Dwifslpreproc fails to generate acquisition parameters file

1

Hi everyone,

I’m running into an issue with FSL’s eddy on a Linux machine. When I try to run it, I get the following error:

EddyInputError: Error when attempting to read --acqp file eddy_config.txt
Terminating program
=========
eddy_cuda
Could not open matrix file eddy_config.txt

The strange part is that the same command and input files work perfectly on my Mac.

I understand that the acquisition parameters file (eddy_config.txt) should normally be created automatically by dwifslpreproc, but for some reason this isn’t happening on this system and I’m not sure why. The command does work on other machines, so it seems to be specific to this setup.

I’m running:

  • Linux Distribution: Ubuntu 22.04.5 LTS (Jammy Jellyfish)

  • Kernel: 6.8.0-65-generic

  • MRtrix3 version: 3.0.7-5-g5ded6caf (built Aug 18 2025)

  • FSL version: 6.0.7.18

  • Python: 3.12.11 (python3) and 3.10.12 (python)

  • FreeSurfer: 7.4.1-20230614-7eb8460

I can manually fix the issue by creating the config file myself, but I’m still unclear why it’s not being generated automatically.

Has anyone run into this before or found a cause?

Thank you for creating this software and for helping users!

Thanks,

Tom

2

Hi Tom,

I have never encountered this error, and have no idea how there could possibly be a plausible path that reaches the eddy invocation without generating that file given that the generating command is unavoidable. Given that, I think the only way I could possibly make anything resembling progress (assuming you don’t want me SSHing around in your machine) would be if you could define a Docker recipe and provide sample data that reproduces the fault. Though it’s entirely likely that reproducing your environment in a container won’t reproduce the fault…

Also make sure that you’re not running out of HDD space. That can sometimes cause strange behaviour.

Cheers
Rob