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FSL Experts, I am currently trying to register a T1 MPRAGE to diffusion space (e.g., FA map) to draw ROIs for tractography in Trackvis. I have tried using FLIRT, but continually receive odd results (see attachment). I am using the Affine 12 parameter model option in FLIRT to register my T1 (high resolution image) to my FA map obtained from TBSS preprocessing steps (reference image). Upon reading the FSL listserv and various online resources, it was suggested that I run the three step model or use a white matter mask obtained from segmentation. For the former, It is unclear to me what I should use as my low resolution image. Any help or advice would me greatly appreciated. Thank you in advance for your attention and help! C.Roman