Unsuccessful Registration fmriprep 23.0.2

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.

Any advice for what do do in this situation?

Functional boldref (in orange) laid on top of T1 (white)

Ses-1 Run 1

Ses-5 Run 5

Hi @zachladwig,

Would you mind giving the 23.2.0alpha a try? It can be pulled under the nipreps/fmriprep:next tag.


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As suggested in the thread you reference:
you can try --bold2t1w-init header and/or --force-no-bbr to see if that improves your registration issue.

@Steven 23.2.0 had the same result

@jsein its strange. it actually used mri_coreg rather than bbreg but still the output was terrible (see above)

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.

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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.