I have been using the surfacemetrics -closest_node command to derive distance from the cortex to skull.
surface metrics -closest_node dlpfc.1D.txt -i skullsurf_outerskull.ply -sv T1.nii
I am wondering if anybody is aware of a way to view a 3D representation of the two points (i.e. the points on the cortex and skull) on a T1 nifti file in relation to each other.
There are a few ways you might go about doing this. One way is to show spheres in the 3D volume in the afni GUI slice view. There using 3dUndump -srad will create datasets with spheres, but the resolution is limited by the voxel grid. Another way is to create a NIML dataset composed of a set of spheres and edges (connections). Displaying with suma combined with volumes and surfaces produces nice results that show spheres and lines connecting them. You can create that kind of dataset with ConvertDset. You need to provide a list of names and coordinates, and another file with a list of connections by index and edge strengths, e.g. 1 10 2. What might be a surprising example is given as a graph of collaborations. There is a link here:
Review the scripts and files included for how you might want to do what you want.