I am actually using python's Nipype which includes both FSL and AFNI functions, the pre-processing pipeline is:
motion correction using MCFLT-> Despiking -> high-pass filtering -> smoothing. And after the pre-processing I am generating the activation maps.
Aligning and co-registering of my functional images were not something that I intended to do, but if it's a solution to the obliquity issue, then it's something that i would incorporate in my processing pipeline.
While we're on the subject of obliquity, is it absolutely necessary to deoblique my images? Would I be compromising my dataset by not deobliquing them? (I am working on building a classifier to differentiate between 2 classes of patients (resting-state) by using their activation maps)
(I apologise if my queries sound too trivial and thanks for your prompt reply)