Dwifslpreproc fails with "unknown option -import_pe_table" (MRtrix3 3.0.7)

[raz27289]

Hello,

I am running into an error with dwifslpreproc when preprocessing DWI data on macOS.

• System: macOS
• MRtrix version: 3.0.7 (mrconvert -version confirms)
• FSL: installed and available in $PATH
• Python: the wrapper script /usr/local/bin/dwifslpreproc uses Python3

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A script executes dwifslpreproc which calls. mrconvert like this:

mrconvert se_epi.mif topup_in.nii \
    -import_pe_table se_epi_manual_pe_scheme.txt \
    -strides -1,+2,+3,+4 \
    -export_pe_topup topup_datain.txt

---

The error

mrconvert: [ERROR] unknown option "-import_pe_table"
dwifslpreproc: [ERROR] mrconvert se_epi.mif topup_in.nii -import_pe_table ...

After this, the pipeline fails with a cascade of “No image files match …” errors, because the expected preproc files are never created.

---

What I checked

• Running mrconvert -help shows that the available options are:
  • -import_pe_topup
  • -import_pe_eddy
  • -export_pe_topup
  • -export_pe_eddy
    There is no -import_pe_table in my version.
• Grepping inside /usr/local/bin/dwifslpreproc shows it is hard-coded to call mrconvert with -import_pe_table.

---

My questions

1. Is this a known mismatch between my dwifslpreproc script and MRtrix 3.0.7?
2. Is there an updated version of the script I should install?
3. Alternatively, is the recommended workflow now to bypass this step?

[namrauf]

Check this:

Preprocessing error

ya, it’s based on an older MRtrix version. like HannesAlmgren said, it is probably due to the renaming of certain commands. I switched to older version of python and the dwifslpreproc runs now. Afterwards when I try to generate a mask, the -ants option gives this error: antsRegistration: error while loading shared libraries: libITKIOBruker-5.3.so.1: cannot open shared object file: No such file or directory I tried to run it with fsl, and it works. But it’s not recommended to use fsl option. I…

[rsmith]

Hi Raj

This is a bug introduced into 3.0.7 by yours truly in #3128.
I was trying to resolve a fundamental ambiguity by removing one command-line option and replacing it with another, but neglected to recall that I was still myself making use of the original command-line option in dwifslpreproc. A little out of practise with releases unfortunately.
The relevant fix is #3146; note in particular requisite additions to documentation.
I will tag and release 3.0.8 as soon as I have code reviews for merging additional fixes to the master branch.

You should be able to execute with 3.0.7 by ensuring that the phase encoding information is embedded in the input image headers and using the -rpe_header option.

Regards
Rob

[johnfoley23]

Hi Robert,

I recently downloaded MRTrix3 to a new computer and ran into this issue when using dwifslpreproc. You mention releasing 3.0.8 soon, and I see that the fix has been merged to the master branch in Github, but when I download via the installer it isn’t pulling the fixed version.

I have had this issue before and solved it through cloning and building from Github; however, this isn’t an option I can use for this new computer.

So, my question is, when will the latest master branch of the software be available through the installer?

Many thanks,

John