.. _scil_tractogram_apply_transform:

scil_tractogram_apply_transform
===============================

::

	usage: __main__.py [-h] [--inverse] [--in_deformation file]
	                   [--reverse_operation]
	                   [--cut_invalid | --remove_invalid | --keep_invalid]
	                   [--no_empty] [--reference REFERENCE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_moving_tractogram in_target_file in_transfo
	                   out_tractogram
	
	Transform a tractogram using an affine/rigid transformation and nonlinear
	deformation (optional).
	
	For more information on how to use the registration script, follow this link:
	https://scilpy.readthedocs.io/en/latest/documentation/tractogram_registration.html
	
	Applying transformation to a tractogram can lead to invalid streamlines (out of
	the bounding box), and thus three strategies are available:
	1) Do nothing, may crash at saving if invalid streamlines are present.
	   [This is the default]
	2) --keep_invalid, save invalid streamlines. Leave it to the user to run
	    scil_tractogram_remove_invalid if needed.
	3) --remove_invalid, automatically remove invalid streamlines before saving.
	    Should not remove more than a few streamlines. Typically, the streamlines
	    that are rejected are the ones reaching the limits of the brain, ex, near
	    the pons.
	4) --cut_invalid, automatically cut invalid streamlines before saving, i.e. the
	   streamlines are kept but the points out of the bounding box are cut.
	
	Example:
	To apply a transformation from ANTs to a tractogram, if the ANTs command was
	MOVING->REFERENCE...
	1) To apply the original transformation:
	scil_tractogram_apply_transform${MOVING_FILE} ${REFERENCE_FILE}
	                                   0GenericAffine.mat ${OUTPUT_NAME}
	                                   --inverse
	                                   --in_deformation 1InverseWarp.nii.gz
	
	2) To apply the inverse transformation, i.e. REFERENCE->MOVING:
	scil_tractogram_apply_transform${MOVING_FILE} ${REFERENCE_FILE}
	                                   0GenericAffine.mat ${OUTPUT_NAME}
	                                   --in_deformation 1Warp.nii.gz
	                                   --reverse_operation
	
	positional arguments:
	  in_moving_tractogram  Path of the tractogram to be transformed.
	                        Bounding box validity will not be checked (could 
	                        contain invalid streamlines).
	  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_tractogram        Output tractogram filename (transformed data).
	
	options:
	  -h, --help            show this help message and exit
	  --no_empty            Do not write file if there is no streamline.
	                        You may save an empty file if you use remove_invalid.
	  --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