You can find the job scripts and instructions for running the following pipelines at the links below:
DWI pre-processing with FreeSurfer T1 processing.
DWI pre-processing with FastSurfer T1 processing /wiki/spaces/FN/pages/2557411524
/wiki/spaces/FN/pages/2558722126 (requires slightly more set up but will work better in most cases).
DWI pre-processing with FastSurfer + Connectomics.Just FastSurfer for T1 processing.
** I need to add synb0 ref files set up + edit ref_path into these instructions. **