.. _scil_surface_apply_transform:

scil_surface_apply_transform
============================

::

	usage: __main__.py [-h] [--inverse] [--in_deformation file]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_moving_surface in_transfo out_surface
	
	Script to apply a transform to a surface (FreeSurfer or VTK supported),
	using output from ANTs registration tools (i.e. vtk_transfo.txt, output1InverseWarp.nii.gz).
	
	Example usage from T1 to b0 using ANTs transforms:
	> ConvertTransformFile 3 output0GenericAffine.mat vtk_transfo.txt --hm
	> scil_surface_apply_transform lh_white_lps.vtk vtk_transfo.txt lh_white_b0.vtk\
	    --in_deformation output1InverseWarp.nii.gz --inverse
	
	Important: The input surface needs to be in *T1 world LPS* coordinates
	(aligned over the T1 in MI-Brain).
	
	The script will use the linear affine first and then the warp image.
	The resulting surface will be in *b0 world LPS* coordinates
	(aligned over the b0 in MI-Brain).
	
	-------------------------------------------------------------------
	Reference:
	[1] St-Onge, E., Daducci, A., Girard, G. and Descoteaux, M. 2018.
	    Surface-enhanced tractography (SET). NeuroImage.
	-------------------------------------------------------------------
	
	positional arguments:
	  in_moving_surface     Input surface (.vtk).
	  in_transfo            Path of the file containing the 4x4 
	                        transformation, matrix (.txt, .npy or .mat).
	  out_surface           Output surface (.vtk).
	
	options:
	  -h, --help            show this help message and exit
	  -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.
	
	Transformation options:
	  --inverse             Apply the inverse linear transformation.
	  --in_deformation file
	                        Path to the file containing a deformation field.
	
	2.2.2