Preprocessing error

1

Hi!

I am trying to preprocess diffusion data using MRtrix3 following Andy’s tutorial. I am getting this error when I try to do topup eddy correction using command:
dwifslpreproc Par-8_den.mif Par-8_den_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled"

Error:
mrconvert se_epi_pad2.mif topup_in.nii -import_pe_table se_epi_manual_pe_scheme.txt -strides -1,+2,+3,+4 -export_pe_topup topup_datain.txt

mrconvert: [ERROR] unknown option “-import_pe_table”

can anyone guide me in resolving it. thanks!

2

I get the same error. dwifslpreproc probably still uses the old tag ‘-import_pe_table’ for mrconvert, which is renamed to ‘-import_pe_topup’ in the latest mrtrix version. Will raise the issue on github.

3

Thank you! till then any workaround?

4

Hi @namrauf,

This can be easily fixed by running topup and Eddy through FSL - then pipe it back to MRtrix.

I hope this helps,

John

5

Can it be Andy’s tutorial is based on an old MRtrix version, and you are using a newer one, which expects ‘-import_pe_topup’ ?

6

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 found that it’s issue with Conda installation (missing shared libraries when installed from conda / mamba · Issue #1696 · ANTsX/ANTs · GitHub). Any info how can I run -ants option in dwibiascorrect in conda?

7

I also encountered this error this morning after updating MRtrix to v3.0.7

After some investigation, I did find a way to get dwifslpreproc to execute with some alterations to bin/dwifslpreproc.ccp. I’ll listed I changes I made here, in case someone finds them useful. The outputs look good, but I’m not very familiar with the MRtrix code base, so I won’t make any bold claims about their correctness in case I’ve missed something

The changes

  • Line 512 : import_dwi_pe_table_option = ’ -import_pe_topup dwi_manual_pe_scheme.txt’
  • Line 828 : run.command('mrconvert ’ + dwi_path + import_dwi_pe_table_option + STRIDES_OPTION_FSL_COMPAT_4D + ’ dwi.nii ’
  • Line 829 : ‘-export_pe_eddy applytopup_config.txt applytopup_indices.txt’)

Some notes - the change to line 512 addresses ‘mrconvert: [ERROR] unknown option “-import_pe_table”’. The MRtrix reference guide for mrconvert states that import_pe_topup ‘imports a phase-encoding table intended for FSL TOPUP from file’, and the reference for mrinfo states that ‘If extracting phase encoding information to interface with FSL tools, use the -export_pe_topup or -export_pe_eddy options.’, so this seems to be the intended replacement for import_pe_table

The changes to lines 828 and 829 fixes a subsequent error that arose with mrinfo (‘mrinfo: [ERROR] Only export phase encoding table to FSL eddy format in conjunction with MGH / NIfTI format images’). Converting dwi.mif to .nii and feeding it into mrinfo did not work, as the phase encoding data was not preserved. So I dropped the use of mrinfo entirely, and had mrconvert export the phase encoding directly when it did the .nii conversion

Hope this helps

8

Hi all, note that this issue is address in PR Fix phase encoding handling on 3.0.7 by Lestropie · Pull Request #3146 · MRtrix3/mrtrix3 · GitHub which will almost certainly make it to the next bug-fix version. If you want to use it before it is released, you can build it yourself, e.g. using:

git clone https://github.com/MRtrix3/mrtrix3.git -b fix_pehandling_307 mrtrix3_fixpe
cd mrtrix3_fixpe
python3 ./configure
python3 ./build
9

I appreciate your help but the git clone is not working.

git clone https://github.com/MRtrix3/mrtrix3.git -b fix_pehandling_307 mrtrix3_fixpe

Cloning into ‘mrtrix3_fixpe’… fatal: Remote branch fix_pehandling_307 not found in upstream origin