afni.nimh.nih.gov

1. Deobliquing will make the data cardinal, and often the data will overlap if the origins are accurate for the acquisition space. Alternatively, you can use -card2oblique to make the data match the obliquity of the other dataset.

2. Alignment is a better choice. The align_epi_anat.py script will take care of obliquity by default, so deobliquing separately is not necessary.