Dear Freesurfer users,
My first run of recon1&2 left some white and grey matter at temporal pole region excluded. So I edited the wm.mgz by adding a bunch of control points intending to get more white matter and expand the pial surface (please see the coronal slice in the attachment where the control points were placed). Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT '-autorecon3'. From my understanding, Freesurfer would recalculate the wm.mgz as well as the white matter and pial surfaces in temporal pole according to the control points. However, I got wm.mgz corrected and pial surface wrong (as the attached graph indicated).
Did I do something wrong? Why wm.mgz got fixed while pial surface not? Thanks for help in advanced!
Veronica