.. _scil_dwi_detect_volume_outliers:

scil_dwi_detect_volume_outliers
===============================

::

	usage: __main__.py [-h] [--std_scale STD_SCALE] [--b0_threshold thr]
	                   [--skip_b0_check] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_dwi in_bval in_bvec
	
	This script simply finds the 3 closest angular neighbors of each direction
	(per shell) and compute the voxel-wise correlation.
	If the angles or correlations to neighbors are below the shell average (by
	args.std_scale x STD) it will flag the volume as a potential outlier.
	
	This script supports multi-shells, but each shell is independant and detected
	using the --b0_threshold parameter.
	
	This script can be run before any processing to identify potential problem
	before launching pre-processing.
	
	positional arguments:
	  in_dwi                The DWI file (.nii) to concatenate.
	  in_bval               The b-values files in FSL format (.bval).
	  in_bvec               The b-vectors files in FSL format (.bvec).
	
	options:
	  -h, --help            show this help message and exit
	  --std_scale STD_SCALE
	                        How many deviation from the mean are required to be considered an outlier. [2.0]
	  --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.
	
	2.2.2