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.
- is the wb_command -volume-to-surface-mapping the best way to go? or better to use bbregister and vol2surf from FreeSurfer?
- 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.
- how to add subcortical areas?
thanks for any pointers or suggestions.