.. _scil_tractogram_smooth:

scil_tractogram_smooth
======================

::

	usage: __main__.py [-h] (--gaussian SIGMA | --spline SIGMA NB_CTRL_POINT)
	                   [--compress [COMPRESS_TH]] [--reference REFERENCE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_tractogram out_tractogram
	
	This script will smooth the streamlines, usually to remove the 'wiggles' in
	probabilistic tracking.
	
	Two choices of methods are available:
	- Gaussian will use the surrounding coordinates for smoothing. Streamlines are
	resampled to 1mm step-size and the smoothing is performed on the coordinate
	array. The sigma will be indicative of the  number of points surrounding the
	center points to be used for blurring.
	- Spline will fit a spline curve to every streamline using a sigma and the
	number of control points. The sigma represents the allowed distance from the
	control points. The final streamlines are obtained by evaluating the spline at
	constant intervals so that it will have the same number of points as initially.
	
	This script enforces endpoints to remain the same.
	
	WARNING:
	- too low of a sigma (e.g: 1) with a lot of control points (e.g: 15)
	will create crazy streamlines that could end up out of the bounding box.
	- data_per_point will be lost.
	
	positional arguments:
	  in_tractogram         Input tractography file.
	  out_tractogram        Output tractography file.
	
	options:
	  -h, --help            show this help message and exit
	  --gaussian SIGMA      Sigma for smoothing. Use the value of surronding
	                        X,Y,Z points on the streamline to blur the streamlines.
	                        A good sigma choice would be around 5.
	  --spline SIGMA NB_CTRL_POINT
	                        Sigma for smoothing. Model each streamline as a spline.
	                        A good sigma choice would be around 5 and control point around 10.
	  --compress [COMPRESS_TH]
	                        If set, compress the resulting streamline. Value is the maximum 
	                        compression distance in mm.[0.1]
	  --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.
	
	2.2.2