.. _scil_dwi_powder_average:

scil_dwi_powder_average
=======================

::

	usage: __main__.py [-h] [-f] [--mask file] [--b0_thr B0_THR]
	                   [--shells SHELLS [SHELLS ...]] [--shell_thr SHELL_THR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_dwi in_bval out_avg
	
	Script to compute powder average (mean diffusion weighted image) from set of
	diffusion images.
	
	By default will output an average image calculated from all images with
	non-zero bvalue.
	
	Specify --bvalue to output an image for a single shell
	
	Script currently does not take into account the diffusion gradient directions
	being averaged.
	
	positional arguments:
	  in_dwi                Path of the input diffusion volume.
	  in_bval               Path of the bvals file, in FSL format.
	  out_avg               Path of the output file.
	
	options:
	  -h, --help            show this help message and exit
	  -f                    Force overwriting of the output files.
	  --mask file           Path to a binary mask.
	                        Only data inside the mask will be used for powder avg. (Default: None)
	  --b0_thr B0_THR       Exclude b0 volumes from powder average with bvalue less than specified threshold.
	                        (Default: remove volumes with bvalue < 50
	  --shells SHELLS [SHELLS ...]
	                        bvalue (shells) to include in powder average passed as a list 
	                        (e.g. --shells 1000 2000). If not specified will include all volumes with a non-zero bvalue.
	  --shell_thr SHELL_THR
	                        Include volumes with bvalue +- the specified threshold.
	                        (Default: [50]
	  -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