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Dear Stephen, [log in to unmask] said: > I want to enter the realignment parameters as nuisance variables in > SPM99b, inorder to account for movement effects. I have a text file > from the realignment process with six columns of numbers. Are these in > left to right order x,y,z,pitch, roll, yaw and if so what units are > being used for these figures? Yes, that's right; translations in mm in x, y, and z, followed by rotations in radians around the x y and z axes (pitch, roll and yaw). [log in to unmask] said: > If these figures are the realignment parameters, I was also wondering > why the first figure in each column is zero, since I understood that > all of the scans, including the first were realigned to a mean image. Yes, that's right again (for PET), but the figures are in terms of parameters needed to realign to the first scan, calculated after they have all been realigned to the mean. See you, Matthew