FROM JESPER: Yes,
the skull is only used for the initial, low resolution, iterations. It is useful there as it sometimes "stabilises" things and prevents fnirt from finding some silly local minima while it is still far from the "global" minimum. After the we use a brain mask that basically covers the standard brain and a couple of voxels outside the brain (to make sure we get the edge). That means that for the rest of the iterations the skull can go pretty much anywhere as dictated by the warps on the brain surface and the regularisation function. The reasons for this is i) We don't want to "waste" warp resolution by reconciling warps on the brain surface and the skull and ii) We find that the variability (across scanners and sequences) in signal is greater outside the brain than inside. Probably because physicists don't really care what is going on outside the brain when they optimise sequences/protocols. If you do want to revisit the phrenology field you can easily turn the masking off in the config file. I can also recommend the phrenology museum in Edinburgh. Very fascinating. Jesper On 9/16/13 11:48 AM, "Jesper Andersson" <[email protected]> wrote: >Yes, > >the skull is only used for the initial, low resolution, iterations. It is >useful there as it sometimes "stabilises" things and prevents fnirt from >finding some silly local minima while it is still far from the "global" >minimum. > >After the we use a brain mask that basically covers the standard brain >and a couple of voxels outside the brain (to make sure we get the edge). >That means that for the rest of the iterations the skull can go pretty >much anywhere as dictated by the warps on the brain surface and the >regularisation function. > >The reasons for this is >i) We don't want to "waste" warp resolution by reconciling warps on the >brain surface and the skull and >ii) We find that the variability (across scanners and sequences) in >signal is greater outside the brain than inside. Probably because >physicists don't really care what is going on outside the brain when they >optimise sequences/protocols. > >If you do want to revisit the phrenology field you can easily turn the >masking off in the config file. I can also recommend the phrenology >museum in Edinburgh. Very fascinating. > >Jesper > ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
