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On Mon, 24 Jan 2005 16:05:08 +0100, Chiara Begliomini <[log in to unmask]> wrote: >Dear SPM experts, > > > >I am pretty new in the fMRI world and I am trying to analize some fMRI data coming from a grasping experiment (event-related design, with variable SOA). Subjects are requested to grasp real objects while being scanned, thus they really have to move their right arm and grasp objects presented in front of them. > >We usually observe a lot of head motion (more than 6 mm translation, and 2°-3° degrees rotation) but we also noticed that movement occurs mostly between runs, during the break between a run and the following one. During the run, so when subjects are performing the grasping task, motion is usually not worse than 1.5 mm for translation and 1° degree rotation. How could I deal with such a problem? Am I methodologically allowed to perform the realign for each run separately (like if I were performing the realign for different subjects) and then do the following steps (coregistration, normalisation and smoothing) as usual, considering data coming from the realignment step as coming from only one subject (like they really are)? If not, which is the best procedure to try to exclude head movement as much as possible from data? FWIW my feeling is that motion between runs isn't as important as motion within a run, *IF* subtractions are not primarily "between runs." (Of course, really large movement even between runs could be a problem, but 6 mm might be OK.) For example, if events A and B occur in all runs in a relatively balanced manner, and you're subtracting B from A, then you can think of this as averaging the results of doing a separate subtraction in each run. If A were mostly in run1 and B were mostly in run2 (which is somewhat problematic and unusual for fMRI anyway), then taking A - B "subtracts" the runs and inter-run motion becomes a more important consideration. Assuming what I just said is reasonable, then in terms of realignment, if the inter-run motion isn't too outlandish (6mm doesn't sound ridiculous, though you should visually check quality after the realignment is done), then it's probably OK to just realign all the runs together the usual way. That's because SPM essentially first aligns the volumes of each run separately, then aligns the first volumes of runs 2, 3, ... with the first volume of the first run, and pulls the other volumes along with those. HTH, S > >I thank you in advance for your help, > > > >Chiara >