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Hi, Yes - just run BET on the magnitude image and use the BET-generated mask. All the best, Mark On 29 Jun 2007, at 09:17, Renate Schweizer wrote: > Hi, > > I would like to do an unwarping of an Epi measurement. Our > fieldmap aquisition sequence gives us a magnitude image and an > unmasked real field map image. If I then use Prelude and the B0 > unwarping option in Feat, it's the Flirt registration that terribly > fails. So far I accounted that to the unmasked real field map, > which is very "noisy" outside the brain/skull. Is there a way to > create an appropriate mask with FSL? > > regards, > > Renate > > > > Renate Schweizer > > Biomedizinische NMR Forschungs GmbH am > Max-Planck-Institut fuer biophysikalische Chemie > Am Fassberg 11 > 37077 Goettingen > Phone: +49 - 551 - 201 - 1724