.. _scil_frf_ssst:

scil_frf_ssst
=============

::

	usage: __main__.py [-h] [--mask MASK] [--mask_wm MASK_WM]
	                   [--fa_thresh FA_THRESH] [--min_fa_thresh MIN_FA_THRESH]
	                   [--min_nvox MIN_NVOX]
	                   [--roi_radii ROI_RADII [ROI_RADII ...]]
	                   [--roi_center tuple(3) tuple(3) tuple(3)]
	                   [--b0_threshold thr] [--skip_b0_check]
	                   [--precision PRECISION] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_dwi in_bval in_bvec frf_file
	
	Compute a single Fiber Response Function from a DWI.
	
	A DTI fit is made, and voxels containing a single fiber population are
	found using a threshold on the FA.
	
	----------------------------------------------------------------------
	Reference:
	[1] Tournier et al. NeuroImage 2007
	----------------------------------------------------------------------
	
	positional arguments:
	  in_dwi                Path of the input diffusion volume.
	  in_bval               Path of the bvals file, in FSL format.
	  in_bvec               Path of the bvecs file, in FSL format.
	  frf_file              Path to the output FRF file, in .txt format, saved by Numpy.
	
	options:
	  -h, --help            show this help message and exit
	  --mask MASK           Path to a binary mask. Only the data inside the mask will be used 
	                        for computations and reconstruction. Useful if no white matter mask 
	                        is available.
	  --mask_wm MASK_WM     Path to a binary white matter mask. Only the data inside this mask 
	                        and above the threshold defined by --fa_thresh will be used to estimate the 
	                        fiber response function.
	  --fa_thresh FA_THRESH
	                        If supplied, use this threshold as the initial threshold to select 
	                        single fiber voxels. [0.7]
	  --min_fa_thresh MIN_FA_THRESH
	                        If supplied, this is the minimal value that will be tried when looking 
	                        for single fiber voxels. [0.5]
	  --min_nvox MIN_NVOX   Minimal number of voxels needing to be identified as single fiber voxels 
	                        in the automatic estimation. [300]
	  --roi_radii ROI_RADII [ROI_RADII ...]
	                        If supplied, use those radii to select a cuboid roi to estimate the 
	                        response functions. The roi will be a cuboid spanning from the middle of 
	                        the volume in each direction with the different radii. The type is either 
	                        an int (e.g. --roi_radii 10) or an array-like (3,) (e.g. --roi_radii 20 30 10). [[20]]
	  --roi_center tuple(3) tuple(3) tuple(3)
	                        If supplied, use this center to span the roi of size roi_radius. [center of the 3D volume]
	  --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.
	  --precision PRECISION
	                        Precision for floating point values. Numbers are rounded up to 
	                        the number of decimals provided. [Default: 12]
	  -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