Problem in dwifslpreproc

1

Hi, it’s my first time to use the MRtrix3 in processing the DTI data. When I use dwifslpreproc, error message tells “Could not find any version of FSL eddy command”. In fact, I have installed FSL and eddy_correct could work. Could anyone here help to solve this problem, thanks.

2

First thing to check is if your FSLDIR is set correctly:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup

You can add the appropriate lines (specific to your OS) from the link above into your file that loads your environment variables on startup. For me that’s the .bashrc file in Ubuntu 18.04.

Then reload your shell. Or “source” the file.

You can verify that this works by typing “echo $FSLDIR” and you see the path to your FSL install displayed.

3

Hi @maomaojin369,

“eddy_correct” is a much older FSL command and is not utilised in the dwifslpreproc script. In addition to verifying your FSL installation, you should check which version you have installed: for a little while the eddy command was only provided as a separate standalone executable, whereas with FSL version 6 it is included in the main installation.

Rob

4

Hi, thanks for your reply. I have found that old FSL version 5.0.9 without eddy tool is the origin of the problem. A patch named eddy_openmp can help to solve this or update the FSL version. Thanks so much again for you.

5

Hi rsmith,

Thanks so much for your kind reply. I have downloaded a patch named eddy_openmp to add it into the FSL path. And then dwifslpreproc can work. As you mentioned, FSL have updated its version 5.0.10 with eddy tool. However, when we use web link to install FSL, version 5.0.9 but not new version 6.0.4 will just be automatically installed. Thanks again for your times.