.. _scil_dwi_to_sh:

scil_dwi_to_sh
==============

::

	usage: __main__.py [-h] [--sh_order SH_ORDER]
	                   [--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
	                   [--smooth SMOOTH] [--use_attenuation] [--mask MASK]
	                   [--b0_threshold thr] [--skip_b0_check]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec out_sh
	
	Script to compute the SH coefficient directly on the raw DWI signal.
	
	positional arguments:
	  in_dwi                Path of the dwi volume.
	  in_bval               Path of the b-value file, in FSL format.
	  in_bvec               Path of the b-vector file, in FSL format.
	  out_sh                Name of the output SH file to save.
	
	options:
	  -h, --help            show this help message and exit
	  --sh_order SH_ORDER   SH order to fit (int). [4]
	  --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.
	  --smooth SMOOTH       Lambda-regularization coefficient in the SH fit (float). [0.006]
	  --use_attenuation     If set, will use signal attenuation before fitting the SH (i.e. divide by the b0).
	  --mask MASK           Path to a binary mask.
	                        Only data inside the mask will be used for computations and reconstruction 
	  --b0_threshold thr    Threshold under which b-values are considered to be b0s.
	                        [Default: 20] 
	                        * Note. We would expect to find at least one b-value in the 
	                          range [0, b0_threshold]. To skip this check, use --skip_b0_check.
	  --skip_b0_check       By default, we supervise that at least one b0 exists in your data
	                        (i.e. b-values below the default --b0_threshold). Use this option to 
	                        allow continuing even if the minimum b-value is suspiciously high.
	                        If no b-value is found below the threshold, the script will continue 
	                        with your minimal b-value as new --b0_threshold.
	                        Use with care, and only if you understand your data.
	  -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.
	
	2.2.2