Sure, 3drefit can be used to reverse the order. I hadn't understood this might be a potential flipping problem. The orientation can be flipped by switching the side of the minimum direction. For example, if the orientation is currently stored as RAI, but the data is really stored "left to right", then "3drefit -orient LAI" would change the orientation. You can do this when you read the data into AFNI too if the defaults don't work. Dimon includes -rev_org_dir and -rev_sort_dir options. to3d has the "-reverse_list" option to reverse slice entries. Another way is to actually flip the voxels with 3dLRflip. If the data doesn't have a flipping problem, then 3dresample or cropped similarly with 3dZeropad -master.