Hi Brad,

Thanks for your continued effort on this one!

Regarding sub96591. We backtraced our steps and realized we used a 7 DOF linear EPI to skull-stripped MPRAGE for the images in the paper. However, the 7 vs. 6 DOF is not the full solution. If you look in our preprocessing scripts, you can see that we get the example func image that is used for later registration after skull-stripping the EPI. If you use the skull-stripped EPI in combination with the 7 DOF FLIRT registration the alignment appears to be good. I attached an image comparing 6 DOF to 7 DOF and 7 DOF on the skull-stripped EPI for this subject. The differences in results are pretty clear.

As to why 7 DOF appears to work better, one possibility is that some degree of scaling may have occurred for the EPI on the scanner. As indicated before, we are not sure whether the EPI and MPRAGE for these subjects were collected on the same day.

Regarding the left-right issue we are continuing to look into this issue with the contributors.

Hope this helps,
Thanks!
Maarten