I work in a lab that is currently using the Freesurfer algorithm to collect data from MRI images of individuals with Multiple Sclerosis. In order to increase the precision of our white matter masks we have combined your algorithm with ANTS, hoping to achieve more accurate surface volumes and aparc+aseg masks. 

   Unfortunately we have had some issues when we edit our ANTS white matter mask (using value of 255) and then put it through freesurfer again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w <subID>). Our wm_surface and aparc+aseg mask do not change based on the edits we have made, and do not follow the white matter volume surface volume. How can we be sure that our white matter mask, and the edits we make to it, are considered in the creation of wm_surface and aparc+aseg mask? Please let me know if any of this is unclear and I will explain it in more detail.

Thank you,

Tristan