Hi, I previously had an issue with one of our data sets which I ended up chalking up to poor white/gray matter contrast in our multi-echo dataset and fmriprep not successfully using the sbref for registration.
Here, I am using a different (single echo) dataset. And for some subjects I am getting terrible anatomical/functional registration. Here are a few examples. It seems to vary quite a bit by run and session. Here there is no sbref with better wm/gm contrast that I can use. I’m not sure what to do.
but, if I take the preprocessed intermediate file (after hmc) and then I do mri_coreg manually, it looks great. This should be the exact same thing right? I guess I am not sure what extra parameters they use on mri_coreg, i picked the most basic. I guess one solution is for me to manually register all of these from that intermediate step, but it seems like what you’re saying should have worked.
also @jsein I had played around with bold2t12-init header but I never felt like I understood exactly what it was doing. What exactly does that do?
Registration is a two-step: a bulk affine registration (mri_coreg) and a boundary-based registration refinement (bbregister). --bold2t1w-init header says to skip mri_coreg. --force-no-bbr says to skip bbregister. If you do both, fMRIPrep will not attempt to perform any coregistration.
I re-ran it with force-no-bbr and the registration looks solid now for all of the runs/sessions! Even true for the runs which already didn’t use bbr (so used mri_coreg) in my last run and looked bad then. I don’t know why that is!
But maybe it will make sense for us to do force-no-bbr when we suspect our gray/white contrast is not good.