.. _scil_dwi_prepare_eddy_command:

scil_dwi_prepare_eddy_command
=============================

::

	usage: __main__.py [-h] [--n_reverse N_REVERSE] [--topup TOPUP]
	                   [--topup_params TOPUP_PARAMS]
	                   [--eddy_cmd {eddy_openmp,eddy_cuda,eddy_cuda8.0,eddy_cuda9.1,eddy_cuda10.2,eddy,eddy_cpu}]
	                   [--b0_thr B0_THR] [--encoding_direction {x,y,z}]
	                   [--readout READOUT] [--slice_drop_correction]
	                   [--lsr_resampling] [--out_directory OUT_DIRECTORY]
	                   [--out_prefix OUT_PREFIX] [--out_script] [--fix_seed]
	                   [--eddy_options EDDY_OPTIONS]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_dwi in_bvals in_bvecs in_mask
	
	Prepare a typical command for eddy and create the necessary files. When using
	multiple acquisitions and/or opposite phase directions, images, b-values and
	b-vectors should be merged together using scil_dwi_concatenate. If using
	topup prior to calling this script, images should be concatenated in the same
	order as the b0s used with prepare_topup.
	
	positional arguments:
	  in_dwi                Input DWI Nifti image. If using multiple acquisition and/or opposite phase directions, please merge in the same order as for prepare_topup using scil_dwi_concatenate.
	  in_bvals              Input b-values file in FSL format.
	  in_bvecs              Input b-vectors file in FSL format.
	  in_mask               Binary brain mask.
	
	options:
	  -h, --help            show this help message and exit
	  --n_reverse N_REVERSE
	                        Number of reverse phase volumes included in the DWI image [0].
	  --topup TOPUP         Topup output name. If given, apply topup during eddy.
	                        Should be the same as --out_prefix from scil_dwi_prepare_topup_command.
	  --topup_params TOPUP_PARAMS
	                        Parameters file (typically named acqparams) used to run topup.
	  --eddy_cmd {eddy_openmp,eddy_cuda,eddy_cuda8.0,eddy_cuda9.1,eddy_cuda10.2,eddy,eddy_cpu}
	                        Eddy command [eddy_openmp].
	  --b0_thr B0_THR       All b-values with values less than or equal to b0_thr are considered
	                        as b0s i.e. without diffusion weighting [20].
	  --encoding_direction {x,y,z}
	                        Acquisition direction, default is AP-PA [y].
	  --readout READOUT     Total readout time from the DICOM metadata [0.062].
	  --slice_drop_correction
	                        If set, will activate eddy's outlier correction,
	                        which includes slice drop correction.
	  --lsr_resampling      Perform least-square resampling, allowing eddy to combine forward and reverse phase acquisitions for better reconstruction. Only works if directions and b-values are identical in both phase direction.
	  --out_directory OUT_DIRECTORY
	                        Output directory for eddy files [.].
	  --out_prefix OUT_PREFIX
	                        Prefix of the eddy-corrected DWI [dwi_eddy_corrected].
	  --out_script          If set, will output a .sh script (eddy.sh).
	                        else, will output the lines to the terminal [False].
	  --fix_seed            If set, will use the fixed seed strategy for eddy.
	                        Enhances reproducibility.
	  --eddy_options EDDY_OPTIONS
	                        Additional options you want to use to run eddy.
	                        Add these options using quotes (i.e. "--ol_nstd=6 --mb=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