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Hi - to use different BET options for the two images, you would need to edit the $FSLDIR/bin/siena script (I suggest you take a local copy) - it's easy to edit the lines in that calling bet, near the beginning. Cheers. On 8 Jul 2010, at 16:13, Michele Placci wrote: > Thank you very much, I have another question. If I have two different images with different centre > of gravity, how can I set the parameters -f -c in SIENA? > > I try this command: > > siena <input1> <input2> -B "-f 0.45 -c 220 249 87" -B "-f 0.40 -c 200 249 87" > > but it doesn't resolve my problem. > > Any suggenstions? > > Thank you. > > > > 2010/7/7 Stamatios Sotiropoulos <[log in to unmask]> > Hi Michelle, > > by default BET assumes that the centre of the brain is in the centre of the field of view. This is not the case if the image have lots of neck, as the centre will be too low. You can initialise the centre of gravity using the -c option in BET. Open the image in fslview and get the coordinates for what you think is approximately the centre of the brain. Then, feed these coordinates to BET, it should give you a better estimate. > > Cheers, > Stam > > > On 7 Jul 2010, at 09:35, Michele Placci wrote: > > > Dear FSL Experts, can you tell me why I get this picture after performing the function BET and pick -o option? > > I mean, why there is part of the neck and mouth in the extraction of the brain? > > > > > > > > Thank you all for any help. > > Michele. > > <Copia di Anonym2.GIF> > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------