Hi,
I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem.
I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects.
Thank you, YP