# \`omitted axis "4"\` Error in dwipreproc of Siemens Vida (XA11A) data

**URL:** <https://community.mrtrix.org/t/omitted-axis-4-error-in-dwipreproc-of-siemens-vida-xa11a-data/2019>\
**Category:** Uncategorized\
**Tags:** error, preprocessing\
**Created:** [October 31, 2018, 4:25pm UTC](https://community.mrtrix.org/t/omitted-axis-4-error-in-dwipreproc-of-siemens-vida-xa11a-data/2019 "2018-10-31T16:25:04Z")\
**Posts on this page:** 1\
**Showing post:** 8

<div class="post-metadata">

**Author:** ![Ingomar\_Gutmann](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/i/e36b37/32.png) [@Ingomar\_Gutmann](https://community.mrtrix.org/u/Ingomar_Gutmann)\
**Post date:** [February 20, 2019, 6:31pm UTC](https://community.mrtrix.org/t/omitted-axis-4-error-in-dwipreproc-of-siemens-vida-xa11a-data/2019/8 "2019-02-20T18:31:04Z")

</div>

Dear mrtrix community,

Sorry for answering so late - another topic and the clinical use test of a major new software at my university grabbed my attention completely. My sincere apologies.

Coming back to your answers I want to ask you for the correct syntax and inputs for the `continue` option. The last file I generate with the

```auto
dwipreproc -force -pe_dir AP APPA_denoised_unrung.mif APPA_denoised_unrung_preprocessed.mif -rpe_all -se_epi b0_AP_PA.mif -eddy_options "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --slspec=slspec_AP.txt"

```

command is `field_deriv_pe_1.mif` as invoked by

```auto
[...]
dwipreproc: Detected matching DWI volumes with opposing phase encoding; performing explicit volume recombination
Command: mrcalc field_map.nii.gz 0.0681 -mult -1.0 -mult - | mrfilter - gradient - | mrconvert - field_deriv_pe_1.mif -coord 3 1 -axes 0,1,2
dwipreproc: 
dwipreproc: [ERROR] Command failed: mrcalc field_map.nii.gz 0.0681 -mult -1.0 -mult - | mrfilter - gradient - | mrconvert - field_deriv_pe_1.mif -coord 3 1 -axes 0,1,2 (dwipreproc:996)
dwipreproc: Output of failed command:
            mrconvert: [ERROR] omitted axis "4" has dimension greater than 1

```

I then followed the suggestion given by @jdtournier and extracted the first volume of `field_map.nii.gz` as described by him.

However

```auto
dwipreproc -force -pe_dir AP APPA_denoised_unrung.mif APPA_denoised_unrung_preprocessed.mif -rpe_all -se_epi b0_AP_PA.mif -eddy_options "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --slspec=slspec_AP.txt" -continue dwipreproc-tmp-1YXW7U field_deriv_pe_1.mif

```

and

```auto
dwipreproc -force -pe_dir AP APPA_denoised_unrung.mif APPA_denoised_unrung_preprocessed.mif -rpe_all -se_epi b0_AP_PA.mif -eddy_options "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --slspec=slspec_AP.txt" -continue "dwipreproc-tmp-1YXW7U" "field_deriv_pe_1.mif

```

and

```auto
dwipreproc -force -pe_dir AP APPA_denoised_unrung.mif APPA_denoised_unrung_preprocessed.mif -rpe_all -se_epi b0_AP_PA.mif -eddy_options "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --repol --ol_type=both --mporder=8 --s2v_niter=8 --slspec=slspec_AP.txt" -continue "dwipreproc-tmp-1YXW7U" "dwi_post_eddy.nii.gz"

```

all produce the same error message:

```auto
mrinfo: [ERROR] failed to open key/value file "dwi.mif": No such file or directory
mrinfo: [ERROR] error opening image "dwi.mif"
dwipreproc: [ERROR] Could not access header information for image 'dwi.mif'

```

I am very grateful for your assistance 🙂

On a the good side I can give you the feedback that if your workflow is ok with the Siemens Magnetom Vida XA11A _enhanced_ DICOMs it will be so too with XA11B.  
The important point is to _always_ have selected _ **enhanced** _ _ **DICOM** _ (in the total chain of storage, i.e. if you are getting them directly from the scanner as well as if you push it via the PACS before exporting)

---

_[View the full topic](https://community.mrtrix.org/t/omitted-axis-4-error-in-dwipreproc-of-siemens-vida-xa11a-data/2019)._