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Dear Lukas, You may want to align your first time series manually (and roughly) to the mid-line, prior to realignment, using, for example, the Display option, and apply the rotation to all your images of the respective session. After that, you perform the realignment of the two series, as usual. That should give you the result you want. It actually should also work to create just one single image with the wanted orientation and use that as first image for the time series, but I think, it will be better to roughly align the entire session to the midline and perform a proper realignment afterwards. Best regards, Karsten Fra: Lukas Scheef <[log in to unmask]> Svar til: Lukas Scheef <[log in to unmask]> Dato: 12Mittwoch, 20. März 2013 12:50 Til: <[log in to unmask]> Emne: Re: [SPM] fMRI preprocessing for longitudinal data Dear Ella and Cyril! Thanks a lot for your response. The motivation for motion correction is clear. I like to realign two fMRI sessions to a volume, which lies in the middle of the two series. You may call it half through coregistration. If I follow the path Cyril pointed out (using the standard spm realign batch I end up with a coregistration (or realignment) to the first volume of the first session or the (mean) of the first session. I have attached an pdf to clarify it: Upper row: The images on the left and right symbolize fMRI-session 1 and 2 and are tilted by -0.2 and 0.2 relative to the middle one. The lower row shows the result after the running the realign batch (1 subject, two sessions). Unfortunately, the result was not the intended one. What I like to do is to set up a batch that realign (and coregister) to the middle one (in space) ... not onto the first series or the second series. All the best, Luke(See attached file: IntersessionAlignment.pdf)