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Hi FSL experts, Im' running FSL-VBM analyses. By following the instructions, I was able to run the first step successfully using fslvbm_1_bet -N. Everything seems right utill I check the "template_GM_4D" image after the 'fslvbm_2_template -n' script using fslview. About half of the brains get wrong orientations. The "_struc_GM_to_T" images of each subject get right orientations. And "_struc_GM_to_T_init" get wrong orientations, same as the corresponding image in "template_GM_4D". I notice that this problem has been posted on the mailing list, as you can see here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=FSL&F=&S=&P=194531. But it was not solved or at least the solution was not posted. Can anyone give some help ? Thanks in advance. Wen Miao -- State Key Laboratory of Intelligent Control and Management of Complex Systems Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190, P.R.CHINA ----- http://nica.ia.ac.cn/?q=wenmiao