Midthickness for fsaverage

Hi, there,

I put all my BOLD signals onto the fsaverage surface by fmriprep and try to do analysis on surface. I saw the midthickness surface/geometry file (fsnative space) in each subject’s anat folder and freesurfer/surf folder. However, I didn’t find any midthickness geometry file for fsaverage. Could anyone help me with that? Or is there a way to generate the midthickness file for fsavearge, which fmriprep put my BOLD on?


Some short answers:

  1. When you have data sampled to the cortical surfaces, which specific surface that you place the data on does not affect the data. white, pial, midthickness, or inflated can be chosen only on what is most useful to view.
  2. The “correct” way to generate a midthickness file is something like mris_expand -thickness lh.white 0.5 graymid. In a surf/ directory, this will create a lh.graymid file.
  3. The cheap way to generate a midthickness file is to average the coordinates from white and pial.

There seems to be some confusion, though, so here are some longer ramblings:

fMRIPrep samples from 5 points evenly space between the white and pial surfaces, not just the halfway point. The coordinates are used during resampling, but once sampled to the surface, the data is abstracted from the volume it was sampled from. It is just a series of values at each vertex.

If you want to smooth your data, then you do need to know the relative distances between vertices, or at least your algorithm does. To smooth on the midthickness surface, it’s easier to use mri_surf2surf with a projfrac 0.5 than to coax FreeSurfer into using a custom-generated surface. See SurfaceSmooth.

Similarly, if you want to sample your surface to the volume, you’ll probably want to play with --proj-frac or --fill-ribbon or similar, which will be features of mri_surf2vol. I can’t think of a good reason for doing this, though.

Otherwise, again, it’s just a choice of surfaces to plot on. Fine to use midthickness for it, but I just want to make sure you’re clear that there’s nothing in the way the data that was processed that makes it more suitable than the other surfaces.

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Thank you very much for your clarification. I just started to do surface-based analysis. That is very helpful!