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Dear Fsl experts, I am trying to make a transformation between aal template and T2 acquisition in native space using my T1.to.T2.mat (obtained with flirt) and using applywarp command. Now, I am not using warp and matrix at the same command (twice! as Wolf and Mark told me), just only the transformation matrix,...but I am having problems with my results: the images seem moved and cutted... Any suggestion would be very appreciated. Best regards, Rosalia.