And here is an example where you can see the mismatch in the back of the brain, especially on the right hemisphere. The third image shows the boldref image on top of the T1 and the pial surface outline. no signal to be found.
The gray/white contrast in your BOLD is extremely low, so boundary-based registration has little to work with. If you can find some other way to register it and update the header, you can use --bold2t1w-init header --force-no-bbr to tell fMRIPrep not to attempt any registration.
I do have single band reference files for each echo which all seem to have at least decent gray/white contrast (much better than what is shown in the registration screen shot i included in the last post).
Does fmriprep use them? From the documentation it looks like it should but then I saw some posts that sbrefs aren’t used for multiecho data?
Thanks for your patience. Yes, I think that is probably best. I looked at the code again, and we are using the sbrefs for the initial bold reference, which is used for head motion correction, but not for the final, which is used for coregistration. This needs fixing in an updated 23.2 series. That is unlikely to happen this month.