Dwifslpreproc Fails with EDDY::: Eddy failed with message Error

Hello everyone,

I am experiencing an issue while running the dwifslpreproc script on my dataset. The process appears to be running fine until it reaches the eddy_cpu command, after which it fails with a vague error message “EDDY::: Eddy failed with message.”

Software Versions:

  • MRTRIX3: == mrinfo 3.0.4 == 64 bit release version, built Dec 14 2022, using Eigen 3.4.0
  • FSL: FLIRT version 6.0
  • Operating System: macOS; Apple M1 Max; 32GB Memory; Ventura 13.5.1


  1. I started by running the dwifslpreproc command as follows:
dwifslpreproc dwi_unringed.mif dwi_preprocessed.mif -rpe_header -pe_dir AP -eddy_options " --slm=linear --verbose"
  1. The script proceeds through several steps like loading headers, executing topup, etc., until it fails at the eddy_cpu command.

Error Message:

The error message I received is as follows:

dwifslpreproc: [ERROR] eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --slm=linear --verbose --out=dwi_post_eddy --verbose (dwifslpreproc:972)
dwifslpreproc: [ERROR] Information from failed command:
               Reading images
               EDDY::: Eddy failed with message

Additional Information:

  • The dwi_unringed.mif was generated from DICOMs using dcm2niix and further processed using dwidenoise and mrdegibbs.
  • The b0_AP_PA.mif used in dwifslpreproc is an average of B0s from both the AP and PA directions.
  • The shell indices and b-values show the following:
    • Shell Indices:
dwifslpreproc: Result: 0,45,91,92 46,47,93,94,138,139 1,2,3,4,5,6,7,48,49,50,51,52,53,54,95,96,97,98,99,100 8,9,10,11,12,13,14,55,56,57,58,59,60,101,102,103,104,105,106,107 15,16,17,18,19,20,21,22,23,24,61,62,63,64,65,66,67,68,69,70,108,109,110,111,112,113,114,115,116,117 25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137
  • Shell B-values: 0 250 1000 1500 2000 2500

I would really appreciate any guidance or suggestions to resolve this issue.

Thank you!

Hi Shai,

Not a solution,but a suggestion: Had encountered a similar problem,and in my specific case,was a problem with how the indices.txt was created.


@archithrajan1 Thanks. I think it may be a similar case for me. How did you specify the dwifslpreproc command to include the correct indicies.txt file?

I’m trying:

dwifslpreproc DKI_all_unringed.mif DKI_all_eddy_corrected.mif -pe_dir ap -rpe_pair -se_epi b0_pair.mif -fslgrad bvecs.txt bvals.txt -eddy_options " --slm=linear --index=/path/to/index.txt"

but it still creates its own indecies.txt file in the tmp folder

Hi Shai,

I think I did the same thing.But in my specific case, text file genereted from notepad in windows didn’t work, but with gedit (in Ubuntu WSL) worked.Again, Id like to put in a disclaimer that it was a specific issue, and not likely to be a solution.