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Hi, I posted a similar message to this previously but did not get a reply. Hopefully someone out there can help though. I have a few very basic questions that are specific to spm5. I am a little confused by the documentation and options. I have read the manual but still dont understand all the options (as I dont know how to check if they have worked). I'm sure I can get by but I would like to understand completely. Could someone answer the following questions please? I would like to do a two pass realignment on my fMRI data e.g. 1) create a mean 2) realign all images to that mean. In earlier versions of SPM, two separate realignment passes had to be performed to accomplish this. In SPM5 does the user interface options combine realignments (mean image creation and realignment to that mean image) to make this possible by selecting the realignment option (and your images) only once?? If this is the case, do the operations described below do what I want? Initially I select all my raw images (I do not have a mean image). In the user interface options for realignment I have chosen "estimate and reslice" There is an option under "number of passes". The default option is "register to mean". This is what I have done, but I wonder if a mean image has to be present before it can do this (or if it creates a virtual one for the job at hand)?? Later in the interface there is the option (as default) to reslice "all images + mean image". This is also what I have selected. If I select exactly what I have described above and run the model is it: 1) Going to do the 2 pass procedure I would like, by first creating a mean and then realigning to that mean? 2) Do something else? If I need to actually do 2 separate realignment passes (and select two realignment - estimate and reslice options, one at a time), do I 1) initially select all my images, change the number of passes to "register to first" and reslice a "mean image only". 2) input my images again (adding the mean image as the very first image) and select estimate and reslice again, only this time select "register to first" and reslice "images 2...n"? Thanks in advance. Cheers Will