Volume to surface after fmriprep and denoising for connectome analysis

Dear all, I’ve been scouring the internet but so far to little avail. After running fmriprep I have denoised (and smoothed using SUSAN) the data in functional space using the great denoiser (https://github.com/arielletambini/denoiser).
Now I want to go from volume to surface to extract timeseries using an atlas already in fsnative space (the Brainnetome atlas) and construct a connectome.
I know that fmriprep also outputs a minimally processed surface representation of the fMRI but as far as I can tell denoiser doesn’t work with these types of files and I actually want to have done thorough denoising before moving on.
I’ve been looking at the connectome workbench for the volume to surface mapping but I’m in need of some guidance.

  1. is the wb_command -volume-to-surface-mapping the best way to go? or better to use bbregister and vol2surf from FreeSurfer?
  2. I read some articles where they said they used this for the volume to surface mapping using *_midthickness.surf.gii and applied the ribbon-constrained option with the white matter and pial surface but what files in fmriprep should you use for this? *_pial.surf.gii and *_smoothwm.surf.gii? I thought the latter wasn’t a surface map of the white matter.
  3. how to add subcortical areas?

thanks for any pointers or suggestions.

bw, Chris