autorecon2-wm without mri_fill in v4.5? - Freesurfer

20 Jul 2013


      Hi Freesurfer Experts,
I am working on a primate anatomy and I am having problems with the
white matter filling in the temporal lobe in version 4.5.
I manually edited wm.mgz and recreated filled.mgz using mri_fill. I
then manually edited filled.mgz.
However, when I then run autorecon-all -autorecon2-wm, all my manual
edits in filled.mgz are overwritten.
Is there a way to autorecon2-wm without mri_fill in v4.5?
Thank you very much,
Caspar