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Hi again, I decided to use FLIRT to register them to each other. Thanks. Hi, thank you for your answer. But I still don't understand how I can co-register the two structural images to each other and then use this aligned (combined) image for further analysis in FEAT? Thanks so much Hi, I would not use SIENA for this, I would just use the functionality in FEAT, which allows you to use the structurals as part of the registration process. Cheers. On 9 Feb 2009, at 22:44, SUBSCRIBE FSL Kim wrote: > Hi everybody, > > I have a very basic question: I am examining test-retest reliability, > so I thought I register two structural images from the same subject > tested on two different days, and then use this aligned structural > image to register the functional runs to. Correct? I ran Sienna, but > can't figure out which output file to use for further analysis in > FEAT. What am I missing? Any ideas and suggestions are greatly > appreciated. > > Thanks > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------