.. _scil_surface_create:

scil_surface_create
===================

::

	usage: __main__.py [-h]
	                   (--in_labels IN_LABELS | --in_mask IN_MASK | --in_volume IN_VOLUME)
	                   [--list_indices LIST_INDICES [LIST_INDICES ...] |
	                   --each_index] [--value VALUE] [--smooth SMOOTH]
	                   [--erosion EROSION] [--dilation DILATION]
	                   [--opening OPENING] [--closing CLOSING] [--fill]
	                   [--vtk2vox] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   out_surface
	
	Script to create a surface with marching cube from a mask or a label image.
	The surface will be readable with software like MI-Brain.
	
	Example : use wmparc.a2009s.nii.gz with some aseg.stats indices
	
	scil_surface_create out_surface.vtk \
	    --in_labels s1a1/mask/S1-A1_wmparc.a2009s.nii.gz\
	    --list_indices 16:32 --opening 2 --smooth 2 -v
	-----------------------------------------------------------------
	Reference:
	[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
	    Surface-enhanced tractography (SET). NeuroImage.
	-----------------------------------------------------------------
	
	positional arguments:
	  out_surface           Output surface (.vtk)
	
	options:
	  -h, --help            show this help message and exit
	  --fill                Fill holes in the image. [False]
	  --vtk2vox             Keep output surface in voxel space. [False]
	  -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.
	
	Input (Labels or Mask):
	  --in_labels IN_LABELS
	                        Path of the atlas (nii or nii.gz).
	                        You can provide a list of indices with --list_indices or create a surface per index with --each_index.
	                        If no indices are provided, it will merge all indices and converted to a binary mask.
	  --in_mask IN_MASK     Path of the mask (nii or nii.gz).
	  --in_volume IN_VOLUME
	                        Path of the volume (nii or nii.gz).
	
	Options for labels input:
	  --list_indices LIST_INDICES [LIST_INDICES ...]
	                        List of labels indices to use for the surface.
	  --each_index          Create a surface per index. It will use the out_surface basename to create the output files.
	
	Options for volume input:
	  --value VALUE         Isosurface threshold value used. This value is called isovalue in mbcube.
	                        Example: For a binary mask (with 0 and 1), 0.5 will generate a surface in the middle of the transition. [0.5]
	
	Morphology options:
	  --smooth SMOOTH       Smoothing size with 1 implicit step. [None]
	  --erosion EROSION     Erosion: number of iterations. [None]
	  --dilation DILATION   Dilation: number of iterations. [None]
	  --opening OPENING     Opening (dilation of the erosion): number of iterations. [None]
	  --closing CLOSING     Closing (erosion of the dilation): number of iterations. [None]
	
	2.2.2