fMRIPrep poor registration between functionals and anatomical


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!


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