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Hi, I'm trying to help based on my knowledge to SPM. On Sun, Nov 22, 2009 at 11:25 PM, Avia Abramovitz <[log in to unmask]>wrote: > Dear SPM users, > > I'm a new user and have some beginner's questions... > I'm trying to understand what is the right way to use the realignment > stage: > So far I understoodd that this stage should realign my scans to the first > scan or the mean one. the scans are within-subject in time difference, > right? > Yes, it is within subject. > Lets say I have a a sequence of 56 T2 scans- > If I want to realign them is it correct to upload all of them and than the > SPM will realign each scan to the first one or the mean one depending on my > choice. > If all the 56 scans (volumes) are for one subject, then, yes. > If so, what sense does it make? the different scans obviously doesn't show > the same slice height, and the brain shape in scan 1 is very different from > scan 56, so I don't understand how does the realignment make sense. > This is to compensate the headmovement of one subject during the scan period. For example, you can't guarantee that your subject doesn't move his head a little during the scan time, right? And , I'm not sure what you mean by ' the different scans obviously doesn't show the same slice height'... Do you mix up the concept of "slice" and "scan"? > If not- what should I basically do? should I upload scans of the same > subject > of the same slice only in different times. > > This might sound confused, so If someone can explain me what exactly is > realigned to what, I will be greatly thankful... > > Avia > -- Regards, Jidan