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

1

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.

Thanks!

Best regards,
Ziqi

2

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,
Donald

3

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.

4

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…

1 Like