fMRIPrep poor registration between functionals and anatomical

registration
multi-echo
fmriprep
#1

Hi NeuroStars,

We’re running fMRIPrep v1.4.1 on multiband, multiecho data and are running into poor registration issues between the functionals and anatomical for several subjects. We’re trying to troubleshoot this (test case is a subject with enlarged ventricles) and have a couple of questions:

  1. Which image is used for registration to the T1? Is it a temporary image?
  2. Is it possible to register the images manually, and then continue with the pipeline?

Thank you!
ali

#2

@oesteban could you please advise on how to proceed for datasets showing poor registration between functionals and anatomicals?