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Hi Rolf, This is very helpful, thank you, I will try this and the papers you have suggested! Thanks again! Sasha -- Vicente Grabovetsky, Alejandro (Sasha) Postdoctoral researcher Donders Centre for Cognitive Neuroimaging http://www.doellerlab.com On 24 Jan 2012, at 22:43, Rolf A. Heckemann wrote: > Hi Sasha > > Something that works reasonably well for me is this approach: > > standard_space_roi target ssroi -b > cog=$(fslstats ssroi -C) > bet target bet1 -c $cog -f 0.3 > bet ssroi bet2 -c $cog -f 0.2 > > Whether bet1 or bet2 is the better extraction depends on how well the > pre-extraction works. Occasionally, ssroi will be undersegmented, in > which case bet2 is hopeless. Also, you can get holes in the mask if > you pre-extract > (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;ce7862f8.1201), so > in most cases bet1 will be better, especially if you can tolerate > oversegmentations (reduce -f further if this is the case). > > For alternatives, see the papers by Eskildsen et al., Neuroimage 2011 > (BEaST) and Leung et al., Neuroimage 2011 (Brain MAPS) -- one or the > other may be worth implementing if you have lots of data to process. > > Hope this helps > > Rolf > > > On 24 January 2012 19:40, Alejandro Vicente Grabovetsky > <[log in to unmask]> wrote: >> Hello FSLers, >> >> I'm attempting to brain extract some high-field MP2RAGEs, affected by both >> inhomogeneity (which I can bias correct to some extent), but sometimes other >> artefacts. I know there is an option in BET to include both T1 and T2 >> images, is there something equivalent for MP2RAGE, or some other option >> (besides -R, which does not always work) to make things more robust? >> >> Thank you very much in advance! >> Sasha >> -- >> Vicente Grabovetsky, Alejandro (Sasha) >> Postdoctoral researcher >> Donders Centre for Cognitive Neuroimaging >> http://www.doellerlab.com >> >> >> > > > > -- > Rolf A Heckemann, MD PhD > Médecin chercheur > Fondation Neurodis > CERMEP - Imagerie du Vivant > Hôpital Neurologique Pierre Wertheimer > 59 Boulevard Pinel > 69003 Lyon > France