# lots of work was done to get to this point ... to re-cap, we've created:
#   PErev_PEreg.nii ... which are the "PE-reversed" and "PE-regular" scans 
#          (1 volume each) glued together
#   topup_params.txt ... which is a text file specifying which one has 
#          which phase encode direcetion

topup --imain=PErev_PEreg.nii --datain=topup_params.txt --config=b02b0.cnf --out=./sample_results/topup_coef

applytopup --imain=run01_wedge.nii --inindex=2 --datain=topup_params.txt --method=jac --topup=./sample_results/topup_coef --out=./sample_results/run01_wedge_topup.nii