why do you want to create a volume? You can run mris_fill to fill the interior of the pial surface, but you will lose orientation info and resolution. Why not just use the pial surface model itself for dipole analysis?

On Tue, 18 Mar 2008, Cochrane Jamison wrote:

Hello. I am still very new to freesurfer. I have finished running a complete recon all process on one mri. I used a very good scan, which produced great results from freesurfer. However, I am having trouble producing some usable output. I want to create a volume from the finished pial surface so that I can load it into another program for dipole analysis. I have read through the archives and come across the command mri_surf2vol that seems to be able to do what I am trying to do. I am having problems with is though. Here is where I started:

MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial

gdiagno = -1

A surface value path must be supplied

In another post, I saw where the user had used the lh.thickness for the surface values, so I tried the same and got this:

MEG-PC:~/freesurfer/subjects/C0668_Duck/mri> mri_surf2vol --hemi lh --surfval ../surf/lh.thickness --template ../orig/001.mgz --outvol left_filled_pial.img --fillribbon --surf pial

gdiagno = -1

A volume registration file must be supplied

I have read the help file about tksurfer2 and creating a volume registration file, but I cannot exactly figure out what all I need for inputs, and what kind of output I want exactly. I know this may not be as much detail as you need, so please let me know if you have any questions. Thank you for the help.

William