Mrtrix3 copying an empty slspec file into the tmp directory, when specifying -eddyslspec option in the dwifslpreproc command

Hi Experts,

I’m using the latest versions of mrtrix3 and FSL, and have encountered a problem with dwifslpreproc. The error happens to be with the slspec file being copied into the dwifslpreproc’s tmp directory.The resulting file named slspec seems to be empty. When I manually copy paste it into the same and run the eddy command within the tmp directory, it seems to be working fine,running the eddy_cuda. I’m using a WSL version of Ubuntu 20.04LTS.


Hi Experts,

Also, while trying to run it under -eddy_options, received the following error:

dwifslpreproc: [ERROR] Cannot provide eddy slice specification file via -eddy_options “–slspec=…” as manipulations are required; use -eddy_slspec option instead