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

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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

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?
2

Check this: