Dear Chiara,
Maybe you can provide some more information on the templates and exact preprocessing steps. Based on your description it sounds as if you just provide a single image (a T1 template?). However, the Normalise module in SPM12 now corresponds to the (improved) unified segmentation algorithm, which requires tissue probability maps (e.g. GM, WM, CSF).
Thus, if you only have a T1 (or T2) template image, go with SPM \ Tools \ Old Normalise. It might be useful to change the "Affine Regularisation" settings depending on brain/head size of your images relative to that of the template.
If you have tissue probability maps I would go with "Segment", as it allows to specify each of the different TPMs separately and also the no. of TPMs overall (in contrast to "Normalise", which relies on the default maps for 6 different tissue types). Again, "Affine Regularisation" settings might have to be changed.
Hope this helps
Helmut
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