3T Diffusion Preprocessing Re-run with fewer hard-coded eddy options

The previous version (v3.18.0) had a number of hard-coded options supplied to the eddy binary. In order not to force all uses of these scripts to use all of those hard-coded options, some of them were removed from the run_eddy.sh script and left to be passed in via multiple uses of the --extra-eddy-arg= parameter.