.. _scil_lesions_info:

scil_lesions_info
=================

::

	usage: __main__.py [-h]
	                   [--bundle BUNDLE | --bundle_mask BUNDLE_MASK | --bundle_labels_map BUNDLE_LABELS_MAP]
	                   [--min_lesion_vol MIN_LESION_VOL] [--out_lesion_atlas FILE]
	                   [--out_lesion_stats FILE] [--out_streamlines_stats FILE]
	                   [--indent INDENT] [--sort_keys] [--reference REFERENCE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_lesion out_json
	
	This script will output informations about lesion load in bundle(s).
	The input lesion file is a labeled volume (.nii.gz) where each lesion is
	represented by a unique label. To label a lesion file use
	scil_labels_from_mask.
	
	Then, the second input can either be streamlines, binary bundle mask, or a
	bundle voxel label map.
	
	positional arguments:
	  in_lesion             Lesions file as labels (.nii.gz).
	  out_json              Output file for lesion information (.json).
	
	options:
	  -h, --help            show this help message and exit
	  --bundle BUNDLE       Path of the bundle file (.trk).
	  --bundle_mask BUNDLE_MASK
	                        Path of the bundle binary mask (.nii.gz).
	  --bundle_labels_map BUNDLE_LABELS_MAP
	                        Path of the bundle labels map (.nii.gz).
	  --min_lesion_vol MIN_LESION_VOL
	                        Minimum lesion volume in mm3 [7].
	  --out_lesion_atlas FILE
	                        Save the labelized lesion(s) map (.nii.gz).
	  --out_lesion_stats FILE
	                        Save the lesion-wise volume measure (.json).
	  --out_streamlines_stats FILE
	                        Save the lesion-wise streamline count (.json).
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	  -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.
	
	Json options:
	  --indent INDENT       Indent for json pretty print.
	  --sort_keys           Sort keys in output json.
	
	2.2.2