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}]]
[-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.py. If using
topup prior to calling this script, images should be concatenated in the same
order as the b0s used with prepare_topup.
Formerly: scil_prepare_eddy_command.py
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.py.
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.py.
--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}]
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.