Dear SPMers,

The order of my preprocessing steps are realignment (estimate only), reslice (only to create mean image), coregistration (reference: mean image, source: structural scan), segmentation, normalization and smoothing.

I wish to manually align the structural scan so that the origin is located at the AC. I just don't understand why one should manually align the structural scan to the AC before coregistration (as I've seen recommended): the structural scan will be moved about to fit the reference image during coregistration, which means the origin defined manually by me will not be the at the same place by the time I perform normalization. It makes more sense to me to manually align the structural scan after coregistration but not before. Am I missing something here? Should I actually manually re-align the scan again after coregistration?

Thank you very much in advance,
Angela