.. _scil_labels_combine:

scil_labels_combine
===================

::

	usage: __main__.py [-h] --volume_ids VOLUME_IDS [VOLUME_IDS ...]
	                   [--out_labels_ids OUT_LABELS_IDS [OUT_LABELS_IDS ...] |
	                   --unique | --group_in_m] [--background BACKGROUND]
	                   [--merge_groups] [--not_save_empty]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   output
	
	Script to combine labels from multiple volumes. If there is overlap, it will
	overwrite them based on the input order.
	
	    >>> scil_labels_combine out_labels.nii.gz
	            --volume_ids animal_labels.nii 20
	            --volume_ids DKT_labels.nii.gz 44 53
	            --out_labels_ids 20 44 53
	    >>> scil_labels_combine slf_labels.nii.gz
	            --volume_ids a2009s_aseg.nii.gz all
	            --volume_ids clean/s1__DKT.nii.gz 1028 2028
	
	------------------------------------------------------------------------------
	Reference:
	[1] Al-Sharif N.B., St-Onge E., Vogel J.W., Theaud G.,
	    Evans A.C. and Descoteaux M. OHBM 2019.
	    Surface integration for connectome analysis in age prediction.
	------------------------------------------------------------------------------
	
	positional arguments:
	  output                Combined labels volume output.
	
	options:
	  -h, --help            show this help message and exit
	  --volume_ids VOLUME_IDS [VOLUME_IDS ...]
	                        List of volumes directly followed by their labels:
	                          --volume_ids atlasA  id1a id2a 
	                          --volume_ids atlasB  id1b id2b ... 
	                          "all" can be used instead of id numbers.
	  --out_labels_ids OUT_LABELS_IDS [OUT_LABELS_IDS ...]
	                        List of labels indices for output images.
	  --unique              If set, output id with unique labels, excluding first background value.
	  --group_in_m          Add (x * 10 000) to each volume labels, where x is the input volume order number.
	  --background BACKGROUND
	                        Background id, excluded from output [0],
	                         the value is used as output background value.
	  --merge_groups        Each group from the --volume_ids option will be merged as a single labels.
	  --not_save_empty      If set, the output will not be saved if it is empty.
	  -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