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Dear FSL users, I want to use probtrackX, but first I have to register my structural image to the diffusion space by using the registration after running Bedpost. I wanted to check how the registration went, and used the ApplyXFM GUI to apply the transform matrix on my structural image: Transformation Matrix: str2diff.mat Input Volume: the structural image, and the mask (or the ROI) that I made in the structural image Output SIze: Base on: Existing Volume: I chose here my nodif_brain image as the reference volume Is this the correct way to do it? Escpecially the last part, is it correct to use the nodif_brain image as the reference volume. When I check the results, the registration of the structural image to the diffusion space is ok, but the mask (or the ROI) selected in the structural image, becomes much larger in the diffusion space. Do someone have any idea what might have happened? Where did i do wrong? Hope to get some answers! Best regards, Live Eikenes. --