Why not do 3D scanning on each subject each time? On our scanners, a 3D SPGR at about 1 mm resolution only takes 4-5 minutes. Not much of a time penalty.
Are your 10 2D slices thin or thick? How much brain coverage do they provide? If they provide approximately the same coverage as the 3D volume, just with thicker slices, perhaps something could be worked out.
bob cox