We’re collecting multiecho T1s. We have individual T1 images with different echoes, and the RMS files. 

I’ve run freesurfer using both the RMS files, and the multiple echo files (labelled as 001, 002…).

I get slightly different results in the parcellation outcomes with the two different methods. Why would that be?

What do you recommend for input — the RMS file, or the individual echo files?

Thanks,

massieh