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Hi - if I remember correctly, SIENA doesn't register to MNI152 by default (though SIENAX does). So I would just try running it with the -d flag so that you can check all the different stages are working ok. As well as the SIENA manual page, see the SIENA lecture and practical examples in the FSL course stuff. Cheers, Steve. On 10 Jun 2007, at 17:22, Katie Karlsgodt wrote: > Hi, > I was wondering if it is possible to use Siena for monkey brains? > We have > some pre-post treatment images and want to see the difference in > changes > between the treated and non-treated groups (n=4 per group). I > haven't used > this tool before, but can see from the web page that at some point > it seems > to register the brains to MNI-152 space. Is it possible to change the > standard space (to a custom made average brain made out of our > subjects or > of control monkeys, or something?). Also, are there any other > assumptions it > makes that would make it not work for a non-human brain? > > thanks! > Katie > > > > _________________________________________ > Katie Karlsgodt, Ph.D. > Post Doctoral Fellow, Neurogenetics Affinity Group > Dept of Psychology/Cognitive Neuroscience > University of California, Los Angeles > > phone: 310-794-9673 > fax: 310-794-9740 ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---