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Hi, On 9 Jul 2007, at 17:20, [log in to unmask] wrote: > Hi, > > I am am running FSL 3.3 and have the following two questions, which > might be silly, but nevertheless I can't answer for myself. > > 1. When defining the input 4D data set during a firdt level > analysis, I get the following warning: > "Warning - have auto-set BET preprocessing option and/or > registration DoF on the basis of image fields; check settings" > > Any idea why this is coming up. Is this warning important? This is probably because you have limited field-of-view in your data, probably in the Z direction. > In the design setup, I have "BET brain extraction" selected, and > "main structural image" for registration is skull-stripped. > > 2. For a different analysis I want to display the 1stlevel results > on the high-res anatomical of the individual subject without > distorting the high-res structural in any way. Under "Registration" > I have selected only "Standard Space" and have supplied the high- > res skull-stripped structural MRI of that subject. Other options > are linear normal search. I obviously want to do rigid-body > registration only, so I select DOF = 6. But for some reason FSL > seems tyo default back onto DOF = 7. What is the difference here? > Would you recommend 6 or 7 DOFs? It probably doesn't matter. You could try both, but either should be ok if your EPI is well calibrated in the same way as the structural. Cheers. > > Thanks a lot! > > Sandy > > > The fish are biting. > Get more visitors on your site using Yahoo! Search Marketing. ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---