recon-all -all -s <subjID> -i path/to/nifti 

attatched is the error recon log 

I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.