Is it possible to specify a target EPI volume to realign to (motion correct to) in fmriprep?

[oesteban]

@12552

My (potentially incorrect) understanding is that fmriprep:

1. aligns each run to some type of mean image,
2. transforms each run to the desired output space (T1w, fsaverage. Or, if using the ‘func’ option, then the output is in the ‘native’ EPI space but not aligned across sessions/runs )

This is correct.

@12552

I have done some quick comparisons between fmriprep (output in T1w) and our existing pipeline and found that fmriprep indeed results in lower signal to noise ratio (estimated as response reliability). Happy to share more details about this as/if required.

I would love to see these results, it could make a good case for us to push towards an EPI norm style of workflow (as you referenced with one of your links).

@12552

We think that maybe the additional inter-run alignments in fmriprep hurts the signal to noise ratio, though we cannot rule out something else.

I would bet against you here

@12552

All and all I’ve found fmriprep really excellent and, aside from the reduced signal to noise ratio, much better than my current processes. It’d be great if this extra alignment option was available.

Thanks for the nice words, looking forward to maxing out the priority of the EPI alignment.

@12552

Cheers and apologies if I missed something obvious.

No need, your feedback is really necessary to make fMRIPrep better. Thank you!