.. _scil_tractogram_seed_density_map:

scil_tractogram_seed_density_map
================================

::

	usage: __main__.py [-h] [--binary [FIXED_VALUE]] [--no_bbox_check]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   tractogram_filename seed_density_filename
	
	Compute a density map of seeds saved in .trk file.
	
	* They are saved as a data_per_streamline 'seeds' when using our tractography
	scripts with option --save_seeds.
	- scil_tracking_local
	- scil_tracking_local_dev
	- scil_tracking_pft
	
	If you use your own tractograms, you can create a 'seeds' data_per_streamline.
	Don't forget to save the coordinates in voxel space, corner origin.
	
	positional arguments:
	  tractogram_filename   Tracts filename. Format must be .trk. 
	                        File should contain a "seeds" value in the data_per_streamline.
	                        These seeds must be in space: voxel, origin: corner.
	  seed_density_filename
	                        Output seed density filename. Format must be Nifti.
	
	options:
	  -h, --help            show this help message and exit
	  --binary [FIXED_VALUE]
	                        If set, will store the same value for all intersected voxels, creating a binary map.
	                        When set without a value, 1 is used (and dtype uint8).
	                        If a value is given, it will be used as the stored value.
	  --no_bbox_check       Activate to ignore validity of the bounding box during loading / saving of 
	                        tractograms (ignores the presence of invalid streamlines).
	  -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