Bruce
Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below:
mri_surf2vol --hemi lh --template <path to>/orig.mgz --outvol <path to where I want the file>/leftfrontallobe.nii.gz --surfval <path to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07
Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR.
Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc.
Thank you again for your help.
Dan
Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fischl@nmr.mgh.harvard.edu To: doclumsden@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol
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
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