.. _scil_tractogram_convert_trk_to_hdf5:

scil_tractogram_convert_trk_to_hdf5
===================================

::

	usage: __main__.py [-h] [--stored_space {rasmm,voxmm,vox}]
	                   [--stored_origin {nifti,trackvis}] [--include_dps]
	                   [--save_empty] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_bundles [in_bundles ...] out_hdf5
	
	Save connections as TRK to HDF5.
	
	This script is useful to convert a set of connections or bundles to a single
	HDF5 file. The HDF5 file will contain a group for each input file, with the
	streamlines stored in the specified space and origin (keep the default if you
	are going to use the connectivity scripts in scilpy).
	
	To make a file compatible with scil_tractogram_commit or
	scil_connectivity_compute_matrices you will have to follow this nomenclature
	for the input files:
	in_dir/
	    |-- LABEL1_LABEL1.trk
	    |-- LABEL1_LABEL2.trk
	    |-- [...]
	    |-- LABEL90_LABEL90.trk
	The value of first labels should be smaller or equal to the second labels.
	Connectivity scripts in scilpy only consider the upper triangular part of the
	connectivity matrix.
	
	By default, ignores the empty connections. To save them, use --save_empty.
	Note that data_per_point is never included.
	
	positional arguments:
	  in_bundles            Path of the input connection(s) or bundle(s).
	  out_hdf5              Output HDF5 filename (.h5).
	
	options:
	  -h, --help            show this help message and exit
	  --stored_space {rasmm,voxmm,vox}
	                        Space convention in which the streamlines are stored [vox].
	  --stored_origin {nifti,trackvis}
	                        Voxel origin convention in which the streamlines are stored [trackvis].
	  --include_dps         Include the data_per_streamline the metadata.
	  --save_empty          Save empty connections.
	  -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