afni.nimh.nih.gov

Ah yes, sorry I forgot to mention this, but I've been using FSL's MELODIC ICA toolbox for pre-processing. So after despiking my images the toolbox does the following pre-processing steps for me:

brain extraction->spatial smoothing->high-pass filtering-> registration to the standard MNI 152 template

I am hoping that the registration step would be good enough for aligning my images with the standard template.