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
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