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These are separate issues rp*.txt is generated from the realignment process for the functional images. That file contains a line for every image that was realigned, and 6 columns corresponding to the affine parameters. All the parameters in the file have also been applied to the *.mat file associated with each image. The file is simply a listing of the parameters defining the movements of each scan relative to the first one. This information can be used in an analysis by as 6 covariates, in order to model scan-to-scan movement related variance. The normalization parameters in the *_sn.mat file, define how the functionals and the t1 (usually) can be warped to a standardized space. This warping does not change from scan-to-scan and so is not part of the statistical design. However, the goodness or badness of the warping can affect the combining of subjects at the second level of analysis. So you should always realign first and then if you want to, warp/normalize the data. Since the parameters in the realignment are already part of the mat file for each image, the normalization parameters are applied afterwards. You would not normalize first then realign, else you would have to normalize each image separately since they would not be aligned to each other. hope this helps, darren ==============Original message text=============== On Thu, 08 Feb 2007 2:45:58 pm CST Amir Tahmasebi wrote: Dear Experts, I am a bit confused about how rp*.txt is being used after preporcessing in fMRI analysis. If we do normalization, the origin of the EPI data changes based on the deformation applied at this stage, Right? On the other hand, when we realign EPI data and the rp*.txt is generated, every param. in rp*.txt file will be with respect to the center of the original data which is not the same as warped data. Maybe this doesn't make sense but the part that I don't understand is that later how are the warped fMRI data from normalization and the rp*.txt used for the analysis? Are they being combined at some point? Thanks a lot. Regards, Amir ===========End of original message text=========== -------------------------------- Darren R. Gitelman, M.D. Department of Neurology 710 N. Lake Shore Dr. #1122 Chicago, IL 60611 Voice: (312) 908-8614 Fax: (312) 908-5073 --------------------------------