.. _scil_connectivity_compute_simple_matrix:

scil_connectivity_compute_simple_matrix
=======================================

::

	usage: __main__.py [-h] [--keep_background] [--hide_labels label [label ...]]
	                   [--hide_fig] [--out_fig file.png] [--binary | --percentage]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [--reference REFERENCE]
	                   [-f]
	                   in_tractogram in_labels out_matrix out_labels
	
	Computes a very simple connectivity matrix, using the streamline count and the
	position of the streamlines' endpoints.
	
	This script is intented for exploration of your data. For a more thorough
	computation (using the longest streamline segment), and for more options about
	the weights of the matrix, see:
	>> scil_connectivity_compute_matrices
	
	Contrary to scil_connectivity_compute_matrices, works with an incomplete
	parcellation (i.e. with streamlines ending in the background).
	
	In the output figure, 4 matrices are shown, all using the streamline count:
	    - Raw count
	    - Raw count (log view)
	    - Binary matrix (if at least 1 streamline connects the two regions)
	    - Percentage of the total streamline count.
	
	You may select which matrix to save to disk (as .npy) using options --binary or
	--percentage. Default ouput matrix is the raw count.
	
	positional arguments:
	  in_tractogram         Tractogram (trk or tck).
	  in_labels             Input nifti volume.
	  out_matrix            Out .npy file.
	  out_labels            Out .txt file. Will show the ordered labels (i.e. the columns and lines' tags).
	
	options:
	  -h, --help            show this help message and exit
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	  -f                    Force overwriting of the output files.
	
	Label management options:
	  --keep_background     By default, the background (label 0) is not included in the matrix. 
	                        Use this option to keep it.
	  --hide_labels label [label ...]
	                        Set given labels' weights to 0 in the matrix. 
	                        Their row and columns wil be kept but set to 0.
	
	Figure options:
	  --hide_fig            If set, does not show the matrices with matplotlib (you can still use --out_fig)
	  --out_fig file.png    If set, saves the figure to file. 
	                        Extension can be any format understood by matplotlib (ex, .png).
	
	Output matrix (.npy) options:
	  --binary              If set, saves the result as binary. Else, the streamline count is saved.
	  --percentage
	
	2.2.2