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The images probably have differing distortions. If you have no other way of undistorting the images, you could use the config file posted by Jesper for nonlinearly registering a FA to a T1 a while back and use it on both images. You could then apply any warp field to your original datasets and undistort them. You would need to take into account any linear rotations that occurred as a part of the registration process in the gradient files. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Markus Gschwind Sent: Wednesday, March 04, 2009 3:36 AM To: [log in to unmask] Subject: [FSL] Two DTI series from 1 subject form different scanners Hello Experts! I have 2 DTI series from the same subject but one from a Siemes 3T platform, and one from a Philips 3T platform. They used the identical table of gradients but the image dimensions are unfortunately different. I am not satisfied with the output of FLIRTing the one dti_FA to the other (12deg) and neither with FLIRTing each of them to the T1 of the subject (12deg). Is there another way how I could compare those images directly? Does anyone has got an experience whith that problem? Thank you in advance! Markus