Hi all,
We just updated mrtrix from github with the intent of using the new -eddy_option
in dwipreproc
. Yet the option does not work well:
dwipreproc -pe_dir $dwiphaseencoding DWI_denois.mif DWI_denois_preproc.mif -rpe_none -quiet -nthreads $mrtrixthreads $force -eddy_options "--data_is_shelled"
Error: argument -eddy_options: expected one argument
Usage: dwipreproc input output [ options ]
(Run dwipreproc -help for more information)
Any help on how to fix this?
Thank you
Hi DorianP,
I noticed the problem as well. For the time being, you can get around it by appending a space to the option value, as in: -eddy_option "--data_is_shelled "
.
Cheers,
Ben
1 Like
Thanks for raising this; I can see a lot of people encountering the same issue. Unfortunately this is a problem with the internals of how Python’s argparse
module parses the user’s command-line input. This is yet another justification for me to do away with argparse
altogether and write my own MRtrix3 Python command-line parser…
Using -eddy_options="--data_is_shelled"
(i.e. putting a ‘=
’ sign between the option and value rather than a space) also works, as does appending a space to the value string as mentioned by @bjeurissen. I’m adding a relevant instruction to the script’s help page so that hopefully less people will stumble across the same issue.