.. _scil_lesions_generate_nawm:

scil_lesions_generate_nawm
==========================

::

	usage: __main__.py [-h] [--nb_ring NB_RING] [--ring_thickness RING_THICKNESS]
	                   [--mask MASK] [--split_4D OUT_DIR]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_image out_image
	
	The NAWM (Normal Appearing White Matter) is the white matter that is
	neighboring a lesion. It is used to compute metrics in the white matter
	surrounding lesions.
	
	This script will generate concentric rings around the lesions, with the rings
	going from 2 to nb_ring + 2, with the lesion being 1.
	
	The optional mask is used to compute the rings only in the mask
	region. This can be useful to avoid useless computation.
	
	If the lesion_atlas is binary, the output will be 3D. If the lesion_atlas
	is a label map, the output will be either:
	  - 4D, with each label having its own NAWM.
	  - 3D, if using --split_4D and saved into a folder as multiple 3D files.
	
	WARNING: Voxels must be isotropic.
	
	positional arguments:
	  in_image              Lesions file as mask OR labels (.nii.gz).
	                        (must be uint8 for mask, uint16 for labels).
	  out_image             Output NAWM file (.nii.gz).
	                        If using --split_4D, this will be the prefix of the output files.
	
	options:
	  -h, --help            show this help message and exit
	  --nb_ring NB_RING     Integer representing the number of rings to be created.
	  --ring_thickness RING_THICKNESS
	                        Integer representing the thickness (in voxels) of the rings to be created.
	  --mask MASK           Mask where to compute the NAWM (e.g WM mask).
	  --split_4D OUT_DIR    Provided lesions will be split into multiple files.
	                        The output files will be named using out_image as a prefix.
	  -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