.. _scil_dwi_prepare_topup_command:

scil_dwi_prepare_topup_command
==============================

::

	usage: __main__.py [-h] [--config CONFIG] [--synb0]
	                   [--encoding_direction {x,y,z}] [--readout READOUT]
	                   [--out_b0s OUT_B0S] [--out_directory OUT_DIRECTORY]
	                   [--out_prefix OUT_PREFIX] [--out_params OUT_PARAMS]
	                   [--out_script] [--topup_options TOPUP_OPTIONS]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_forward_b0 in_reverse_b0
	
	Prepare a typical command for topup and create the necessary files.
	The reversed b0 must be in a different file.
	
	positional arguments:
	  in_forward_b0         Input b0 Nifti image with forward phase encoding.
	  in_reverse_b0         Input b0 Nifti image with reversed phase encoding.
	
	options:
	  -h, --help            show this help message and exit
	  --config CONFIG       Topup config file [b02b0.cnf].
	  --synb0               If set, will use SyNb0 custom acqparams file.
	  --encoding_direction {x,y,z}
	                        Acquisition direction of the forward b0 image, default is AP [y].
	  --readout READOUT     Total readout time from the DICOM metadata [0.062].
	  --out_b0s OUT_B0S     Output fused b0 file [fused_b0s.nii.gz].
	  --out_directory OUT_DIRECTORY
	                        Output directory for topup files [.].
	  --out_prefix OUT_PREFIX
	                        Prefix of the topup results [topup_results].
	  --out_params OUT_PARAMS
	                        Filename for the acquisition parameters file [acqparams.txt].
	  --out_script          If set, will output a .sh script (topup.sh).
	                        else, will output the lines to the terminal [False].
	  --topup_options TOPUP_OPTIONS
	                        Additional options you want to use to run topup.
	                        Add these options using quotes (i.e. "--fwhm=6 --miter=4").
	  -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