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Thanks Darren for your reply. As you mentioned that rp*.txt info is already included in the .mat files, would it be the case if I choose "coregister and reslice" and then "All image (1..n)"? If I choose "mean image only", would it include rp* in .mat files as well? Thanks. Amir [log in to unmask] wrote: > 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 > -------------------------------- > > > > -- ________________________________ Amir M. Tahmasebi Ph.D. Student, Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 ________________________________ Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb