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Yes, precisely what I needed to know. Thanks! David On Thu, Apr 18, 2013 at 3:33 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > It is worth pointing out here that we don't recommend this approach to > registration (using an intermediate T2) and I would advise you to just go > from the epi to the T1 to standard. If you turn on fieldmap correction, > FSL currently assumes that the "initial highres" is a wholebrain EPI, and > applies the fieldmap distortion correction to it. At the moment this > behaviour cannot be turned off in the GUI and if you really want to use > both an intermediate T2 image _and_ fieldmaps, then you will have to run it > yourself outside of the GUI. You can always do this and then copy the > resulting registration into the FEAT directory and run "updatefeatreg" to > incorporate these results into the FEAT pipeline. > > I hope this helps. > All the best, > Mark > > > On 18 Apr 2013, at 02:05, David Grayson <[log in to unmask]> wrote: > > > 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 >