Hello,

I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren’t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is volume-based or surface-based and when it’s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths.

Thanks, Alissa