I will check with the Emory group that I know has been scanning canines. Don't know if they are interested in the extra work to get FreeSurfer output but since they are doing FMRI maybe they would be OK with sharing their AMRI data.
It would be good to ask C. Destrieux on the progress with pig and sheep pipelines as he was at the conference in Nantes last year for this but they weren't quite ready to share their templates at that time. I'd love to know what the status of that work is as I would guess it would be useful for making a canine pipeline to some degree. All great model systems and interesting points came up about the labeling across species.
Cheers,
-Morgan