I am new to fMRI analysis, so I've been having some problems with which I hope you can help me. My biggest problem seems to have to do with my NIFTI images (or that's what I think might be happening). I have 14 EPI runs of 120 TRs each, and I have 14 .nii files (one for each run). However, SPM5 seems to treat each .nii image as one TR, and not one run. The reason I believe that is that a) I only have one value instead of 120 per run for each of my six estimated movement parameters in the realignment step, b) my design matrix acts as if e.g. a block with an onset at 0 and duration of 2 TRs lasts for more than one .nii file. I am not convinced that the error is necessarily specific to SPM5, but I just don't know how to deal with it. I was hoping that someone could give me good advice.
