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}]] [-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.
Formerly: scil_prepare_topup_command.py
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}]
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.