.. _scil_tractogram_register:

scil_tractogram_register
========================

::

	usage: __main__.py [-h] [--out_name OUT_NAME] [--only_rigid]
	                   [--moving_tractogram_ref MOVING_TRACTOGRAM_REF]
	                   [--static_tractogram_ref STATIC_TRACTOGRAM_REF]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   moving_tractogram static_tractogram
	
	Generate a linear transformation matrix from the registration of 2 tractograms.
	Typically, this script is run before scil_tractogram_apply_transform
	
	For more information on how to use the various registration scripts, see the
	doc at:
	https://scilpy.readthedocs.io/en/latest/documentation/tractogram_registration.html
	
	----------------------------------------------------------------------------------
	Reference:
	[1] E. Garyfallidis, O. Ocegueda, D. Wassermann, M. Descoteaux
	    Robust and efficient linear registration of white-matter fascicles in the
	    space of streamlines, NeuroImage, Volume 117, 15 August 2015, Pages 124-140
	    (http://www.sciencedirect.com/science/article/pii/S1053811915003961)
	----------------------------------------------------------------------------------
	
	positional arguments:
	  moving_tractogram     Path of the moving tractogram.
	  static_tractogram     Path of the target tractogram.
	
	options:
	  -h, --help            show this help message and exit
	  --out_name OUT_NAME   Filename of the transformation matrix. 
	                        The registration type will be appended as a suffix,
	                        [<out_name>_<affine/rigid>.txt]. 
	                        Default: [transformation.txt]
	  --only_rigid          If set, will only use a rigid transformation (uses affine by default).
	  --moving_tractogram_ref MOVING_TRACTOGRAM_REF
	                        Reference anatomy for moving_tractogram (if tck/vtk/fib/dpy) file
	                        support (.nii or .nii.gz).
	  --static_tractogram_ref STATIC_TRACTOGRAM_REF
	                        Reference anatomy for static_tractogram (if 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.
	
	2.2.2