.. _scil_dwi_extract_shell:

scil_dwi_extract_shell
======================

::

	usage: __main__.py [-h] [--out_indices OUT_INDICES] [--block-size INT]
	                   [--tolerance INT] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bval in_bvec in_bvals_to_extract
	                   [in_bvals_to_extract ...] out_dwi out_bval out_bvec
	
	Extracts the DWI volumes that are on specific b-value shells. Many shells
	can be extracted at once by specifying multiple b-values. The extracted
	volumes are in the same order as in the original file.
	
	If the b-values of a shell are not all identical, use the --tolerance
	argument to adjust the accepted interval. For example, a b-value of 2000
	and a tolerance of 20 will extract all volumes with a b-values from 1980 to
	2020.
	
	Files that are too large to be loaded in memory can still be processed by
	setting the --block-size argument. A block size of X means that X DWI volumes
	are loaded at a time for processing.
	
	positional arguments:
	  in_dwi                The DW image file to split.
	  in_bval               The b-values file in FSL format (.bval).
	  in_bvec               The b-vectors file in FSL format (.bvec).
	  in_bvals_to_extract   The list of b-values to extract. For example 0 2000.
	  out_dwi               The name of the output DWI file.
	  out_bval              The name of the output b-value file (.bval).
	  out_bvec              The name of the output b-vector file (.bvec).
	
	options:
	  -h, --help            show this help message and exit
	  --out_indices OUT_INDICES
	                        Optional filename for valid indices in input dwi volume
	  --block-size INT, -s INT
	                        Loads the data using this block size. Useful
	                        when the data is too large to be loaded in memory.
	  --tolerance INT, -t INT
	                        The tolerated gap between the b-values to  extract
	                        and the actual b-values. [20]
	  -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