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