Dwinormalise dwiextract: [ERROR] No b=0 volumes present

Dear MRtrix Community,

First of all, thanks to the developers for providing such a powerful tool and maintaining it so well. It helps me a lot in learning dMRI processing.

I got a dataset where the b values are unstable; specifically, the b=0 turns out to be b=15 mm/s2. And when I was running dwinormalise, I got the error

dwiextract: [ERROR] No b=0 volumes present
mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
mrmath: [ERROR] error opening image “-”
mrstats: [ERROR] no filename supplied to standard input (broken pipe?)
mrstats: [ERROR] error opening image “-”

Therefore, I’m wondering:

  1. For a temporary solution, can I modify my bval file so that all of my b=15 are converted to b=0?
  2. Could we implement a feature in which we tolerate a certain extent of b-value fluctuation? This would be especially helpful for data in 7T.


Best regards,

Hi @ziqi,

We’re already do! Look up the BZeroTreshold config file option, explained in the docs. It’s set to 10 by default, which is why you’re having trouble…

All the best,

Thank you so much, Donald. I created a ~/.mrtrix.conf, and it works!
However, if I do not have the ~/.mrtrix.conf file, the “-config BZeroThreshold 20” option seems not to be working with dwinormalise command.
Did I do anything wrong? Or, to change the default parameter, we have to have a ~/.mrtrix.conf file.

Ah, that’ll probably be due to dwinormalise being a python script – there’s a chance that option doesn’t get forwarded through to the commands invoked within the script. Hopefully @rsmith or @daljit46 will be able to confirm…

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