Hi Dan

try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote:

Dear All

Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the  the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command.

From the terminal window I can see that the commands required are:

surf2vol <surf> <refvol> <outvol> <convention>

I presume that <surf> is the .gii file I'm trying to visualise, and <outvol> is to specify the name of the output volume the command will generate, but what should I be using as the <refvol>? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance.

Dan Lumsden Clinical Research Fellow