, smooth TODI (angular and spatial).
--asymmetric If set, compute asymmetric TODI.
Cannot be used with --smooth_todi.
--n_steps N_STEPS Number of steps for streamline segments subdivision prior to binning [1].
Output files. Saves only when filename is set:
--out_mask OUT_MASK Mask showing where TDI > 0.
--out_tdi OUT_TDI Output Track Density Image (TDI).
--out_todi_sf OUT_TODI_SF
Output TODI, with SF (each directions
on the sphere, requires a lot of memory)
--out_todi_sh OUT_TODI_SH
Output TODI, with SH coefficients.
References:
[1] Dhollander T, Emsell L, Van Hecke W, Maes F, Sunaert S, Suetens P.
Track orientation density imaging (TODI) and
track orientation distribution (TOD) based tractography.
NeuroImage. 2014 Jul 1;94:312-36.