# Dwifslpreproc unsuccessful after 12h with no error message

**URL:** https://community.mrtrix.org/t/dwifslpreproc-unsuccessful-after-12h-with-no-error-message/8859
**Category:** Uncategorized
**Tags:** preprocessing
**Created:** [October 6, 2026, 1:43pm UTC](https://community.mrtrix.org/t/dwifslpreproc-unsuccessful-after-12h-with-no-error-message/8859 "2026-10-06T13:43:17Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![LM10](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/l/c37758/32.png) [@LM10](https://community.mrtrix.org/u/LM10)
#### Post date: [October 6, 2026, 1:43pm UTC](https://community.mrtrix.org/t/dwifslpreproc-unsuccessful-after-12h-with-no-error-message/8859/1 "2026-10-06T13:43:17Z")

</div>

Hi everyone,

I’m having issues with dwifslpreproc in subjects where I know it should run correctly because I have previously successfully processed them with micapipe which also uses dwifslpreproc. The processing for one subject remains unfinished even after 12 hours, but no error message is shown.

This is a multi-shell dataset with 104 directions in total and 3 shells, I have AP and PA data so 208 volumes in total.

I’m running the following commands using MRtrix 3.0.8 and Rocky Linux 8.10:

```bash
$ mrconvert AP_dwi.nii.gz AP_dwi.mif -fslgrad AP_dwi.bvec AP_dwi.bval
$ dwidenoise AP_dwi.mif AP_dwi_denoised.mif
$ mrdegibbs AP_dwi_denoised.mif AP_dwi_denoised_unr.mif
$ # mrconvert, dwidenoise and mrdegibbs for PA images
$ mrcat AP_dwi_denoised_unr.mif PA_dwi_denoised_unr.mif AP_PA.mif -axis 3
$ dwifslpreproc AP_PA.mif AP_PA_preproc.mif -rpe_all -pe_dir ap -readout_time 0.0708501 -eddy_options " --data_is_shelled --verbose --slm=linear"

```

I tried running this without --data\_is\_shelled and without --slm=linear, both with the same outcome.

The last few lines of the log file when running the last step are:  
`Command: mrconvert dwi.mif -import_pe_table dwi_manual_pe_scheme.txt eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt`  
`Command: eddy_cuda11.0 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --data_is_shelled --verbose --slm=linear --out=dwi_post_eddy --verbose`  
`dwifslpreproc: CUDA version of 'eddy' was not successful; attempting OpenMP version`  
`Command: eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --data_is_shelled --verbose --slm=linear --out=dwi_post_eddy --verbose`

dwifslpreproc runs successfully on the same system on data that doesn’t have two PE directions where I instead used Synb0 and -rpe\_none. Does anyone have an idea what might be going on? Thank you in advance!