.. _scil_frf_msmt:

scil_frf_msmt
=============

::

	usage: __main__.py [-h] [--mask MASK] [--mask_wm MASK_WM] [--mask_gm MASK_GM]
	                   [--mask_csf MASK_CSF] [--fa_thr_wm FA_THR_WM]
	                   [--fa_thr_gm FA_THR_GM] [--fa_thr_csf FA_THR_CSF]
	                   [--md_thr_gm MD_THR_GM] [--md_thr_csf MD_THR_CSF]
	                   [--min_nvox MIN_NVOX] [--tolerance TOLERANCE]
	                   [--skip_b0_check] [--dti_bval_limit DTI_BVAL_LIMIT]
	                   [--roi_radii ROI_RADII [ROI_RADII ...]]
	                   [--roi_center tuple(3) tuple(3) tuple(3)]
	                   [--wm_frf_mask file] [--gm_frf_mask file]
	                   [--csf_frf_mask file] [--precision PRECISION]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec out_wm_frf out_gm_frf out_csf_frf
	
	Compute response functions for multi-shell multi-tissue (MSMT) constrained
	spherical deconvolution from DWI data.
	
	The script computes a response function for white-matter (wm),
	gray-matter (gm), csf and the mean b=0.
	    - In the wm, we compute the response function in each voxel where the FA is
	      superior at threshold_fa_wm.
	    - In the gm (or csf), we compute the response function in each voxel where
	      the FA is below at threshold_fa_gm (or threshold_fa_csf) and where the MD
	      is below threshold_md_gm (or threshold_md_csf).
	
	We output one response function file for each tissue, containing the response
	function for each b-value (arranged by lines). These are saved as the diagonal
	of the axis-symmetric diffusion tensor (3 e-values) and a mean b0 value.
	For example, a typical wm_frf is [15e-4, 4e-4, 4e-4, 700], where the tensor
	e-values are (15,4,4)x10^-4 mm^2/s and the mean b0 is 700.
	
	Based on B. Jeurissen et al., Multi-tissue constrained spherical deconvolution
	for improved analysis of multi-shell diffusion MRI data. Neuroimage (2014)
	
	positional arguments:
	  in_dwi                Path to the input diffusion volume.
	  in_bval               Path to the bval file, in FSL format.
	  in_bvec               Path to the bvec file, in FSL format.
	  out_wm_frf            Path to the output WM frf file, in .txt format.
	  out_gm_frf            Path to the output GM frf file, in .txt format.
	  out_csf_frf           Path to the output CSF frf file, in .txt format.
	
	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 tissue masks are available.
	  --mask_wm MASK_WM     Path to the input WM mask file, used to improve the final WM frf mask.
	  --mask_gm MASK_GM     Path to the input GM mask file, used to improve the final GM frf mask.
	  --mask_csf MASK_CSF   Path to the input CSF mask file, used to improve the final CSF frf mask.
	  --fa_thr_wm FA_THR_WM
	                        If supplied, use this threshold to select single WM fiber voxels from the FA inside the WM mask defined  by mask_wm. Each voxel above this threshold will be selected. [0.7]
	  --fa_thr_gm FA_THR_GM
	                        If supplied, use this threshold to select GM voxels from the FA inside the GM mask defined by mask_gm. Each voxel below this threshold will be selected. [0.2]
	  --fa_thr_csf FA_THR_CSF
	                        If supplied, use this threshold to select CSF voxels from the FA inside the CSF mask defined by mask_csf. Each voxel below this threshold will be selected. [0.1]
	  --md_thr_gm MD_THR_GM
	                        If supplied, use this threshold to select GM voxels from the MD inside the GM mask defined by mask_gm. Each voxel below this threshold will be selected. [0.0007]
	  --md_thr_csf MD_THR_CSF
	                        If supplied, use this threshold to select CSF voxels from the MD inside the CSF mask defined by mask_csf. Each voxel below this threshold will be selected. [0.003]
	  --min_nvox MIN_NVOX   Minimal number of voxels needed for each tissue masks in order to proceed to frf estimation. [100]
	  --tolerance TOLERANCE
	                        The tolerated gap between the b-values to extract and the current b-value. [20]
	  --skip_b0_check       By default, we supervise that at least one b0 exists in your data
	                        (i.e. b-values below the default --tolerance). 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 the original --tolerance and no b0 volumes.
	                        Use with care, and only if you understand your data.
	  --dti_bval_limit DTI_BVAL_LIMIT
	                        The highest b-value taken for the DTI model. [1200]
	  --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 cuboid roi using roi_radii. [center of the 3D volume] (e.g. --roi_center 66 79 79)
	  --wm_frf_mask file    Path to the output WM frf mask file, the voxels used to compute the WM frf.
	  --gm_frf_mask file    Path to the output GM frf mask file, the voxels used to compute the GM frf.
	  --csf_frf_mask file   Path to the output CSF frf mask file, the voxels used to compute the CSF frf.
	  --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