Hello,
I am a staff research associate for a group that specializes in MRI of Multiple Sclerosis. We use freesurfer's reconstruction approach, however the white matter masks are not very good for the MS disease population. We have combined the FreeSurfer algorithm with ANTS in order to get more precise white matter masks – which in theory should improve the surface volumes and aparc+aseg masks. When we have tried putting the ANTS white matter mask into freesurfer and re-running recon-all (recon-all -autorecon2–wm –autorecon3 –w <subID>), the wm_surface and aparc+aseg mask do not seem to follow the white matter surface volume (see attached pictures for an example). How do we insure that the white matter mask is taken into consideration? I know that edits to the white matter mask are done with a value of 255 but the actual white matter volume is 110 – could this be the problem? Let me know if I need to explain anything further.
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Thank you, Gina
