.. _scil_tractogram_compute_TODI:

scil_tractogram_compute_TODI
============================

::

	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,ERROR}]] [-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.
	
	------------------------------------------------------------------------------------
	Reference:
	[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.
	------------------------------------------------------------------------------------
	
	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,ERROR}]
	                        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.
	
	2.2.2