Inconsistency

1

Hi all,

I’m using RC1-44.

Found inconsistency between command-line usage and documentation.

  • command-line “dwipreproc” has [options] (in man page) first: dwipreproc [ options ] input output
  • doc on website has dwipreproc input output [ options ]

Stefan.

2

Hi @Stefan_Sunaert
I think both are right. In MRtrix, options are generally pairs of name and value, such as -pe_dir PE. So you can put them before or after input and output. It doesn’t matter.
Best,
Zonglei

3

Hi @Zonglei,

you are right!

dwipreproc -pe_dir AP -rpe_pair -se_epi S_004_055_all_b0.mif S_004_055.mif S_004_055_PP.mif

&

dwipreproc S_004_055.mif S_004_055_PP.mif -pe_dir AP -rpe_pair -se_epi S_004_055_all_b0.mif

both work.

Thanks for your quick response.

4

In MRtrix, options are generally pairs of name and value, …

Not always: Some options are just “flags” (i.e. just the option string, no need to provide a value afterwards), and other options take more than one argument (e.g. -export_grad_fsl bvecs bvals).

However the fact that all options take some fixed number of values means that command-line options can appear in any position at the command line, without ambiguity.

5

Yes. Thanks for the add. @rsmith