What I wound up doing is put the MNI152_T1_2mm and the FSL template in the same directory, and use a 6DOF FLIRT transformation to generate a transformation matrix from SPM-->FSL. The underlying brains/spaces are the same, but the padding on the images is different.... so you can just calculate the matrix automatically and then use the Apply_XFM program to convert whatever images you need from FSL-->SPM (and vice versa if you invert the matrix).
Could anyone tell me why and what coordinate difference between FSL and SPM on both using MNI standard as template. When I use GingerALE to transfer, there are different choices on them.
Best regards,
Emma
-- David A Gutman, M.D. Ph.D. Department of Psychiatry & Behavioral Sciences Emory University School of Medicine