Dear Martin,
Considering Christian's idea, maybe you can scan an additional subject (be it healthy or patient) for whom you acquire two anatomies, reflecting the two sequences? Then you could compare normalisation results based on sequence 1, sequence 2 and sequence 2 resliced to resolution of sequence 1.
In general you won't be able to completely rule out a bias, but you could still stick with normalising the EPI means onto an EPI template (with the old routine) or segmenting the EPI means in case the reviewers are not satisfied.
Best regards,
Helmut
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