It will register whichever direction you pick dset2to1 or the dset1to2 (the default). With 1to2, you don't get motion correction. If DSC is the dset2, then you choose the dset2_base/epi_base as the alignment and registration sub-brick.
You can also align to the T1 dataset directly, but you would likely need another cost function. Since this method worked for your dataset with the dset1/2 options used, then the default cost function there is lpa+ZZ. You can use lpc or lpc+ZZ then to align to T1.
Alternatively, once transformations are computed between pairs of datasets, then you can concatenate transformations together, inverting the ones that are going in the opposite direction.
