I agree with Pete.
I would point out that dcm2niix_afni exists within the AFNI distribution-- it is dcm2niix, kindly added for distribution to the AFNI distribution by Chris Rorden. Using that, you wouldn't have to install another package/tool. And AFNI's Dimon might also be useful.
What are your procesing goals for hte data? Dealing with obliquity/possibly obliquity can be a hassle. If at all possible, using the afni_proc.py tool to deal with it while you do other processing steps is probably the most recommended option. But this will depend on what you want to do with the data.
--pt
