.. _scil_tractogram_apply_transform_to_hdf5:

scil_tractogram_apply_transform_to_hdf5
=======================================

::

	usage: __main__.py [-h] [--inverse] [--in_deformation file]
	                   [--reverse_operation]
	                   [--cut_invalid | --remove_invalid | --keep_invalid]
	                   [--reference REFERENCE] [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   [-f]
	                   in_hdf5 in_target_file in_transfo out_hdf5
	
	Transform tractogram(s) contained in the hdf5 output from a connectivity
	script, using an affine/rigid transformation and nonlinear deformation
	(optional).
	
	See scil_tractogram_apply_transformto apply directly to a tractogram.
	
	For more information on how to use the registration script, follow this link:
	https://scilpy.readthedocs.io/en/latest/documentation/tractogram_registration.html
	
	Or use >> scil_tractogram_apply_transform--help
	
	positional arguments:
	  in_hdf5               Path of the hdf5 containing the moving tractogram, to be transformed. (.h5 extension).
	  in_target_file        Path of the reference target file (.trk or .nii).
	  in_transfo            Path of the file containing the 4x4 
	                        transformation, matrix (.txt, .npy or .mat).
	  out_hdf5              Output tractogram filename (transformed data).
	
	options:
	  -h, --help            show this help message and exit
	  --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.
	
	Transformation options:
	  --inverse             Apply the inverse linear transformation.
	  --in_deformation file
	                        Path to the file containing a deformation field.
	  --reverse_operation   Apply the transformation in reverse (see doc), warp
	                        first, then linear.
	
	Management of invalid streamlines:
	  --cut_invalid         Cut invalid streamlines rather than removing them.
	                        Keep the longest segment only.
	  --remove_invalid      Remove the streamlines landing out of the bounding box.
	  --keep_invalid        Keep the streamlines landing out of the bounding box.
	
	2.2.2