Dear FreeSurfer experts,

I am reaching out to kindly ask for some clarification on how to set up mris_pmake to achieve the following:

1. Calculate the distance between pairs of peak vertices on the inflated fsaverage surface using the Dijkstra's algorithm 2. Create fixed-radius ROIs around peak vertices to plot them on the inflated fsaverage surface in Freeview

After reviewing the FreeSurfer mail archive, I understand that mris_pmake should be able to address both tasks. However, I am finding the argument structure a bit challenging to interpret.

For point 1), would the following command be appropriate?

mris_pmake --subj fsaverage --hemi lh --surface inflated --mpmOverlay distance --mpmProg pathFind --mpmArgs vertexStart:{start_vertex},vertexEnd:{end_vertex}

Could you please elaborate on the available options in mris_pmake, particularly in relation to --mpmOverlay and --mpmProg? For example, I have noticed that the total path cost remains unchanged whether I use “distance” or “euclidean” in –mpmOverlay.

As for point 2), could you please provide some guidance on how to set up mris_pmake? Or, more simply, would it be possible to save a number of peak vertices and plot them on the inflated fsaverage surface in Freeview.?

I am using FreeSurfer version 7.1.1.

Thank you in advance for your time, Silvia