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I think empiricism would be the way to find out what works best for your data. I'd guess that if you can achieve a nice segmentation of the EPI, then you are probably better off estimating the alignment based on these data. What works best is likely to depend quite a lot on whether your EPI are spatially distorted. If the are distorted, then (rigid-body) aligning them with a structural scan is unlikely to work well. Best regards, -John On 16 September 2015 at 13:09, Clas Linnman <[log in to unmask]> wrote: > Hi, > > I am working on a 7T dataset where the functional data (1x1x1mm) is > crisp enough to be segmented, especially the realigned mean functional. The > EPI and structural segmentations look slightly different, so my question is > which one to use as input for creating a Dartel template? My thinking is > that by using the EPI, I can avoid coregistration errors. Or should I use > the structural (even crisper), or a combination of the two? > > with my best regards > Clas >