.. _scil_bundle_mean_std:

scil_bundle_mean_std
====================

::

	usage: __main__.py [-h] [--per_point in_labels | --include_dps]
	                   [--density_weighting] [--distance_weighting DISTANCE_NII]
	                   [--correlation_weighting CORRELATION_NII]
	                   [--out_json OUT_JSON] [--reference REFERENCE]
	                   [--indent INDENT] [--sort_keys]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]]
	                   in_bundle in_metrics [in_metrics ...]
	
	Compute mean and std for each metric.
	
	- Default: For the whole bundle. This is achieved by averaging the metric
	  values of all voxels occupied by the bundle.
	- Option --per_point: For all streamlines points in the bundle for each metric
	  combination, along the bundle, i.e. for each point.
	  **To create label_map and distance_map, see
	  scil_bundle_label_map
	
	Density weighting modifies the contribution of voxel with lower/higher
	streamline count to reduce influence of spurious streamlines.
	
	positional arguments:
	  in_bundle             Fiber bundle file to compute statistics on.
	  in_metrics            Nifti file to compute statistics on. Probably some tractometry measure(s) such as FA, MD, RD, ...
	
	options:
	  -h, --help            show this help message and exit
	  --per_point in_labels
	                        If set, computes the metrics per point instead of on the whole bundle.
	                        You must then give the label map (.nii.gz) of the corresponding fiber bundle.
	  --include_dps         Save values from data_per_streamline.
	                        Currently not offered with option --per_point.
	  --density_weighting   If set, weights statistics by the number of fibers passing through each voxel.
	  --distance_weighting DISTANCE_NII
	                        If set, weights statistics by the inverse of the distance between a streamline and the centroid.
	  --correlation_weighting CORRELATION_NII
	                        If set, weight statistics by the correlation strength between longitudinal data.
	  --out_json OUT_JSON   Path of the output file. If not given, the output is simply printed on screen.
	  --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.
	
	Json options:
	  --indent INDENT       Indent for json pretty print.
	  --sort_keys           Sort keys in output json.
	
	2.2.2