-rpe_pair error_dwipreproc

Dear MRtrix experts,

I am using BATMAN structure with these commands:

dwiextract AP.mif dwi.mif -no_bzero
dwidenoise dwi.mif dwi_den.mif
dwiextract AP.mif AP_b0.mif -bzero
mrmath – mean mean_b0_AP.mif –axis 3
mrconvert b0_PA/ - | mrmath – mean mean_b0_PA.mif –axis 3
mrcat mean_b0_AP.mif mean_b0_PA.mif –axis 3 b0_pair.mif

Now I want to run motion and distortion correction with dwipreproc command, but I get this error:
dwipreproc dwi_den.mif dwi_den_preproc.mif -pe_dir AP –rpe_pair -se_epi b0_pair.mif
Error: unrecognized arguments: –rpe_pair
Usage: dwipreproc input output [ options ]
(Run dwipreproc -help for more information)

Please help me, I’m confused.

Thanks in advanced.
Best regards.


I think the problem is that you wrote — instead of - infront of rpe_pair. One thing I noticed, why do you remove the B0 before the denoising? I think the denoise step should include the B0s. I hope this helps.

Best regards,


1 Like

Hi dear Manuel,

You’re absolutely right about both.:+1:

Thanks so much.:rose: