Hi, My bbregistration finished with the warnning" --------------------------------------------------------------------------------------------- WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 --------------------------------------------------------------------------------------------

and does not create subj_RS_register.dat file... I thought, it is only warning so it should create the files. Here is the command, I run to do bbregistration, where ${sub} is substituted by subject number: -------------------------------------- bbregister --s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg ${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o ${sub}.RS.template.mgz -------------------------------------------------------------------------

Thanks Priyank