Hello Dr. Fischl,

I had question about Freesurfer, I am trying to correct the gray matter volume. So I made changes by adding pixels to the contour, and ran recon-all. Subsequently, when I opened up the file after performing recon-all I saw were the pixels (which are white) that I added when I was making the changes. How do you make changes to the gray matter, and what type of recon command should I run after making the changes.

I searched through the various tutorials, but that further confused me. 

I am attaching a screen shot of the brain as well as the tool that I used to add the pixel, and you will be able to see the white pixels I am mentioning above.

Thank you for your time.