incorporate non-linear registration when not using topup correction

[akhanf]

could make use of the same ANTS SyN approach used by fmriprep

[akhanf]

for now, incorporated niftyreg for nlin registration; looks good qualitatively, can validate later using scans with AP-PA (leaving out PA scan)

[akhanf]

Some failures in rigid alignment of T1w to b0 prior to non-linear warping -- need to add a quality check for this registration, and this step in general