change volume ROI to surface dset

AFNI Message Board
1

Hi, I’m trying to change my ROI volume data to surface dset. Is it correct to use 3dVol2Surf in this case? If so, should I put my volume ROI file as input for -grid_parent or -map_func (or -mask?)?

Eventually what I would like to do is to visualize only the boundaries (contours) of the ROIs on the surface…

2

Hi-

Yes, to project data from a volume onto a surface, you can use 3dVol2Surf.

How did you create your surface? Did you use FreeSurfer’s recon-all and then convert all the output to NIFTI+GIFTI dsets (where standard meshes are created, which are quite useful) with AFNI’s @SUMA_Make_Spec_FS?

If you did use those couple of commands, then an example if your ROI is in the right hemisphere (rh) might be:


3dVol2Surf                          \
    -spec std.141.${subj}_rh.spec   \
    -surf_A  std.141.rh.smoothwm.gii \
    -map_func mask                   \
    -sv          DSET_ROI \
    -grid_parent DSET_ROI \
    -out_niml     std.141.rh.ROI_NAME.niml.dset

To view in suma, open your surfaces in SUMA:


suma -onestate -spec std.141.${subj}_both.spec -sv ${subj}_SurfVol.nii

… then open the Surface Controller, select “Load Dset”, (might have to change the list of dsets shown to have rh in it), and then view your dset. Is that reasonable?

NB: This video shows some of the visualization options for loading+viewing a dset:
https://www.youtube.com/watch?v=k4T9nLDSOp0&list=PL_CD549H9kgqSs51SCNZQ4q57IguXvFI8&index=5
(as well as drawing one, and other things with the SUMA GUI).

A lot of optionality with the mapping process dependes on:

  • does your ROI intersect clearly with the surface, or just bound on it?
  • are you aiming to project the ROI from being between two surfaces (like the GM-WM border and the pial), or just using one?

But the above is a starting point for mapping an ROI.

–pt