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Thankyou for the quick reply. tbss_2_reg has this output for me (Below). It seems to end very quickly without error but obviously without completing properly. Any idea of what might be happening? I have tried -t and -T options with the FMRIB58 template. Thank you, -James output: # tbss_2_reg -t /root/Desktop/tbss/FAi/FMRIB58_FA_1mm_FAi.hdr FMRIB58_FA_1mm_FAi_to_target PCON_s100fa_FAi_to_target PCON_s101fa_FAi_to_target PCON_s102fa_FAi_to_target PCON_s103fa_FAi_to_target PCON_s105fa_FAi_to_target PCON_s106fa_FAi_to_target PCON_s107fa_FAi_to_target PCON_s108fa_FAi_to_target PCON_s109fa_FAi_to_target PCON_s110fa_FAi_to_target PCON_s111fa_FAi_to_target PCON_s112fa_FAi_to_target PCON_s113fa_FAi_to_target PCON_s114fa_FAi_to_target PCON_s115fa_FAi_to_target PEXP_s101fa_FAi_to_target PEXP_s102fa_FAi_to_target PEXP_s103fa_FAi_to_target PEXP_s104fa_FAi_to_target PEXP_s106fa_FAi_to_target PEXP_s107fa_FAi_to_target PEXP_s108fa_FAi_to_target PEXP_s109fa_FAi_to_target PEXP_s111fa_FAi_to_target PEXP_s112fa_FAi_to_target PEXP_s114fa_FAi_to_target PEXP_s115fa_FAi_to_target 20503 [root@Nineset-PC tbss]#