Dear List,
I've been quite frustrated with the BBRegister results when trying to register a partial field of view EPI mean functional image to a T1 scan. I've tried different init arguments (fsl, spm, header) and none really work. I've found that the initial registration is causing the problem, since the T1 and mean EPi are in reasonable alignment, but not perfect. As soon as it passes the initial alignment it's totally off and obviously fails in the BBR step. I have no full head EPI, unfortunately. I have a full head scout which seems to be a T1 image with really poor contrast. If I try to register this to the T1 through BBRegister it works. But if I use it as an intermediate file it still fails. What can I do? How does the intermediate file come into play? Will it get registered to the T1 initially and then the resulting matrix is used further? I also tried to feed the resulting registration matrix as init-reg but that didn't work either.
Is there a way to skip the initial registration?
Can I mask the T1 image with the FoV of the functional scan if they are initially in reasonable alignment? Would that work? Would that mean that I have to re-run ReconAll with the masked T1?
Would love to hear back from someone.
Regards, Glad