Dear Paul,

you can also try to play with "reposition surface" tool in freeview, where you (apart from other options) can directly edit coordinates of the surface vertices.
However, this tool is not well documented and I myself would like to know the significance of some of the parameters - see my unanswered post from 4th january 2017:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50759.html

And, I am not sure how this works in 5.3 version of freeview, I have used it only in V6beta (dev) version.

Regards,

Antonin


I think this problem is fixed in 6.0 (if and when we get it out)

Thanks bruce for your response. I accidentally listed number 3 twice instead
of 4. Here's my 4th question: Which of the mris_make_surfaces can I use to
correct the pial surface when it does cross the white matter and also, which
is helpful with white matter surface extension? Please see attached
screenshot. I came across a post with similar error in the forum and you
diagnosed but it wasn'tfix 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-April/045097
.html 
Best, 
Paul