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Dear FSLusers, I have both standard masks obtained from T1 images (1mm isotropic) as well as masks which were drawn on a high-resolution scan for the medial temporal lobe (0.4x0.4mm in coronal plane, 3mm thick slices). The resolution of my DTI data is 2mm isotropic. I would like to extract MD and FA values from these masks and I would appreciate very much if you could give me your opinion on the best way to proceed. -For the T1 masks: 1) Register FA or MD maps to T1 brain extracted volumes (flirt options –interp nearestneighbour and 6DOF) 2) Invert the transformation file (convert_xfm -inverse) 3) Register masks to FA or MD maps (flirt options –interp nearestneighbour, 6DOF and use of the inverted .mat file) 4) Extract values (fslmeants) Does it look like a good way to proceed? I read in some publications that transformation matrices obtained from registrations of FA maps to T1 images could be applied to MD maps. Is this a step I’m forgetting here? - For the T2 high res masks: This might be very obvious but I’m wondering if I should follow the same steps or add a step and register the masks to T1 images first. I also read that the epi_reg function could be recommended. In my case, should I apply the same steps using the epi_reg command instead of FLIRT? I apologize for the basic questions. Thanks in advance for your help! Alix