# Dwifslpreproc - Eddy failed with message
**URL:** https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180
**Category:** Uncategorized
**Created:** [November 29, 2023, 2:13pm UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180 "2023-11-29T14:13:36Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@ejanson6](https://community.mrtrix.org/u/ejanson6)
#### Post date: [November 29, 2023, 2:13pm UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/1 "2023-11-29T14:13:36Z")
Dear MRtrix community,
Although another topic about this error was poster previously ([Dwifslpreproc Fails with EDDY::: Eddy failed with message Error](https://community.mrtrix.org/t/dwifslpreproc-fails-with-eddy-eddy-failed-with-message-error/6930)), I did not find a solution yet.
I’m trying to run dwifslpreproc on my multi-shell neonatal data, including a B0 pair, using the following command:
```auto
for_each * : dwifslpreproc IN/dwi_denoised_unringed.mif IN/dwi_denoised_unringed_preproc.mif -pe_dir j- -rpe_pair -se_epi IN/B0_pair.mif
```
However, I receive the following error:
```auto
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 --out=dwi_post_eddy --verbose (dwifslpreproc:972)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
Reading images
@��v�
EDDY::: Eddy failed with message
```
Once I open the textile ‘error.txt’ in the scratch directory, I see no additional error information.
The images loaded for the eddy\_cpu command can be opened manually using mrview and are present in the scratch directory.
Any advice on how to continue?
Many thanks in advance!!
Els
---
### Author:  [@Shai\_P](https://community.mrtrix.org/u/Shai_P)
#### Post date: [December 5, 2023, 12:58am UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/2 "2023-12-05T00:58:37Z")
@ejanson6 Im the original poster of the question you referenced. I think this may be an issue with mac OS and fsl eddy/cuda compatibility but I am not certain.
---
### Author:  [@mschira](https://community.mrtrix.org/u/mschira)
#### Post date: [December 5, 2023, 2:42am UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/3 "2023-12-05T02:42:13Z")
Hm it looks like the following command failed:
```auto
eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --out=dwi_post_eddy --verbose (dwifslpreproc:972
```
did you check in the temp directory if the input imgages (eddy\_in.nii, eddy\_mask.nii, eddy\_config.txt ) exist?
Do they look fine or are they faulty?
M.
---
### Author:  [@j-tseng](https://community.mrtrix.org/u/j-tseng)
#### Post date: [December 6, 2023, 8:06pm UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/4 "2023-12-06T20:06:02Z")
+1 to this - I’ve seen this eddy error before and in my case, the auto-generated `eddy_mask.nii` file was way off from a proper brain mask. I was able to circumvent this by using the `-eddy_mask` argument for `dwifslpreproc` since I already had a mask from some other processing step.
---
### Author:  [@ejanson6](https://community.mrtrix.org/u/ejanson6)
#### Post date: [December 14, 2023, 1:01pm UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/5 "2023-12-14T13:01:54Z")
Thanks for your response! In my case, the eddy\_in and eddy\_mask file look okay to me. See here the mask with reduced opacity on top of the input file:
---
### Author:  [@ejanson6](https://community.mrtrix.org/u/ejanson6)
#### Post date: [December 14, 2023, 1:01pm UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/6 "2023-12-14T13:01:59Z")
Dear mschira, thank you so much for thinking along. These files do exist, can be opened and look good.
---
### Author:  [@mschira](https://community.mrtrix.org/u/mschira)
#### Post date: [December 18, 2023, 12:23am UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/7 "2023-12-18T00:23:39Z")
> [@mschira](#):
>
> `eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --out=dwi_post_eddy --verbose (dwifslpreproc:972`
Do you have fsl installed? If so I would recommend trying the command:
_ **eddy\_openmp --imain=eddy\_in.nii --mask=eddy\_mask.nii --acqp=eddy\_config.txt --index=eddy\_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --out=dwi\_post\_eddy --verbose** _
That should do exactly the same as eddy\_cpu, but forgoing the mrtrix wrapper.
---
### Author:  [@ejanson6](https://community.mrtrix.org/u/ejanson6)
#### Post date: [December 19, 2023, 10:23am UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/8 "2023-12-19T10:23:14Z")
Dear mschira, thank you for the suggestion. FSL is installed, but the command eddy\_openmp and the ‘normal’ eddy do not work. I still receive the error message about reading images…
dwifslpreproc-tmp-1WCNWH % eddy\_openmp --imain=eddy\_in.nii --mask=eddy\_mask.nii --acqp=eddy\_config.txt --index=eddy\_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --out=dwi\_post\_eddy --verbose
zsh: command not found: eddy\_openmp
dwifslpreproc-tmp-1WCNWH % eddy --imain=eddy\_in.nii --mask=eddy\_mask.nii --acqp=eddy\_config.txt --index=eddy\_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --out=dwi\_post\_eddy --verbose
Reading images
??
---
### Author:  [@mschira](https://community.mrtrix.org/u/mschira)
#### Post date: [December 21, 2023, 12:14am UTC](https://community.mrtrix.org/t/dwifslpreproc-eddy-failed-with-message/7180/9 "2023-12-21T00:14:39Z")
Maybe that is where the problem lies?
I think eddy\_cpu calls essentially eddy\_openmp.
Can you try and locate if the program eddy\_openmp exists on your computer maybe using the search function? What system are you using?
I don’t think troubleshooting your FSL or MRtrix installation is my forte.
I would recommend you to use the Neurodesk app. You can find it at [neurodesk.org](http://neurodesk.org).
We have working modules for MRtrix 3.0.2 and 3.0.3.
I would probably recommend in the neurodesk app you would need to type
> ml mrtrix3/3.0.3
and then do your dwifslpreproc again.
If you are running it on a server you can use neurocommand. Let me know, I can help you.
Best
M.