.. _scil_dti_convert_tensors:

scil_dti_convert_tensors
========================

::

	usage: __main__.py [-h] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_file out_file in_format out_format
	
	Conversion of tensors (the 6 values from the triangular matrix) between various
	software standards. We cannot discover the input format type, user must know
	how the tensors were created.
	
	    Dipy's order is [Dxx, Dxy, Dyy, Dxz, Dyz, Dzz]
	       Shape: [i, j , k, 6].
	       Ref: https://github.com/dipy/dipy/blob/master/dipy/reconst/dti.py#L1639
	    
	    MRTRIX's order is : [Dxx, Dyy, Dzz, Dxy, Dxz, Dyz]
	       Shape: [i, j , k, 6].
	       Ref: https://mrtrix.readthedocs.io/en/dev/reference/commands/dwi2tensor.html
	    
	    ANTS's order ('nifti format') is : [Dxx, Dxy, Dyy, Dxz, Dyz, Dzz].
	       Shape: [i, j , k, 1, 6] (Careful, file is 5D).
	       Ref: https://github.com/ANTsX/ANTs/wiki/Importing-diffusion-tensor-data-from-other-software
	    
	    FSL's order is [Dxx, Dxy, Dxz, Dyy, Dyz, Dzz]
	       Shape: [i, j , k, 6].
	       Ref: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide
	       (Also used for the Fibernavigator)
	    
	
	positional arguments:
	  in_file               Input tensors filename.
	  out_file              Output tensors filename.
	  in_format             Input format. Choices: ['fsl', 'nifti', 'mrtrix', 'dipy']
	  out_format            Output format. Choices: ['fsl', 'nifti', 'mrtrix', 'dipy']
	
	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.
	  -f                    Force overwriting of the output files.
	
	2.2.2