@oesteban Feel free to split this off to a separate issue but I do have a question related to this. You and I have discussed this at length in terms of re-using pre-run FS, particularly for longitudinal analyses.
What is the difference between what fMRIPrep is doing to average the T1s and running FS vs. the subject-specific template step of running longitudinal FS? The values appear to be slightly different but could the same approach for re-using fMRIPrep’s FS (here: FMRIPREP confounds error (copied columns for multiple subjects)) be applied to the subject-specific templates?