Freesurfer preprocessing -fmriprepr

Dear fmriprep fellows,

I was wondering to which stage arrives fmriprep with Freesurfer “recon-all” and how I could use the outputs from Freesurfer from fmriprep to use them in further analysis with Freesufer.


fMRIPrep runs all of FreeSurfere 6.0.1’s recon-all, with the exception of injecting a brain mask that is calculated by ANTs. The result should be usable in any workflow that assumes a normal FreeSurfer reconstruction.


This includes tables with stats?

Thank you,

I assume you’re talking about segstats and parcstats? Yes, those steps are run.