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Hi On 16 Jul 2012, at 14:35, N. Doorenweerd wrote: > Hello FSL-experts, > > While working with SIENAX on a cross-sectional study I ran into the following: > > If I understand correctly, SIENAX uses the exterior skull surface as a scaling constraint in the registration by determining the boundary between the low skull intensity and bright scalp. > My first question is what happens if in between these two, abnormally large temporal muscles are present. Will it still be able to reliably determine the outline of the outer skull or is there a chance that the muscle will be included? The rough estimate of the outer skull boundary is only used to set the scaling - so only needs to estimate this one thing globally. Hence hopefully issues such as you raise shouldn't bias this - hopefully. > My second question relates more to the normalization to skull size, with respect to atrophy estimates. I understand that there is a close relationship between normal skull and brain growth, making the skull size a reliable marker, but what if there is a diseased state disrupting normal skull growth? Or, indeed, a study that looks at childhood development - yes in such cases you can't rely on the skull - in which case an alternative is necessary, for example relying on the scanner calibration being exactly correct, and/or using phantoms. Cheers. > How does one dissect for example different skull thickness (low intensity) from more CSF (also low intensity)? > > > I appreciate any and all advice in this matter. > > Nathalie --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------