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Dear FSL experts, I am trying to use the feat command to apply the following registration procedure: epi --> initial T2 structural (dof 6) initial T2 structural --> main T1 structural (dof 6) main T1 structural --> standard atlas (dof 12) fieldmap unwarping is on. I have made these settings in the design.fsf file. However, when I go through the log files where it calls the 'mainfeatreg' command, I see that it has overwritten the dof to 'BBR' for the initial T2 structural --> highres T1 stage. Here is the command as it is called (notice that there are 2 -w options, the first is what I set, the one at the end is apparently what overwrites): /usr/share/fsl/5.0/bin/mainfeatreg -d /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_44 6_func_1_.feat -l /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_446_func_1_.feat/logs/ feat5_reg -R /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_446_func_1_.feat/report_unw arp.html -r /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_446_func_1_.feat/report_reg. html -i /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_446_func_1_.feat/example_func.n ii.gz -n 10 -j /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/T2_late2epi_brain -u 6 -v 90 -h /home/david/Projects/Amyg_Monkeys/Analyses/unknown/processed_data/d_446/d_446_MPRAGE_fslreorient_strip -w 6 -x 90 -s /home/david/Projects/Primate_Atlases/inia19/inia19_t1_brain -y 12 -z 180 -a /home/david/Projects/Amyg_Mo nkeys/Analyses/unknown/processed_data/d_446/uphase_rad -b /home/david/Projects/Amyg_Monkeys/Analyses/unknown/proce ssed_data/d_446/d_446_MAG_fslreorient_strip -e 22 -f 10 -g 0.94 -p y- -w BBR This leads to the fieldmap unwarping being applied to the T2 image, in addition to unwarping being applied to the example_func image, which is clearly not what I want. Is this a bug or what can I do about this? P.S. I am using a design file optimized for use with a previous version of fsl, before bbr was incorporated. In case that matters... Thanks very much for reading, David